Since the completion of the Human Genome Project high-throughput experimentalprojects have been initiated for uncovering genomic information in an extendedsense including transcriptomics proteomics metabolomics glycomics chemicalgenomics and metagenomics We are developing bioinformatics technologies tointegrate and interpret such large-scale datasets especially for medical and phar-maceutical applications

1 KEGG DISEASE and KEGG DRUG

Minoru Kanehisa

KEGG is a database of biological systems thatintegrates genomic chemical and systemic func-tional information It is widely used as a refer-ence knowledge base for understanding higher-order functions and utilities of the cell the or-ganism and the ecosystem from genomic infor-mation This Laboratory is responsible for theapplied areas of KEGG especially in medicaland pharmaceutical sciences We consider dis-eases as perturbed states of the molecular sys-tem that operates the cell and the organism anddrugs as perturbants to the molecular systemWe develop a disease information resourceKEGG DISEASE (httpwwwgenomejpkeggdisease) which is intended for use by compu-tational analysis rather than just for humans toread and understand When the detail of themolecular system is relatively well character-ized we draw KEGG pathway maps When thedetail is not known but disease genes are identi-fied we create KEGG DISEASE entries each ofwhich contains a list of known disease genesand other relevant molecules including environ-

mental factors diagnostic markers and thera-peutic drugs The list simply defines the mem-bership to the underlying molecular system butis useful for integrated analysis with large-scaledatasets We also develop a comprehensive druginformation resource KEGG DRUG (httpwww genome jp kegg drug ) containingchemical structures andor chemical compo-nents of all prescription and OTC drugs in Ja-pan and most prescription drugs in the USAand Europe In KEGG DRUG we also captureknowledge on two types of molecular networksOne is the interaction network of drugs withtarget molecules metabolizing enzymes trans-porters pharmacogenomic markers other drugsand the pathways involving all these moleculesThe other is the chemical structure transforma-tion network in the history of drug developmentwhere drug structures have been continuouslymodified by medicinal chemists

2 KEGG OC Automatic assignments oforthologs and paralogs in completegenomes

Toshiaki Katayama Shuichi Kawashima Aki-hiro Nakaya1 and Minoru Kanehisa 1Graduate

Human Genome Center

Laboratory of Genome Databaseゲノムデータベース分野

Professor Minoru Kanehisa PhDAssistant Professor Toshiaki Katayama MScAssistant Professor Shuichi Kawashima MSc

教 授 理学博士 金 久 實助 教 理学修士 片 山 俊 明助 教 理学修士 川 島 秀 一

94

School of Frontier Sciences The University ofTokyo

The increase in the number of completegenomes has provided clues to gain useful in-sights to understand the evolution of the geneuniverse Among the KEGG suites of databasesthe GENES database contains more than 56 mil-lion genes from over 1300 organisms as of Janu-ary 2011 Sequence similarities among thesegenes are calculated by all-against-all SSEARCHcomparison and stored in the SSDB databaseBased on those databases the ORTHOLOGY da-tabase has been manually constructed to storethe relationships among the genes sharing thesame biological function However in this strat-egy only the well known functions can be usedfor annotation of newly added genes thus thenumber of annotated genes is limited To over-come this situation we have developed a fullyautomated procedure to find candidate ortholo-gous clusters including those without any func-tional annotation The method is based on agraph analysis of the SSDB database treatinggenes as nodes and the Smith-Waterman se-quence similarity scores as edge weights Thecluster is found by our heuristic method forfinding quasi-cliques but the SSDB graph is toolarge to perform quasi-clique finding at a timeTherefore we introduce a hierarchy (evolution-ary relationship) of organisms and treat theSSDB graph as a nested graph The automaticdecomposition of the SSDB graph into a set ofquasi-cliques results in the KEGG OC (OrthologCluster) database We have built a system thatperforms automatic update of KEGG OC whichcan be run on a weekly basis As a result weobtained 959333 clusters including 595004 sin-gleton clusters from 5631381 protein codinggenes Among them 5704 clusters were sharedacross kingdoms and other clusters were king-dom specific The automatic classification of ourortholog clusters is largely consistent with themanually curated ORTHOLOGY database Aweb interface to search and browse genes inclusters is made available at httpochgcjp

3 EGENES A database for expressed se-quence tag indices of plant species

Shuichi Kawashima Yuki Moriya1 ToshiakiTokimatsu1 Susumu Goto1 and Minoru Kane-hisa 1Institute for Chemical Science KyotoUniversity

EGENES is a knowledge-based database forefficient analysis of plant expressed sequencetags (ESTs) It links plant genomic informationto higher order functional information in KEGG

The genomic information in EGENES is a collec-tion of EST contigs constructed from assembledplant ESTs by using EGassembler The EST indi-ces are automatically annotated with the KEGGOrthology identifiers (K numbers) by KEGGAutomatic Annotation Server (KAAS) Cur-rently EGENES contains 3170203 sequencecatalogues in 80 plants among which 21 haveassigned K numbers EGENES is available athttpwwwgenomejpkeggcatalogorg_list2html

4 KEGG API SOAPWSDL interface for theKEGG system

Shuichi Kawashima Toshiaki Katayama andMinoru Kanehisa

KEGG is a suite of databases and associatedsoftware integrating our current knowledge ofmolecular interactionreaction pathways andother systemic functions (PATHWAY and BRITEdatabases) information about the genomic space(GENES database) and information about thechemical space (LIGAND databases) To facili-tate large-scale applications of the KEGG systemprogrammatically we have been developingand maintaining the KEGG API as a stableSOAPWSDL based web service The KEGGAPI is available at httpwwwgenomejpkeggsoap

5 BioRuby Bioinformatics software for theRuby programming language

Naohisa Goto1 Pjotr Prins2 Mitsuteru Nakao3Raoul Bonnal4 Jan Aerts5 and Toshiaki Kata-yama 1Research Institute for Microbial Dis-eases Osaka University 2Database Center forLife Science ROIS 3Groningen BioinformaticsCentre University of Groningen The Nether-lands 4Integrative Biology Program Fondazi-one Istituto Nazionale di Genetica MolecolareItaly 5Katholieke Universiteit Leuven Belgium

The BioRuby software toolkit contains a com-prehensive set of free development tools and li-braries for bioinformatics and molecular biologywritten in the Ruby programming languageBioRuby has components for sequence analysispathway analysis protein modelling and phylo-genetic analysis it supports many widely useddata formats and provides easy access to data-bases external programs and public web serv-ices including BLAST KEGG GenBank MED-LINE and GO BioRuby comes with a tutorialdocumentation and an interactive environmentwhich can be used in the shell and in the webbrowser BioRuby is free and open source soft-

95

ware made available under the Ruby licenseBioRuby runs on all platforms that supportRuby including Linux Mac OS X and Win-dows And with JRuby BioRuby runs on theJava Virtual Machine The source code is avail-able from httpwwwbiorubyorg

6 TogoWS integrated SOAP and REST APIsfor interoperable bioinformatics Web serv-ices

Toshiaki Katayama Mitsuteru Nakao1 andToshihisa Takagi23 1Database Center for LifeScience ROIS 2National Bioscience DatabaseCenter JST 3Graduate School of Frontier Sci-ences The University of Tokyo

Web services have become widely used inbioinformatics analysis but there exist incom-patibilities in interfaces and data types whichprevent users from making full use of a combi-nation of these services Therefore we have de-veloped the TogoWS service to provide an inte-grated interface with advanced features In theTogoWS REST (REpresentative State Transfer)API (application programming interface) we in-troduce a unified access method for major data-base resources through intuitive URIs that canbe used to search retrieve parse and convertthe database entries The TogoWS SOAP API re-solves compatibility issues found on the serverand client-side SOAP implementations The To-goWS service is freely available at httptogowsdbclsjp

7 TogoDB Instantly publish your researchmaterial as a public database

Toshiaki Katayama Mitsuteru Nakao1 andToshihisa Takagi23 1Database Center for LifeScience ROIS 2National Bioscience DatabaseCenter JST 3Graduate School of Frontier Sci-ences The University of Tokyo

Supplemental materials are often provided asseparate files downloadable from the publisherrsquossite along with the publication of a journal arti-cle However these data are not fully utilizedsince they are not available in the form of regu-lar biological databases and hard to find by thepopular Web search engines TogoDB is a sim-ple and intuitive database system to publishtabular formatted data instantly on the Web Us-ers can upload their research materials to theTogoDB through the simple web interface andthe data will be made available as a fully func-tional database in a minute or two TogoWS isan integrated and uniformed interface for themajor bioinformatics web services and also pro-

vides REST API for the contents in the TogoDBRecently we extended TogoDB and TogoWS tobe used as a consolidated platform for the Se-mantic Web by adding a metadata editor and anautomatic Resource Description Framework(RDF) dumper This system fills the gap be-tween userrsquos data and major public databases todeliver effective variations in the Linked Data

8 Characterization of parasite specific genesby ortholog gene clusters and the Seman-tic Web technologies

Toshiaki Katayama Shuichi KawashimaJunichi Watanabe Yutaka Suzuki1 SumioSugano1 and Minoru Kanehisa 1GraduateSchool of Frontier Sciences The University ofTokyo

Characterization of a set of genes is one of themost demanded tasks in bioinformatics Usuallyextensive sequence similarity search is per-formed and the functions of query sequencesare inferred from the annotation of highly simi-lar sequences For more accurate inferenceortholog clusters and protein motif informationare often added for further investigationOrtholog cluster is useful to infer the phyloge-netic distribution of the protein family and mo-tifs provides molecular evidence of the func-tional domains in combination In this way in-formation integration of related data sources isgaining in importance to make the annotationmore reliable or to discover hidden relationsamong data sets However the incompatibleidentifiers and data types have prevented fromintegrating heterogeneous data seamlesslyamong life-science databases Recently the Se-mantic Web technologies are being accepted toresolve this situation We applied these methodsto characterize a set of genes from non-labstrains of Plasmodium falciparum and other para-site species Clinical samples are taken at thehospital in Manado Indonesia and RNA se-quencing was performed to find over-expressedmalarial genes As a result we obtained ~5 oftotal genes which are highly expressed Amongthem we found 20 P falciparum specific 48 Plas-modium specific and 43 Apicomplexa specificgenes Many of them turned out to possessparasite specific domains such as surface anti-gen and exported protein with unknown func-tion We also discovered that some of them arechanged 7-folds in their gene expression levelsamong samples which can be candidates for thedrug target

96

9 Analysis of EST sequences from thehouse dust mite Dermatophagoides fari-nae

Shuichi Kawashima Junichi Watanabe andMinoru Kanehisa

The house dust mite feed on skin scales (dan-der and scurf) and other organic detritus suchas bacteria spores and feathers and produce 20to 30 small fecal particles which are highly al-lergic Thus it is important that we expand ourknowledge of the mites to develop effective al-lergy panels or vaccines Angus et al have initi-ated a project to sequence ESTs of Dermato-phagoides farinae and other mite species associ-ated with allergic diseases Wakaguri et al havealso sequenced ESTs of D farinae which wasfirst established in 1968 and has been main-tained using the method developed by Sasa etal The produced sequences are available at theFullMite database In this study we analyzed therelationships between known mite allergens andthe EST sequences derived from the FullMitedatabase

After removing low quality regions and clip-ping vector sequences from the initial 23040 se-quences a total of 21005 sequences is retainedThen we assembled pair-end sequences if theywere aligned with a strict condition (more than500 bit score and 99 sequence identity in thealigned region) Clustering and assembling withthe CAP3 software resulted in 1717 contigs and3368 singletons The distribution of the numberof ESTs included in each contig showed thatknown allergens were widely distributedthrough the variety of gene expression levelsAs expected the major mite allergens such asDer f 1 or Der f 2 were highly expressed in ourdata On the other hand there were also knownallergens which were lower expressed It isknown at least 20 of adults allergic to mitehave poor reactivity to the group 1 and group 2allergens Furthermore new mite allergens havestill been characterized today (eg Der f 22)Thus there could be unknown mite allergens inour data and we will try to screen potential al-lergens which are still uncharacterized

10 Analysis of a tardigrade proteome withthe Gene Ontology

Shuichi Kawashima Toshiaki Katayama andMinoru Kanehisa

Kunieda et al have been sequencing and ana-lyzing the genome of extremotolerant tardi-grade Rammazzottius cf varieornatus YOKOZUNA-1 Currently they produced about

15000 hypothetical protein coding genes by us-ing ab initio method implemented in SNAP soft-ware Tardigrades form the phylum Tardigradawhich is considered as a member of the su-perphylum Ecdysozoa However the definitivephylogenetic position is still unclear To under-stand the ecdysozoans specific molecular func-tions we compared the Gene Ontology termsannotated to the proteome with those of Dro-sphila melanogaster Daphnia pulex and Caenorhab-ditis elegans as representative Ecdysozoas andfound the 2241 GO temrs common to the fourecdysozoans Interestingly only six ontologieswere found in the proteomes of four species ex-clusively Those are rhabdomere (GO0016028)cation channel complex (GO0034703) septatejunction (GO0005918) signal recognition parti-cle (GO0048500) fusom (GO0045169) and spec-trosome (GO0045170)

11 Functional genome annotation of a tardi-grade by KEGG MODULE database

Toshiaki Katayama Shuichi Kawashima andMinoru Kanehisa

Functional annotation of genes is usually per-formed based on sequence similarities to genesof other organisms However it is difficult tofind out characteristics of the genome onlybased on the each annotated gene Thereforeoverall signature of a genome is often describedwith the help of the Gene Ontology (GO) orKEGG PATHWAY databases Assigning GOterms to genes we can grasp an outline of func-tional categories covered by a set of genes en-coded in a genome Reconstructing KEGGPATHWAY will reveals metabolic and regula-tory pathways that the target organism mayutilize The problem here is the granularityFunctional categories of the GO and coveringarea of each KEGG PATHWAY map are rathercoarse-grained to find key differences among or-ganisms Meanwhile KEGG MODULE is a data-base of functional units in the pathways whichare highly conserved among organisms We arerunning a genome project of a tardigrade whichis expected to explain its phylogenetic positionand to make functional annotation of thegenome Therefore we introduced the KEGGMODULE to see conserved and non-conservedmodules in the tardigrade genome comparedwith closely-related species As a result wefound 184 conserved modules in tardigradewhich are slightly larger than that of C elegans(162) D pulex (181) and D melanogaster (164)Among them we found several module candi-dates describing evolution of the metabolicpathways in animal For example M00029 (urea

97

cycle) which is missing in nematodes partiallyconserved (cytosolic portion) in arthropods andfully conserved in vertebrates (cytosolic and mi-tochondrial portions) Tardigrade had only oneenzyme in this module (in cytosolic portion)showing the same pattern with some protistsAs the number of sequenced genomes increasesvery rapidly KEGG MODULE combined with aphylogenetic profile will be a powerful tool toelucidate characteristics of those genomes effi-ciently

12 HiGet and SSS Search engines for thelarge-scale biological databases

Toshiaki Katayama Shuichi KawashimaKazuhiro Ohi1 Kenta Nakai2 Minoru Kane-hisa 1Hitatchi Ltd 2Laboratory of FunctionalAnalysis In Silico Institute of Medical ScienceThe University of Tokyo

The number of entries in biological databasesis exponentially increasing year by year For ex-ample there were 10106023 entries in the Gen-Bank database in the year 2000 which has nowgrown to 141537514 (Release 181＋daily up-dates) In order for such a vast amount of datato be searched at a high speed we have devel-

oped a high performance database entry re-trieval system named HiGet For this purposethe system is constructed on the HiRDB a com-mercial ORDBMS (Object-oriented RelationalDatabase Management System) developed byHitachi Ltd HiGet can perform full text searchon various biological databases including Gen-Bank RefSeq UniProt Prosite OMIM and PDBAdditional advantage of the HiGet system is thecapability of a field specific search which en-ables users to narrow down the number of re-sults especially useful for collecting sequencesof their specific needs We have also developeda sequence similarity search (SSS) service to findhomologous sequences with various algorithmsincluding BLAST FASTA SSEARCH TRANSand EXONERATE This variety of options isunique among the public services and users canselect an appropriate method to search similarsequences according to their query Because al-gorithms such as TRANS and EXONERATE arehighly time consuming the SSS service is back-ended by the distributed computing environ-ment with the Sun Grid Engine in our supercomputer system HiGet and SSS services areavailable at httphigethgcjp and httpssshgcjp respectively

Publications

Kanehisa M Goto S Furumichi M TanabeM Hirakawa M KEGG for representationand analysis of molecular networks involvingdiseases and drugs Nucleic Acids Research 38D355-D360 2010

Katayama T Nakao M Takagi T TogoWSintegrated SOAP and REST APIs for interop-erable bioinformatics Web services Nucleic Ac-ids Research 38 W706-W711 2010

Katayama T Arakawa K Nakao M Ono KAoki-Kinoshita KF Yamamoto Y Yama-guchi A Kawashima S Chun HW AertsJ Aranda B Barboza LH Bonnal RJBruskiewich R Bryne JC Fernaacutendez JMFunahashi A Gordon PM Goto N Gro-scurth A Gutteridge A Holland R KanoY Kawas EA Kerhornou A Kibukawa EKinjo AR Kuhn M Lapp H LehvaslaihoH Nakamura H Nakamura Y NishizawaT Nobata C Noguchi T Oinn TMOkamoto S Owen S Pafilis E Pocock MPrins P Ranzinger R Reisinger F Salwin-ski L Schreiber M Senger M ShigemotoY Standley DM Sugawara H Tashiro TTrelles O Vos RA Wilkinson MD YorkW Zmasek CM Asai K Takagi T TheDBCLS BioHackathon standardization and in-

teroperability for bioinformatics web servicesand workflows Journal of Biomedical Semantics1 8 2010

Goto N Prins P Nakao M Bonnal R AertsJ Katayama T BioRuby bioinformatics soft-ware for the Ruby programming languageBioinformatics 26 2617-2619 2010

Yamanishi Y Kotera M Kanehisa M GotoS Drug-target interaction prediction fromchemical genomic and pharmacological datain an integrated framework Bioinformatics 26i246-i256 2010

Erguner B Hattori M Goto S Kanehisa MCharacterizing common substructures ofligands for GPCR protein subfamilies GenomeInformatics 24 31-41 2010

Kotera M Kobayashi T Hattori M Toki-matsu T Goto S Mihara H Kanehisa MComprehensive genomic analysis of sulfur-relay pathway genes Genome Informatics 24104-115 2010

Mizutani S Tanaka M Wheelock C Kane-hisa M Goto S Phylogenetic analysis oflipid mediator GPCRs Genome Informatics 24116-126 2010

Nishimura Y Tokimatsu T Kotera M GotoS Kanehisa M Genome-wide analysis of

98

plant UGT family based on sequence and sub-strate information Genome Informatics 24 127-

138 2010

99

The recent advances in biomedical research have been producing large-scaleultra-high dimensional ultra-heterogeneous data Due to these post-genomic re-search progresses our current mission is to create computational strategy for sys-tems biology and medicine towards translational bioinformatics With this missionwe have been developing computational methods for understanding life as systemand applying them to practical issues in medicine and biology

1 Gene Network Analysis

a Inferring dynamic gene networks undervarying conditions for transcriptomic net-work comparison

Teppei Shimamura Seiya Imoto Rui Yama-guchi Masao Nagasaki Satoru Miyano

Elucidating the differences between cellularresponses to various biological conditions or ex-ternal stimuli is an important challenge in sys-tems biology Many approaches have been de-veloped for reverse-engineering a cellular sys-tem called gene network from time series mi-croarray gene expression data in order to under-stand a transcriptomic response under a condi-tion of interest Comparative topological analy-sis has also been applied based on the gene net-

works inferred independently from each of themultiple time series datasets under varying con-ditions to find critical differences between thesenetworks However these comparisons oftenlead to misleading results because each networkcontains considerable noise due to the limitedlength of the time series With this motivationwe developed an integrated approach for infer-ring multiple gene networks from time seriesexpression data under varying conditions Tothe best of our knowledge our approach is thefirst reverse-engineering method that is intendedfor transcriptomic network comparison betweenvarying conditions Furthermore we developeda state-of-the-art parameter estimation methodrelevance-weighted recursive elastic net for pro-viding higher precision and recall than existingreverse-engineering methods We analyze ex-perimental data of MCF-7 human breast cancer

Human Genome Center

Laboratory of DNA Information AnalysisLaboratory of Sequence Data AnalysisDNA情報解析分野シークエンスデータ情報処理分野

Professor Satoru Miyano PhDAssociate Professor Seiya Imoto PhDAssistant Professor Masao Nagasaki PhDProject Assistant Professor Yoshinori Tamada PhDProject Assistant Professor Teppei Shimamura PhDAssociate Professor Tetsuo Shibuya PhDLecturer Rui Yamaguchi PhD

教 授 理学博士 宮 野 悟准教授 博士（数理学） 井 元 清 哉助 教 博士（理学） 長 正 朗特任助教 博士（情報学） 玉 田 嘉 紀特任助教 博士（工学） 島 村 徹 平准教授 博士（理学） 渋 谷 哲 朗講 師 博士（理学） 山 口 類

100

cells stimulated by epidermal growth factor orheregulin with several doses and provide novelbiological hypotheses through network compari-son The software NETCOMP is available athttp bonsai ims u-tokyo ac jp ~shima NETCOMP

b Collocation-based sparse estimation forconstructing dynamic gene networks

Teppei Shimamura Seiya Imoto Masao Na-gasaki Mai Yamauchi13 Rui Yamaguchi An-dreacute Fujita Yoshinori Tamada Noriko Gotoh13Satoru Miyano

One of the open problems in systems biologyis to infer dynamic gene networks describingthe underlying biological process with mathe-matical statistical and computational methodsThe first-order difference equation-based modelssuch as dynamic Bayesian networks and vectorautoregressive models were used to infer time-lagged relationships between genes from time-series microarray data However two primaryproblems greatly reduce the effectiveness of cur-rent approaches The first problem is the tacitassumption that time lag is stationary The sec-ond is the inseparability between measurementnoise and process noise (unmeasured distur-bances that pass through time process) To ad-dress these problems we developed a stochasticdifferential equation model for inferringcontinuous-time dynamic gene networks underthe situation in which both of the process noiseand the observation noise exist We devised acollocation-based sparse estimation for simulta-neous parameter estimation and model selectionin the model The collocation-based approach re-quires considerably less computational effortthan traditional methods in ordinary stochasticdifferential equation models We also incorpo-rated various biological knowledge easily to re-fine the estimation accuracy with this methodThe results using simulated data and real time-series expression data of human primary smallairway epithelial cells demonstrate that this ap-proach outperformed competing approaches andcould provide significant genes influenced byGefitinib

c Gene set-based module discovery de-codes cis-regulatory codes governing di-verse gene expression across human mul-tiple tissues

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Saatoru Miyano

Decoding transcriptional programs governing

transcriptomic diversity across human multipletissues is a major challenge in bioinformatics Toaddress this problem a number of computa-tional methods have focused on cis-regulatorycodes driving overexpression or underexpres-sion in a single tissue as compared to others Onthe other hand we recently proposed a differentapproach to mine cis-regulatory codes startingfrom gene sets sharing common cis-regulatorymotifs the method screens for expression mod-ules based on expression coherence Howeverboth approaches seem to be insufficient to cap-ture transcriptional programs that control geneexpression in a subset of all samples Especiallythis limitation would be serious when analyzingmultiple tissue data To overcome this limita-tion we developed a new module discoverymethod termed BEEM (Biclusering-based Extrac-tion of Expression Modules) in order to discoverexpression modules that are functional in a sub-set of tissues We showed that when applied toexpression profiles of human multiple tissuesBEEM finds expression modules missed by twoexisting approaches that are based on the coher-ent expression and the single tissue-specific dif-ferential expression From the BEEM results weobtained new insights into transcriptional pro-grams controlling transcriptomic diversity acrossvarious types of tissues This study introducesBEEM as a powerful tool for decoding regula-tory programs from a compendium of gene ex-pression profiles

d Model-free unsupervised gene set screen-ing based on information enrichment inexpression profiles

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Andreacute Fujita Teppei Shima-mura Satoru Miyano

A number of unsupervised gene set screeningmethods have recently been developed forsearch of putative functional gene sets based ontheir expression profiles Most of the methodsstatistically evaluate whether the expression pro-files of each gene set are fit to assumed modelseg co-expression across all samples or a sub-group of samples However it is possible thatthey fail to capture informative gene sets whoseexpression profiles are not fit to the assumedmodels To overcome this limitation we devel-oped a model-free unsupervised gene set screen-ing method Matrix Information EnrichmentAnalysis (MIEA) Without assuming any specificmodels MIEA screens gene sets based on infor-mation richness of their expression profiles Weextensively compared the performance of MIEAto those of other unsupervised gene set screen-

101

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

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(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

School of Frontier Sciences The University ofTokyo

The increase in the number of completegenomes has provided clues to gain useful in-sights to understand the evolution of the geneuniverse Among the KEGG suites of databasesthe GENES database contains more than 56 mil-lion genes from over 1300 organisms as of Janu-ary 2011 Sequence similarities among thesegenes are calculated by all-against-all SSEARCHcomparison and stored in the SSDB databaseBased on those databases the ORTHOLOGY da-tabase has been manually constructed to storethe relationships among the genes sharing thesame biological function However in this strat-egy only the well known functions can be usedfor annotation of newly added genes thus thenumber of annotated genes is limited To over-come this situation we have developed a fullyautomated procedure to find candidate ortholo-gous clusters including those without any func-tional annotation The method is based on agraph analysis of the SSDB database treatinggenes as nodes and the Smith-Waterman se-quence similarity scores as edge weights Thecluster is found by our heuristic method forfinding quasi-cliques but the SSDB graph is toolarge to perform quasi-clique finding at a timeTherefore we introduce a hierarchy (evolution-ary relationship) of organisms and treat theSSDB graph as a nested graph The automaticdecomposition of the SSDB graph into a set ofquasi-cliques results in the KEGG OC (OrthologCluster) database We have built a system thatperforms automatic update of KEGG OC whichcan be run on a weekly basis As a result weobtained 959333 clusters including 595004 sin-gleton clusters from 5631381 protein codinggenes Among them 5704 clusters were sharedacross kingdoms and other clusters were king-dom specific The automatic classification of ourortholog clusters is largely consistent with themanually curated ORTHOLOGY database Aweb interface to search and browse genes inclusters is made available at httpochgcjp

3 EGENES A database for expressed se-quence tag indices of plant species

Shuichi Kawashima Yuki Moriya1 ToshiakiTokimatsu1 Susumu Goto1 and Minoru Kane-hisa 1Institute for Chemical Science KyotoUniversity

EGENES is a knowledge-based database forefficient analysis of plant expressed sequencetags (ESTs) It links plant genomic informationto higher order functional information in KEGG

The genomic information in EGENES is a collec-tion of EST contigs constructed from assembledplant ESTs by using EGassembler The EST indi-ces are automatically annotated with the KEGGOrthology identifiers (K numbers) by KEGGAutomatic Annotation Server (KAAS) Cur-rently EGENES contains 3170203 sequencecatalogues in 80 plants among which 21 haveassigned K numbers EGENES is available athttpwwwgenomejpkeggcatalogorg_list2html

4 KEGG API SOAPWSDL interface for theKEGG system

Shuichi Kawashima Toshiaki Katayama andMinoru Kanehisa

KEGG is a suite of databases and associatedsoftware integrating our current knowledge ofmolecular interactionreaction pathways andother systemic functions (PATHWAY and BRITEdatabases) information about the genomic space(GENES database) and information about thechemical space (LIGAND databases) To facili-tate large-scale applications of the KEGG systemprogrammatically we have been developingand maintaining the KEGG API as a stableSOAPWSDL based web service The KEGGAPI is available at httpwwwgenomejpkeggsoap

5 BioRuby Bioinformatics software for theRuby programming language

Naohisa Goto1 Pjotr Prins2 Mitsuteru Nakao3Raoul Bonnal4 Jan Aerts5 and Toshiaki Kata-yama 1Research Institute for Microbial Dis-eases Osaka University 2Database Center forLife Science ROIS 3Groningen BioinformaticsCentre University of Groningen The Nether-lands 4Integrative Biology Program Fondazi-one Istituto Nazionale di Genetica MolecolareItaly 5Katholieke Universiteit Leuven Belgium

The BioRuby software toolkit contains a com-prehensive set of free development tools and li-braries for bioinformatics and molecular biologywritten in the Ruby programming languageBioRuby has components for sequence analysispathway analysis protein modelling and phylo-genetic analysis it supports many widely useddata formats and provides easy access to data-bases external programs and public web serv-ices including BLAST KEGG GenBank MED-LINE and GO BioRuby comes with a tutorialdocumentation and an interactive environmentwhich can be used in the shell and in the webbrowser BioRuby is free and open source soft-

95

ware made available under the Ruby licenseBioRuby runs on all platforms that supportRuby including Linux Mac OS X and Win-dows And with JRuby BioRuby runs on theJava Virtual Machine The source code is avail-able from httpwwwbiorubyorg

6 TogoWS integrated SOAP and REST APIsfor interoperable bioinformatics Web serv-ices

Toshiaki Katayama Mitsuteru Nakao1 andToshihisa Takagi23 1Database Center for LifeScience ROIS 2National Bioscience DatabaseCenter JST 3Graduate School of Frontier Sci-ences The University of Tokyo

Web services have become widely used inbioinformatics analysis but there exist incom-patibilities in interfaces and data types whichprevent users from making full use of a combi-nation of these services Therefore we have de-veloped the TogoWS service to provide an inte-grated interface with advanced features In theTogoWS REST (REpresentative State Transfer)API (application programming interface) we in-troduce a unified access method for major data-base resources through intuitive URIs that canbe used to search retrieve parse and convertthe database entries The TogoWS SOAP API re-solves compatibility issues found on the serverand client-side SOAP implementations The To-goWS service is freely available at httptogowsdbclsjp

7 TogoDB Instantly publish your researchmaterial as a public database

Toshiaki Katayama Mitsuteru Nakao1 andToshihisa Takagi23 1Database Center for LifeScience ROIS 2National Bioscience DatabaseCenter JST 3Graduate School of Frontier Sci-ences The University of Tokyo

Supplemental materials are often provided asseparate files downloadable from the publisherrsquossite along with the publication of a journal arti-cle However these data are not fully utilizedsince they are not available in the form of regu-lar biological databases and hard to find by thepopular Web search engines TogoDB is a sim-ple and intuitive database system to publishtabular formatted data instantly on the Web Us-ers can upload their research materials to theTogoDB through the simple web interface andthe data will be made available as a fully func-tional database in a minute or two TogoWS isan integrated and uniformed interface for themajor bioinformatics web services and also pro-

vides REST API for the contents in the TogoDBRecently we extended TogoDB and TogoWS tobe used as a consolidated platform for the Se-mantic Web by adding a metadata editor and anautomatic Resource Description Framework(RDF) dumper This system fills the gap be-tween userrsquos data and major public databases todeliver effective variations in the Linked Data

8 Characterization of parasite specific genesby ortholog gene clusters and the Seman-tic Web technologies

Toshiaki Katayama Shuichi KawashimaJunichi Watanabe Yutaka Suzuki1 SumioSugano1 and Minoru Kanehisa 1GraduateSchool of Frontier Sciences The University ofTokyo

Characterization of a set of genes is one of themost demanded tasks in bioinformatics Usuallyextensive sequence similarity search is per-formed and the functions of query sequencesare inferred from the annotation of highly simi-lar sequences For more accurate inferenceortholog clusters and protein motif informationare often added for further investigationOrtholog cluster is useful to infer the phyloge-netic distribution of the protein family and mo-tifs provides molecular evidence of the func-tional domains in combination In this way in-formation integration of related data sources isgaining in importance to make the annotationmore reliable or to discover hidden relationsamong data sets However the incompatibleidentifiers and data types have prevented fromintegrating heterogeneous data seamlesslyamong life-science databases Recently the Se-mantic Web technologies are being accepted toresolve this situation We applied these methodsto characterize a set of genes from non-labstrains of Plasmodium falciparum and other para-site species Clinical samples are taken at thehospital in Manado Indonesia and RNA se-quencing was performed to find over-expressedmalarial genes As a result we obtained ~5 oftotal genes which are highly expressed Amongthem we found 20 P falciparum specific 48 Plas-modium specific and 43 Apicomplexa specificgenes Many of them turned out to possessparasite specific domains such as surface anti-gen and exported protein with unknown func-tion We also discovered that some of them arechanged 7-folds in their gene expression levelsamong samples which can be candidates for thedrug target

96

9 Analysis of EST sequences from thehouse dust mite Dermatophagoides fari-nae

Shuichi Kawashima Junichi Watanabe andMinoru Kanehisa

The house dust mite feed on skin scales (dan-der and scurf) and other organic detritus suchas bacteria spores and feathers and produce 20to 30 small fecal particles which are highly al-lergic Thus it is important that we expand ourknowledge of the mites to develop effective al-lergy panels or vaccines Angus et al have initi-ated a project to sequence ESTs of Dermato-phagoides farinae and other mite species associ-ated with allergic diseases Wakaguri et al havealso sequenced ESTs of D farinae which wasfirst established in 1968 and has been main-tained using the method developed by Sasa etal The produced sequences are available at theFullMite database In this study we analyzed therelationships between known mite allergens andthe EST sequences derived from the FullMitedatabase

After removing low quality regions and clip-ping vector sequences from the initial 23040 se-quences a total of 21005 sequences is retainedThen we assembled pair-end sequences if theywere aligned with a strict condition (more than500 bit score and 99 sequence identity in thealigned region) Clustering and assembling withthe CAP3 software resulted in 1717 contigs and3368 singletons The distribution of the numberof ESTs included in each contig showed thatknown allergens were widely distributedthrough the variety of gene expression levelsAs expected the major mite allergens such asDer f 1 or Der f 2 were highly expressed in ourdata On the other hand there were also knownallergens which were lower expressed It isknown at least 20 of adults allergic to mitehave poor reactivity to the group 1 and group 2allergens Furthermore new mite allergens havestill been characterized today (eg Der f 22)Thus there could be unknown mite allergens inour data and we will try to screen potential al-lergens which are still uncharacterized

10 Analysis of a tardigrade proteome withthe Gene Ontology

Shuichi Kawashima Toshiaki Katayama andMinoru Kanehisa

Kunieda et al have been sequencing and ana-lyzing the genome of extremotolerant tardi-grade Rammazzottius cf varieornatus YOKOZUNA-1 Currently they produced about

15000 hypothetical protein coding genes by us-ing ab initio method implemented in SNAP soft-ware Tardigrades form the phylum Tardigradawhich is considered as a member of the su-perphylum Ecdysozoa However the definitivephylogenetic position is still unclear To under-stand the ecdysozoans specific molecular func-tions we compared the Gene Ontology termsannotated to the proteome with those of Dro-sphila melanogaster Daphnia pulex and Caenorhab-ditis elegans as representative Ecdysozoas andfound the 2241 GO temrs common to the fourecdysozoans Interestingly only six ontologieswere found in the proteomes of four species ex-clusively Those are rhabdomere (GO0016028)cation channel complex (GO0034703) septatejunction (GO0005918) signal recognition parti-cle (GO0048500) fusom (GO0045169) and spec-trosome (GO0045170)

11 Functional genome annotation of a tardi-grade by KEGG MODULE database

Toshiaki Katayama Shuichi Kawashima andMinoru Kanehisa

Functional annotation of genes is usually per-formed based on sequence similarities to genesof other organisms However it is difficult tofind out characteristics of the genome onlybased on the each annotated gene Thereforeoverall signature of a genome is often describedwith the help of the Gene Ontology (GO) orKEGG PATHWAY databases Assigning GOterms to genes we can grasp an outline of func-tional categories covered by a set of genes en-coded in a genome Reconstructing KEGGPATHWAY will reveals metabolic and regula-tory pathways that the target organism mayutilize The problem here is the granularityFunctional categories of the GO and coveringarea of each KEGG PATHWAY map are rathercoarse-grained to find key differences among or-ganisms Meanwhile KEGG MODULE is a data-base of functional units in the pathways whichare highly conserved among organisms We arerunning a genome project of a tardigrade whichis expected to explain its phylogenetic positionand to make functional annotation of thegenome Therefore we introduced the KEGGMODULE to see conserved and non-conservedmodules in the tardigrade genome comparedwith closely-related species As a result wefound 184 conserved modules in tardigradewhich are slightly larger than that of C elegans(162) D pulex (181) and D melanogaster (164)Among them we found several module candi-dates describing evolution of the metabolicpathways in animal For example M00029 (urea

97

cycle) which is missing in nematodes partiallyconserved (cytosolic portion) in arthropods andfully conserved in vertebrates (cytosolic and mi-tochondrial portions) Tardigrade had only oneenzyme in this module (in cytosolic portion)showing the same pattern with some protistsAs the number of sequenced genomes increasesvery rapidly KEGG MODULE combined with aphylogenetic profile will be a powerful tool toelucidate characteristics of those genomes effi-ciently

12 HiGet and SSS Search engines for thelarge-scale biological databases

Toshiaki Katayama Shuichi KawashimaKazuhiro Ohi1 Kenta Nakai2 Minoru Kane-hisa 1Hitatchi Ltd 2Laboratory of FunctionalAnalysis In Silico Institute of Medical ScienceThe University of Tokyo

The number of entries in biological databasesis exponentially increasing year by year For ex-ample there were 10106023 entries in the Gen-Bank database in the year 2000 which has nowgrown to 141537514 (Release 181＋daily up-dates) In order for such a vast amount of datato be searched at a high speed we have devel-

oped a high performance database entry re-trieval system named HiGet For this purposethe system is constructed on the HiRDB a com-mercial ORDBMS (Object-oriented RelationalDatabase Management System) developed byHitachi Ltd HiGet can perform full text searchon various biological databases including Gen-Bank RefSeq UniProt Prosite OMIM and PDBAdditional advantage of the HiGet system is thecapability of a field specific search which en-ables users to narrow down the number of re-sults especially useful for collecting sequencesof their specific needs We have also developeda sequence similarity search (SSS) service to findhomologous sequences with various algorithmsincluding BLAST FASTA SSEARCH TRANSand EXONERATE This variety of options isunique among the public services and users canselect an appropriate method to search similarsequences according to their query Because al-gorithms such as TRANS and EXONERATE arehighly time consuming the SSS service is back-ended by the distributed computing environ-ment with the Sun Grid Engine in our supercomputer system HiGet and SSS services areavailable at httphigethgcjp and httpssshgcjp respectively

Publications

Kanehisa M Goto S Furumichi M TanabeM Hirakawa M KEGG for representationand analysis of molecular networks involvingdiseases and drugs Nucleic Acids Research 38D355-D360 2010

Katayama T Nakao M Takagi T TogoWSintegrated SOAP and REST APIs for interop-erable bioinformatics Web services Nucleic Ac-ids Research 38 W706-W711 2010

Katayama T Arakawa K Nakao M Ono KAoki-Kinoshita KF Yamamoto Y Yama-guchi A Kawashima S Chun HW AertsJ Aranda B Barboza LH Bonnal RJBruskiewich R Bryne JC Fernaacutendez JMFunahashi A Gordon PM Goto N Gro-scurth A Gutteridge A Holland R KanoY Kawas EA Kerhornou A Kibukawa EKinjo AR Kuhn M Lapp H LehvaslaihoH Nakamura H Nakamura Y NishizawaT Nobata C Noguchi T Oinn TMOkamoto S Owen S Pafilis E Pocock MPrins P Ranzinger R Reisinger F Salwin-ski L Schreiber M Senger M ShigemotoY Standley DM Sugawara H Tashiro TTrelles O Vos RA Wilkinson MD YorkW Zmasek CM Asai K Takagi T TheDBCLS BioHackathon standardization and in-

teroperability for bioinformatics web servicesand workflows Journal of Biomedical Semantics1 8 2010

Goto N Prins P Nakao M Bonnal R AertsJ Katayama T BioRuby bioinformatics soft-ware for the Ruby programming languageBioinformatics 26 2617-2619 2010

Yamanishi Y Kotera M Kanehisa M GotoS Drug-target interaction prediction fromchemical genomic and pharmacological datain an integrated framework Bioinformatics 26i246-i256 2010

Erguner B Hattori M Goto S Kanehisa MCharacterizing common substructures ofligands for GPCR protein subfamilies GenomeInformatics 24 31-41 2010

Kotera M Kobayashi T Hattori M Toki-matsu T Goto S Mihara H Kanehisa MComprehensive genomic analysis of sulfur-relay pathway genes Genome Informatics 24104-115 2010

Mizutani S Tanaka M Wheelock C Kane-hisa M Goto S Phylogenetic analysis oflipid mediator GPCRs Genome Informatics 24116-126 2010

Nishimura Y Tokimatsu T Kotera M GotoS Kanehisa M Genome-wide analysis of

98

plant UGT family based on sequence and sub-strate information Genome Informatics 24 127-

138 2010

99

The recent advances in biomedical research have been producing large-scaleultra-high dimensional ultra-heterogeneous data Due to these post-genomic re-search progresses our current mission is to create computational strategy for sys-tems biology and medicine towards translational bioinformatics With this missionwe have been developing computational methods for understanding life as systemand applying them to practical issues in medicine and biology

1 Gene Network Analysis

a Inferring dynamic gene networks undervarying conditions for transcriptomic net-work comparison

Teppei Shimamura Seiya Imoto Rui Yama-guchi Masao Nagasaki Satoru Miyano

Elucidating the differences between cellularresponses to various biological conditions or ex-ternal stimuli is an important challenge in sys-tems biology Many approaches have been de-veloped for reverse-engineering a cellular sys-tem called gene network from time series mi-croarray gene expression data in order to under-stand a transcriptomic response under a condi-tion of interest Comparative topological analy-sis has also been applied based on the gene net-

works inferred independently from each of themultiple time series datasets under varying con-ditions to find critical differences between thesenetworks However these comparisons oftenlead to misleading results because each networkcontains considerable noise due to the limitedlength of the time series With this motivationwe developed an integrated approach for infer-ring multiple gene networks from time seriesexpression data under varying conditions Tothe best of our knowledge our approach is thefirst reverse-engineering method that is intendedfor transcriptomic network comparison betweenvarying conditions Furthermore we developeda state-of-the-art parameter estimation methodrelevance-weighted recursive elastic net for pro-viding higher precision and recall than existingreverse-engineering methods We analyze ex-perimental data of MCF-7 human breast cancer

Human Genome Center

Laboratory of DNA Information AnalysisLaboratory of Sequence Data AnalysisDNA情報解析分野シークエンスデータ情報処理分野

Professor Satoru Miyano PhDAssociate Professor Seiya Imoto PhDAssistant Professor Masao Nagasaki PhDProject Assistant Professor Yoshinori Tamada PhDProject Assistant Professor Teppei Shimamura PhDAssociate Professor Tetsuo Shibuya PhDLecturer Rui Yamaguchi PhD

教 授 理学博士 宮 野 悟准教授 博士（数理学） 井 元 清 哉助 教 博士（理学） 長 正 朗特任助教 博士（情報学） 玉 田 嘉 紀特任助教 博士（工学） 島 村 徹 平准教授 博士（理学） 渋 谷 哲 朗講 師 博士（理学） 山 口 類

100

cells stimulated by epidermal growth factor orheregulin with several doses and provide novelbiological hypotheses through network compari-son The software NETCOMP is available athttp bonsai ims u-tokyo ac jp ~shima NETCOMP

b Collocation-based sparse estimation forconstructing dynamic gene networks

Teppei Shimamura Seiya Imoto Masao Na-gasaki Mai Yamauchi13 Rui Yamaguchi An-dreacute Fujita Yoshinori Tamada Noriko Gotoh13Satoru Miyano

One of the open problems in systems biologyis to infer dynamic gene networks describingthe underlying biological process with mathe-matical statistical and computational methodsThe first-order difference equation-based modelssuch as dynamic Bayesian networks and vectorautoregressive models were used to infer time-lagged relationships between genes from time-series microarray data However two primaryproblems greatly reduce the effectiveness of cur-rent approaches The first problem is the tacitassumption that time lag is stationary The sec-ond is the inseparability between measurementnoise and process noise (unmeasured distur-bances that pass through time process) To ad-dress these problems we developed a stochasticdifferential equation model for inferringcontinuous-time dynamic gene networks underthe situation in which both of the process noiseand the observation noise exist We devised acollocation-based sparse estimation for simulta-neous parameter estimation and model selectionin the model The collocation-based approach re-quires considerably less computational effortthan traditional methods in ordinary stochasticdifferential equation models We also incorpo-rated various biological knowledge easily to re-fine the estimation accuracy with this methodThe results using simulated data and real time-series expression data of human primary smallairway epithelial cells demonstrate that this ap-proach outperformed competing approaches andcould provide significant genes influenced byGefitinib

c Gene set-based module discovery de-codes cis-regulatory codes governing di-verse gene expression across human mul-tiple tissues

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Saatoru Miyano

Decoding transcriptional programs governing

transcriptomic diversity across human multipletissues is a major challenge in bioinformatics Toaddress this problem a number of computa-tional methods have focused on cis-regulatorycodes driving overexpression or underexpres-sion in a single tissue as compared to others Onthe other hand we recently proposed a differentapproach to mine cis-regulatory codes startingfrom gene sets sharing common cis-regulatorymotifs the method screens for expression mod-ules based on expression coherence Howeverboth approaches seem to be insufficient to cap-ture transcriptional programs that control geneexpression in a subset of all samples Especiallythis limitation would be serious when analyzingmultiple tissue data To overcome this limita-tion we developed a new module discoverymethod termed BEEM (Biclusering-based Extrac-tion of Expression Modules) in order to discoverexpression modules that are functional in a sub-set of tissues We showed that when applied toexpression profiles of human multiple tissuesBEEM finds expression modules missed by twoexisting approaches that are based on the coher-ent expression and the single tissue-specific dif-ferential expression From the BEEM results weobtained new insights into transcriptional pro-grams controlling transcriptomic diversity acrossvarious types of tissues This study introducesBEEM as a powerful tool for decoding regula-tory programs from a compendium of gene ex-pression profiles

d Model-free unsupervised gene set screen-ing based on information enrichment inexpression profiles

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Andreacute Fujita Teppei Shima-mura Satoru Miyano

A number of unsupervised gene set screeningmethods have recently been developed forsearch of putative functional gene sets based ontheir expression profiles Most of the methodsstatistically evaluate whether the expression pro-files of each gene set are fit to assumed modelseg co-expression across all samples or a sub-group of samples However it is possible thatthey fail to capture informative gene sets whoseexpression profiles are not fit to the assumedmodels To overcome this limitation we devel-oped a model-free unsupervised gene set screen-ing method Matrix Information EnrichmentAnalysis (MIEA) Without assuming any specificmodels MIEA screens gene sets based on infor-mation richness of their expression profiles Weextensively compared the performance of MIEAto those of other unsupervised gene set screen-

101

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

ware made available under the Ruby licenseBioRuby runs on all platforms that supportRuby including Linux Mac OS X and Win-dows And with JRuby BioRuby runs on theJava Virtual Machine The source code is avail-able from httpwwwbiorubyorg

6 TogoWS integrated SOAP and REST APIsfor interoperable bioinformatics Web serv-ices

Toshiaki Katayama Mitsuteru Nakao1 andToshihisa Takagi23 1Database Center for LifeScience ROIS 2National Bioscience DatabaseCenter JST 3Graduate School of Frontier Sci-ences The University of Tokyo

Web services have become widely used inbioinformatics analysis but there exist incom-patibilities in interfaces and data types whichprevent users from making full use of a combi-nation of these services Therefore we have de-veloped the TogoWS service to provide an inte-grated interface with advanced features In theTogoWS REST (REpresentative State Transfer)API (application programming interface) we in-troduce a unified access method for major data-base resources through intuitive URIs that canbe used to search retrieve parse and convertthe database entries The TogoWS SOAP API re-solves compatibility issues found on the serverand client-side SOAP implementations The To-goWS service is freely available at httptogowsdbclsjp

7 TogoDB Instantly publish your researchmaterial as a public database

Toshiaki Katayama Mitsuteru Nakao1 andToshihisa Takagi23 1Database Center for LifeScience ROIS 2National Bioscience DatabaseCenter JST 3Graduate School of Frontier Sci-ences The University of Tokyo

Supplemental materials are often provided asseparate files downloadable from the publisherrsquossite along with the publication of a journal arti-cle However these data are not fully utilizedsince they are not available in the form of regu-lar biological databases and hard to find by thepopular Web search engines TogoDB is a sim-ple and intuitive database system to publishtabular formatted data instantly on the Web Us-ers can upload their research materials to theTogoDB through the simple web interface andthe data will be made available as a fully func-tional database in a minute or two TogoWS isan integrated and uniformed interface for themajor bioinformatics web services and also pro-

vides REST API for the contents in the TogoDBRecently we extended TogoDB and TogoWS tobe used as a consolidated platform for the Se-mantic Web by adding a metadata editor and anautomatic Resource Description Framework(RDF) dumper This system fills the gap be-tween userrsquos data and major public databases todeliver effective variations in the Linked Data

8 Characterization of parasite specific genesby ortholog gene clusters and the Seman-tic Web technologies

Toshiaki Katayama Shuichi KawashimaJunichi Watanabe Yutaka Suzuki1 SumioSugano1 and Minoru Kanehisa 1GraduateSchool of Frontier Sciences The University ofTokyo

Characterization of a set of genes is one of themost demanded tasks in bioinformatics Usuallyextensive sequence similarity search is per-formed and the functions of query sequencesare inferred from the annotation of highly simi-lar sequences For more accurate inferenceortholog clusters and protein motif informationare often added for further investigationOrtholog cluster is useful to infer the phyloge-netic distribution of the protein family and mo-tifs provides molecular evidence of the func-tional domains in combination In this way in-formation integration of related data sources isgaining in importance to make the annotationmore reliable or to discover hidden relationsamong data sets However the incompatibleidentifiers and data types have prevented fromintegrating heterogeneous data seamlesslyamong life-science databases Recently the Se-mantic Web technologies are being accepted toresolve this situation We applied these methodsto characterize a set of genes from non-labstrains of Plasmodium falciparum and other para-site species Clinical samples are taken at thehospital in Manado Indonesia and RNA se-quencing was performed to find over-expressedmalarial genes As a result we obtained ~5 oftotal genes which are highly expressed Amongthem we found 20 P falciparum specific 48 Plas-modium specific and 43 Apicomplexa specificgenes Many of them turned out to possessparasite specific domains such as surface anti-gen and exported protein with unknown func-tion We also discovered that some of them arechanged 7-folds in their gene expression levelsamong samples which can be candidates for thedrug target

96

9 Analysis of EST sequences from thehouse dust mite Dermatophagoides fari-nae

Shuichi Kawashima Junichi Watanabe andMinoru Kanehisa

The house dust mite feed on skin scales (dan-der and scurf) and other organic detritus suchas bacteria spores and feathers and produce 20to 30 small fecal particles which are highly al-lergic Thus it is important that we expand ourknowledge of the mites to develop effective al-lergy panels or vaccines Angus et al have initi-ated a project to sequence ESTs of Dermato-phagoides farinae and other mite species associ-ated with allergic diseases Wakaguri et al havealso sequenced ESTs of D farinae which wasfirst established in 1968 and has been main-tained using the method developed by Sasa etal The produced sequences are available at theFullMite database In this study we analyzed therelationships between known mite allergens andthe EST sequences derived from the FullMitedatabase

After removing low quality regions and clip-ping vector sequences from the initial 23040 se-quences a total of 21005 sequences is retainedThen we assembled pair-end sequences if theywere aligned with a strict condition (more than500 bit score and 99 sequence identity in thealigned region) Clustering and assembling withthe CAP3 software resulted in 1717 contigs and3368 singletons The distribution of the numberof ESTs included in each contig showed thatknown allergens were widely distributedthrough the variety of gene expression levelsAs expected the major mite allergens such asDer f 1 or Der f 2 were highly expressed in ourdata On the other hand there were also knownallergens which were lower expressed It isknown at least 20 of adults allergic to mitehave poor reactivity to the group 1 and group 2allergens Furthermore new mite allergens havestill been characterized today (eg Der f 22)Thus there could be unknown mite allergens inour data and we will try to screen potential al-lergens which are still uncharacterized

10 Analysis of a tardigrade proteome withthe Gene Ontology

Shuichi Kawashima Toshiaki Katayama andMinoru Kanehisa

Kunieda et al have been sequencing and ana-lyzing the genome of extremotolerant tardi-grade Rammazzottius cf varieornatus YOKOZUNA-1 Currently they produced about

15000 hypothetical protein coding genes by us-ing ab initio method implemented in SNAP soft-ware Tardigrades form the phylum Tardigradawhich is considered as a member of the su-perphylum Ecdysozoa However the definitivephylogenetic position is still unclear To under-stand the ecdysozoans specific molecular func-tions we compared the Gene Ontology termsannotated to the proteome with those of Dro-sphila melanogaster Daphnia pulex and Caenorhab-ditis elegans as representative Ecdysozoas andfound the 2241 GO temrs common to the fourecdysozoans Interestingly only six ontologieswere found in the proteomes of four species ex-clusively Those are rhabdomere (GO0016028)cation channel complex (GO0034703) septatejunction (GO0005918) signal recognition parti-cle (GO0048500) fusom (GO0045169) and spec-trosome (GO0045170)

11 Functional genome annotation of a tardi-grade by KEGG MODULE database

Toshiaki Katayama Shuichi Kawashima andMinoru Kanehisa

Functional annotation of genes is usually per-formed based on sequence similarities to genesof other organisms However it is difficult tofind out characteristics of the genome onlybased on the each annotated gene Thereforeoverall signature of a genome is often describedwith the help of the Gene Ontology (GO) orKEGG PATHWAY databases Assigning GOterms to genes we can grasp an outline of func-tional categories covered by a set of genes en-coded in a genome Reconstructing KEGGPATHWAY will reveals metabolic and regula-tory pathways that the target organism mayutilize The problem here is the granularityFunctional categories of the GO and coveringarea of each KEGG PATHWAY map are rathercoarse-grained to find key differences among or-ganisms Meanwhile KEGG MODULE is a data-base of functional units in the pathways whichare highly conserved among organisms We arerunning a genome project of a tardigrade whichis expected to explain its phylogenetic positionand to make functional annotation of thegenome Therefore we introduced the KEGGMODULE to see conserved and non-conservedmodules in the tardigrade genome comparedwith closely-related species As a result wefound 184 conserved modules in tardigradewhich are slightly larger than that of C elegans(162) D pulex (181) and D melanogaster (164)Among them we found several module candi-dates describing evolution of the metabolicpathways in animal For example M00029 (urea

97

cycle) which is missing in nematodes partiallyconserved (cytosolic portion) in arthropods andfully conserved in vertebrates (cytosolic and mi-tochondrial portions) Tardigrade had only oneenzyme in this module (in cytosolic portion)showing the same pattern with some protistsAs the number of sequenced genomes increasesvery rapidly KEGG MODULE combined with aphylogenetic profile will be a powerful tool toelucidate characteristics of those genomes effi-ciently

12 HiGet and SSS Search engines for thelarge-scale biological databases

Toshiaki Katayama Shuichi KawashimaKazuhiro Ohi1 Kenta Nakai2 Minoru Kane-hisa 1Hitatchi Ltd 2Laboratory of FunctionalAnalysis In Silico Institute of Medical ScienceThe University of Tokyo

The number of entries in biological databasesis exponentially increasing year by year For ex-ample there were 10106023 entries in the Gen-Bank database in the year 2000 which has nowgrown to 141537514 (Release 181＋daily up-dates) In order for such a vast amount of datato be searched at a high speed we have devel-

oped a high performance database entry re-trieval system named HiGet For this purposethe system is constructed on the HiRDB a com-mercial ORDBMS (Object-oriented RelationalDatabase Management System) developed byHitachi Ltd HiGet can perform full text searchon various biological databases including Gen-Bank RefSeq UniProt Prosite OMIM and PDBAdditional advantage of the HiGet system is thecapability of a field specific search which en-ables users to narrow down the number of re-sults especially useful for collecting sequencesof their specific needs We have also developeda sequence similarity search (SSS) service to findhomologous sequences with various algorithmsincluding BLAST FASTA SSEARCH TRANSand EXONERATE This variety of options isunique among the public services and users canselect an appropriate method to search similarsequences according to their query Because al-gorithms such as TRANS and EXONERATE arehighly time consuming the SSS service is back-ended by the distributed computing environ-ment with the Sun Grid Engine in our supercomputer system HiGet and SSS services areavailable at httphigethgcjp and httpssshgcjp respectively

Publications

Kanehisa M Goto S Furumichi M TanabeM Hirakawa M KEGG for representationand analysis of molecular networks involvingdiseases and drugs Nucleic Acids Research 38D355-D360 2010

Katayama T Nakao M Takagi T TogoWSintegrated SOAP and REST APIs for interop-erable bioinformatics Web services Nucleic Ac-ids Research 38 W706-W711 2010

Katayama T Arakawa K Nakao M Ono KAoki-Kinoshita KF Yamamoto Y Yama-guchi A Kawashima S Chun HW AertsJ Aranda B Barboza LH Bonnal RJBruskiewich R Bryne JC Fernaacutendez JMFunahashi A Gordon PM Goto N Gro-scurth A Gutteridge A Holland R KanoY Kawas EA Kerhornou A Kibukawa EKinjo AR Kuhn M Lapp H LehvaslaihoH Nakamura H Nakamura Y NishizawaT Nobata C Noguchi T Oinn TMOkamoto S Owen S Pafilis E Pocock MPrins P Ranzinger R Reisinger F Salwin-ski L Schreiber M Senger M ShigemotoY Standley DM Sugawara H Tashiro TTrelles O Vos RA Wilkinson MD YorkW Zmasek CM Asai K Takagi T TheDBCLS BioHackathon standardization and in-

teroperability for bioinformatics web servicesand workflows Journal of Biomedical Semantics1 8 2010

Goto N Prins P Nakao M Bonnal R AertsJ Katayama T BioRuby bioinformatics soft-ware for the Ruby programming languageBioinformatics 26 2617-2619 2010

Yamanishi Y Kotera M Kanehisa M GotoS Drug-target interaction prediction fromchemical genomic and pharmacological datain an integrated framework Bioinformatics 26i246-i256 2010

Erguner B Hattori M Goto S Kanehisa MCharacterizing common substructures ofligands for GPCR protein subfamilies GenomeInformatics 24 31-41 2010

Kotera M Kobayashi T Hattori M Toki-matsu T Goto S Mihara H Kanehisa MComprehensive genomic analysis of sulfur-relay pathway genes Genome Informatics 24104-115 2010

Mizutani S Tanaka M Wheelock C Kane-hisa M Goto S Phylogenetic analysis oflipid mediator GPCRs Genome Informatics 24116-126 2010

Nishimura Y Tokimatsu T Kotera M GotoS Kanehisa M Genome-wide analysis of

98

plant UGT family based on sequence and sub-strate information Genome Informatics 24 127-

138 2010

99

The recent advances in biomedical research have been producing large-scaleultra-high dimensional ultra-heterogeneous data Due to these post-genomic re-search progresses our current mission is to create computational strategy for sys-tems biology and medicine towards translational bioinformatics With this missionwe have been developing computational methods for understanding life as systemand applying them to practical issues in medicine and biology

1 Gene Network Analysis

a Inferring dynamic gene networks undervarying conditions for transcriptomic net-work comparison

Teppei Shimamura Seiya Imoto Rui Yama-guchi Masao Nagasaki Satoru Miyano

Elucidating the differences between cellularresponses to various biological conditions or ex-ternal stimuli is an important challenge in sys-tems biology Many approaches have been de-veloped for reverse-engineering a cellular sys-tem called gene network from time series mi-croarray gene expression data in order to under-stand a transcriptomic response under a condi-tion of interest Comparative topological analy-sis has also been applied based on the gene net-

works inferred independently from each of themultiple time series datasets under varying con-ditions to find critical differences between thesenetworks However these comparisons oftenlead to misleading results because each networkcontains considerable noise due to the limitedlength of the time series With this motivationwe developed an integrated approach for infer-ring multiple gene networks from time seriesexpression data under varying conditions Tothe best of our knowledge our approach is thefirst reverse-engineering method that is intendedfor transcriptomic network comparison betweenvarying conditions Furthermore we developeda state-of-the-art parameter estimation methodrelevance-weighted recursive elastic net for pro-viding higher precision and recall than existingreverse-engineering methods We analyze ex-perimental data of MCF-7 human breast cancer

Human Genome Center

Laboratory of DNA Information AnalysisLaboratory of Sequence Data AnalysisDNA情報解析分野シークエンスデータ情報処理分野

Professor Satoru Miyano PhDAssociate Professor Seiya Imoto PhDAssistant Professor Masao Nagasaki PhDProject Assistant Professor Yoshinori Tamada PhDProject Assistant Professor Teppei Shimamura PhDAssociate Professor Tetsuo Shibuya PhDLecturer Rui Yamaguchi PhD

教 授 理学博士 宮 野 悟准教授 博士（数理学） 井 元 清 哉助 教 博士（理学） 長 正 朗特任助教 博士（情報学） 玉 田 嘉 紀特任助教 博士（工学） 島 村 徹 平准教授 博士（理学） 渋 谷 哲 朗講 師 博士（理学） 山 口 類

100

cells stimulated by epidermal growth factor orheregulin with several doses and provide novelbiological hypotheses through network compari-son The software NETCOMP is available athttp bonsai ims u-tokyo ac jp ~shima NETCOMP

b Collocation-based sparse estimation forconstructing dynamic gene networks

Teppei Shimamura Seiya Imoto Masao Na-gasaki Mai Yamauchi13 Rui Yamaguchi An-dreacute Fujita Yoshinori Tamada Noriko Gotoh13Satoru Miyano

One of the open problems in systems biologyis to infer dynamic gene networks describingthe underlying biological process with mathe-matical statistical and computational methodsThe first-order difference equation-based modelssuch as dynamic Bayesian networks and vectorautoregressive models were used to infer time-lagged relationships between genes from time-series microarray data However two primaryproblems greatly reduce the effectiveness of cur-rent approaches The first problem is the tacitassumption that time lag is stationary The sec-ond is the inseparability between measurementnoise and process noise (unmeasured distur-bances that pass through time process) To ad-dress these problems we developed a stochasticdifferential equation model for inferringcontinuous-time dynamic gene networks underthe situation in which both of the process noiseand the observation noise exist We devised acollocation-based sparse estimation for simulta-neous parameter estimation and model selectionin the model The collocation-based approach re-quires considerably less computational effortthan traditional methods in ordinary stochasticdifferential equation models We also incorpo-rated various biological knowledge easily to re-fine the estimation accuracy with this methodThe results using simulated data and real time-series expression data of human primary smallairway epithelial cells demonstrate that this ap-proach outperformed competing approaches andcould provide significant genes influenced byGefitinib

c Gene set-based module discovery de-codes cis-regulatory codes governing di-verse gene expression across human mul-tiple tissues

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Saatoru Miyano

Decoding transcriptional programs governing

transcriptomic diversity across human multipletissues is a major challenge in bioinformatics Toaddress this problem a number of computa-tional methods have focused on cis-regulatorycodes driving overexpression or underexpres-sion in a single tissue as compared to others Onthe other hand we recently proposed a differentapproach to mine cis-regulatory codes startingfrom gene sets sharing common cis-regulatorymotifs the method screens for expression mod-ules based on expression coherence Howeverboth approaches seem to be insufficient to cap-ture transcriptional programs that control geneexpression in a subset of all samples Especiallythis limitation would be serious when analyzingmultiple tissue data To overcome this limita-tion we developed a new module discoverymethod termed BEEM (Biclusering-based Extrac-tion of Expression Modules) in order to discoverexpression modules that are functional in a sub-set of tissues We showed that when applied toexpression profiles of human multiple tissuesBEEM finds expression modules missed by twoexisting approaches that are based on the coher-ent expression and the single tissue-specific dif-ferential expression From the BEEM results weobtained new insights into transcriptional pro-grams controlling transcriptomic diversity acrossvarious types of tissues This study introducesBEEM as a powerful tool for decoding regula-tory programs from a compendium of gene ex-pression profiles

d Model-free unsupervised gene set screen-ing based on information enrichment inexpression profiles

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Andreacute Fujita Teppei Shima-mura Satoru Miyano

A number of unsupervised gene set screeningmethods have recently been developed forsearch of putative functional gene sets based ontheir expression profiles Most of the methodsstatistically evaluate whether the expression pro-files of each gene set are fit to assumed modelseg co-expression across all samples or a sub-group of samples However it is possible thatthey fail to capture informative gene sets whoseexpression profiles are not fit to the assumedmodels To overcome this limitation we devel-oped a model-free unsupervised gene set screen-ing method Matrix Information EnrichmentAnalysis (MIEA) Without assuming any specificmodels MIEA screens gene sets based on infor-mation richness of their expression profiles Weextensively compared the performance of MIEAto those of other unsupervised gene set screen-

101

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

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strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

9 Analysis of EST sequences from thehouse dust mite Dermatophagoides fari-nae

Shuichi Kawashima Junichi Watanabe andMinoru Kanehisa

The house dust mite feed on skin scales (dan-der and scurf) and other organic detritus suchas bacteria spores and feathers and produce 20to 30 small fecal particles which are highly al-lergic Thus it is important that we expand ourknowledge of the mites to develop effective al-lergy panels or vaccines Angus et al have initi-ated a project to sequence ESTs of Dermato-phagoides farinae and other mite species associ-ated with allergic diseases Wakaguri et al havealso sequenced ESTs of D farinae which wasfirst established in 1968 and has been main-tained using the method developed by Sasa etal The produced sequences are available at theFullMite database In this study we analyzed therelationships between known mite allergens andthe EST sequences derived from the FullMitedatabase

After removing low quality regions and clip-ping vector sequences from the initial 23040 se-quences a total of 21005 sequences is retainedThen we assembled pair-end sequences if theywere aligned with a strict condition (more than500 bit score and 99 sequence identity in thealigned region) Clustering and assembling withthe CAP3 software resulted in 1717 contigs and3368 singletons The distribution of the numberof ESTs included in each contig showed thatknown allergens were widely distributedthrough the variety of gene expression levelsAs expected the major mite allergens such asDer f 1 or Der f 2 were highly expressed in ourdata On the other hand there were also knownallergens which were lower expressed It isknown at least 20 of adults allergic to mitehave poor reactivity to the group 1 and group 2allergens Furthermore new mite allergens havestill been characterized today (eg Der f 22)Thus there could be unknown mite allergens inour data and we will try to screen potential al-lergens which are still uncharacterized

10 Analysis of a tardigrade proteome withthe Gene Ontology

Shuichi Kawashima Toshiaki Katayama andMinoru Kanehisa

Kunieda et al have been sequencing and ana-lyzing the genome of extremotolerant tardi-grade Rammazzottius cf varieornatus YOKOZUNA-1 Currently they produced about

15000 hypothetical protein coding genes by us-ing ab initio method implemented in SNAP soft-ware Tardigrades form the phylum Tardigradawhich is considered as a member of the su-perphylum Ecdysozoa However the definitivephylogenetic position is still unclear To under-stand the ecdysozoans specific molecular func-tions we compared the Gene Ontology termsannotated to the proteome with those of Dro-sphila melanogaster Daphnia pulex and Caenorhab-ditis elegans as representative Ecdysozoas andfound the 2241 GO temrs common to the fourecdysozoans Interestingly only six ontologieswere found in the proteomes of four species ex-clusively Those are rhabdomere (GO0016028)cation channel complex (GO0034703) septatejunction (GO0005918) signal recognition parti-cle (GO0048500) fusom (GO0045169) and spec-trosome (GO0045170)

11 Functional genome annotation of a tardi-grade by KEGG MODULE database

Toshiaki Katayama Shuichi Kawashima andMinoru Kanehisa

Functional annotation of genes is usually per-formed based on sequence similarities to genesof other organisms However it is difficult tofind out characteristics of the genome onlybased on the each annotated gene Thereforeoverall signature of a genome is often describedwith the help of the Gene Ontology (GO) orKEGG PATHWAY databases Assigning GOterms to genes we can grasp an outline of func-tional categories covered by a set of genes en-coded in a genome Reconstructing KEGGPATHWAY will reveals metabolic and regula-tory pathways that the target organism mayutilize The problem here is the granularityFunctional categories of the GO and coveringarea of each KEGG PATHWAY map are rathercoarse-grained to find key differences among or-ganisms Meanwhile KEGG MODULE is a data-base of functional units in the pathways whichare highly conserved among organisms We arerunning a genome project of a tardigrade whichis expected to explain its phylogenetic positionand to make functional annotation of thegenome Therefore we introduced the KEGGMODULE to see conserved and non-conservedmodules in the tardigrade genome comparedwith closely-related species As a result wefound 184 conserved modules in tardigradewhich are slightly larger than that of C elegans(162) D pulex (181) and D melanogaster (164)Among them we found several module candi-dates describing evolution of the metabolicpathways in animal For example M00029 (urea

97

cycle) which is missing in nematodes partiallyconserved (cytosolic portion) in arthropods andfully conserved in vertebrates (cytosolic and mi-tochondrial portions) Tardigrade had only oneenzyme in this module (in cytosolic portion)showing the same pattern with some protistsAs the number of sequenced genomes increasesvery rapidly KEGG MODULE combined with aphylogenetic profile will be a powerful tool toelucidate characteristics of those genomes effi-ciently

12 HiGet and SSS Search engines for thelarge-scale biological databases

Toshiaki Katayama Shuichi KawashimaKazuhiro Ohi1 Kenta Nakai2 Minoru Kane-hisa 1Hitatchi Ltd 2Laboratory of FunctionalAnalysis In Silico Institute of Medical ScienceThe University of Tokyo

The number of entries in biological databasesis exponentially increasing year by year For ex-ample there were 10106023 entries in the Gen-Bank database in the year 2000 which has nowgrown to 141537514 (Release 181＋daily up-dates) In order for such a vast amount of datato be searched at a high speed we have devel-

oped a high performance database entry re-trieval system named HiGet For this purposethe system is constructed on the HiRDB a com-mercial ORDBMS (Object-oriented RelationalDatabase Management System) developed byHitachi Ltd HiGet can perform full text searchon various biological databases including Gen-Bank RefSeq UniProt Prosite OMIM and PDBAdditional advantage of the HiGet system is thecapability of a field specific search which en-ables users to narrow down the number of re-sults especially useful for collecting sequencesof their specific needs We have also developeda sequence similarity search (SSS) service to findhomologous sequences with various algorithmsincluding BLAST FASTA SSEARCH TRANSand EXONERATE This variety of options isunique among the public services and users canselect an appropriate method to search similarsequences according to their query Because al-gorithms such as TRANS and EXONERATE arehighly time consuming the SSS service is back-ended by the distributed computing environ-ment with the Sun Grid Engine in our supercomputer system HiGet and SSS services areavailable at httphigethgcjp and httpssshgcjp respectively

Publications

Kanehisa M Goto S Furumichi M TanabeM Hirakawa M KEGG for representationand analysis of molecular networks involvingdiseases and drugs Nucleic Acids Research 38D355-D360 2010

Katayama T Nakao M Takagi T TogoWSintegrated SOAP and REST APIs for interop-erable bioinformatics Web services Nucleic Ac-ids Research 38 W706-W711 2010

Katayama T Arakawa K Nakao M Ono KAoki-Kinoshita KF Yamamoto Y Yama-guchi A Kawashima S Chun HW AertsJ Aranda B Barboza LH Bonnal RJBruskiewich R Bryne JC Fernaacutendez JMFunahashi A Gordon PM Goto N Gro-scurth A Gutteridge A Holland R KanoY Kawas EA Kerhornou A Kibukawa EKinjo AR Kuhn M Lapp H LehvaslaihoH Nakamura H Nakamura Y NishizawaT Nobata C Noguchi T Oinn TMOkamoto S Owen S Pafilis E Pocock MPrins P Ranzinger R Reisinger F Salwin-ski L Schreiber M Senger M ShigemotoY Standley DM Sugawara H Tashiro TTrelles O Vos RA Wilkinson MD YorkW Zmasek CM Asai K Takagi T TheDBCLS BioHackathon standardization and in-

teroperability for bioinformatics web servicesand workflows Journal of Biomedical Semantics1 8 2010

Goto N Prins P Nakao M Bonnal R AertsJ Katayama T BioRuby bioinformatics soft-ware for the Ruby programming languageBioinformatics 26 2617-2619 2010

Yamanishi Y Kotera M Kanehisa M GotoS Drug-target interaction prediction fromchemical genomic and pharmacological datain an integrated framework Bioinformatics 26i246-i256 2010

Erguner B Hattori M Goto S Kanehisa MCharacterizing common substructures ofligands for GPCR protein subfamilies GenomeInformatics 24 31-41 2010

Kotera M Kobayashi T Hattori M Toki-matsu T Goto S Mihara H Kanehisa MComprehensive genomic analysis of sulfur-relay pathway genes Genome Informatics 24104-115 2010

Mizutani S Tanaka M Wheelock C Kane-hisa M Goto S Phylogenetic analysis oflipid mediator GPCRs Genome Informatics 24116-126 2010

Nishimura Y Tokimatsu T Kotera M GotoS Kanehisa M Genome-wide analysis of

98

plant UGT family based on sequence and sub-strate information Genome Informatics 24 127-

138 2010

99

The recent advances in biomedical research have been producing large-scaleultra-high dimensional ultra-heterogeneous data Due to these post-genomic re-search progresses our current mission is to create computational strategy for sys-tems biology and medicine towards translational bioinformatics With this missionwe have been developing computational methods for understanding life as systemand applying them to practical issues in medicine and biology

1 Gene Network Analysis

a Inferring dynamic gene networks undervarying conditions for transcriptomic net-work comparison

Teppei Shimamura Seiya Imoto Rui Yama-guchi Masao Nagasaki Satoru Miyano

Elucidating the differences between cellularresponses to various biological conditions or ex-ternal stimuli is an important challenge in sys-tems biology Many approaches have been de-veloped for reverse-engineering a cellular sys-tem called gene network from time series mi-croarray gene expression data in order to under-stand a transcriptomic response under a condi-tion of interest Comparative topological analy-sis has also been applied based on the gene net-

works inferred independently from each of themultiple time series datasets under varying con-ditions to find critical differences between thesenetworks However these comparisons oftenlead to misleading results because each networkcontains considerable noise due to the limitedlength of the time series With this motivationwe developed an integrated approach for infer-ring multiple gene networks from time seriesexpression data under varying conditions Tothe best of our knowledge our approach is thefirst reverse-engineering method that is intendedfor transcriptomic network comparison betweenvarying conditions Furthermore we developeda state-of-the-art parameter estimation methodrelevance-weighted recursive elastic net for pro-viding higher precision and recall than existingreverse-engineering methods We analyze ex-perimental data of MCF-7 human breast cancer

Human Genome Center

Laboratory of DNA Information AnalysisLaboratory of Sequence Data AnalysisDNA情報解析分野シークエンスデータ情報処理分野

Professor Satoru Miyano PhDAssociate Professor Seiya Imoto PhDAssistant Professor Masao Nagasaki PhDProject Assistant Professor Yoshinori Tamada PhDProject Assistant Professor Teppei Shimamura PhDAssociate Professor Tetsuo Shibuya PhDLecturer Rui Yamaguchi PhD

教 授 理学博士 宮 野 悟准教授 博士（数理学） 井 元 清 哉助 教 博士（理学） 長 正 朗特任助教 博士（情報学） 玉 田 嘉 紀特任助教 博士（工学） 島 村 徹 平准教授 博士（理学） 渋 谷 哲 朗講 師 博士（理学） 山 口 類

100

cells stimulated by epidermal growth factor orheregulin with several doses and provide novelbiological hypotheses through network compari-son The software NETCOMP is available athttp bonsai ims u-tokyo ac jp ~shima NETCOMP

b Collocation-based sparse estimation forconstructing dynamic gene networks

Teppei Shimamura Seiya Imoto Masao Na-gasaki Mai Yamauchi13 Rui Yamaguchi An-dreacute Fujita Yoshinori Tamada Noriko Gotoh13Satoru Miyano

One of the open problems in systems biologyis to infer dynamic gene networks describingthe underlying biological process with mathe-matical statistical and computational methodsThe first-order difference equation-based modelssuch as dynamic Bayesian networks and vectorautoregressive models were used to infer time-lagged relationships between genes from time-series microarray data However two primaryproblems greatly reduce the effectiveness of cur-rent approaches The first problem is the tacitassumption that time lag is stationary The sec-ond is the inseparability between measurementnoise and process noise (unmeasured distur-bances that pass through time process) To ad-dress these problems we developed a stochasticdifferential equation model for inferringcontinuous-time dynamic gene networks underthe situation in which both of the process noiseand the observation noise exist We devised acollocation-based sparse estimation for simulta-neous parameter estimation and model selectionin the model The collocation-based approach re-quires considerably less computational effortthan traditional methods in ordinary stochasticdifferential equation models We also incorpo-rated various biological knowledge easily to re-fine the estimation accuracy with this methodThe results using simulated data and real time-series expression data of human primary smallairway epithelial cells demonstrate that this ap-proach outperformed competing approaches andcould provide significant genes influenced byGefitinib

c Gene set-based module discovery de-codes cis-regulatory codes governing di-verse gene expression across human mul-tiple tissues

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Saatoru Miyano

Decoding transcriptional programs governing

transcriptomic diversity across human multipletissues is a major challenge in bioinformatics Toaddress this problem a number of computa-tional methods have focused on cis-regulatorycodes driving overexpression or underexpres-sion in a single tissue as compared to others Onthe other hand we recently proposed a differentapproach to mine cis-regulatory codes startingfrom gene sets sharing common cis-regulatorymotifs the method screens for expression mod-ules based on expression coherence Howeverboth approaches seem to be insufficient to cap-ture transcriptional programs that control geneexpression in a subset of all samples Especiallythis limitation would be serious when analyzingmultiple tissue data To overcome this limita-tion we developed a new module discoverymethod termed BEEM (Biclusering-based Extrac-tion of Expression Modules) in order to discoverexpression modules that are functional in a sub-set of tissues We showed that when applied toexpression profiles of human multiple tissuesBEEM finds expression modules missed by twoexisting approaches that are based on the coher-ent expression and the single tissue-specific dif-ferential expression From the BEEM results weobtained new insights into transcriptional pro-grams controlling transcriptomic diversity acrossvarious types of tissues This study introducesBEEM as a powerful tool for decoding regula-tory programs from a compendium of gene ex-pression profiles

d Model-free unsupervised gene set screen-ing based on information enrichment inexpression profiles

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Andreacute Fujita Teppei Shima-mura Satoru Miyano

A number of unsupervised gene set screeningmethods have recently been developed forsearch of putative functional gene sets based ontheir expression profiles Most of the methodsstatistically evaluate whether the expression pro-files of each gene set are fit to assumed modelseg co-expression across all samples or a sub-group of samples However it is possible thatthey fail to capture informative gene sets whoseexpression profiles are not fit to the assumedmodels To overcome this limitation we devel-oped a model-free unsupervised gene set screen-ing method Matrix Information EnrichmentAnalysis (MIEA) Without assuming any specificmodels MIEA screens gene sets based on infor-mation richness of their expression profiles Weextensively compared the performance of MIEAto those of other unsupervised gene set screen-

101

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

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Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

cycle) which is missing in nematodes partiallyconserved (cytosolic portion) in arthropods andfully conserved in vertebrates (cytosolic and mi-tochondrial portions) Tardigrade had only oneenzyme in this module (in cytosolic portion)showing the same pattern with some protistsAs the number of sequenced genomes increasesvery rapidly KEGG MODULE combined with aphylogenetic profile will be a powerful tool toelucidate characteristics of those genomes effi-ciently

12 HiGet and SSS Search engines for thelarge-scale biological databases

Toshiaki Katayama Shuichi KawashimaKazuhiro Ohi1 Kenta Nakai2 Minoru Kane-hisa 1Hitatchi Ltd 2Laboratory of FunctionalAnalysis In Silico Institute of Medical ScienceThe University of Tokyo

The number of entries in biological databasesis exponentially increasing year by year For ex-ample there were 10106023 entries in the Gen-Bank database in the year 2000 which has nowgrown to 141537514 (Release 181＋daily up-dates) In order for such a vast amount of datato be searched at a high speed we have devel-

oped a high performance database entry re-trieval system named HiGet For this purposethe system is constructed on the HiRDB a com-mercial ORDBMS (Object-oriented RelationalDatabase Management System) developed byHitachi Ltd HiGet can perform full text searchon various biological databases including Gen-Bank RefSeq UniProt Prosite OMIM and PDBAdditional advantage of the HiGet system is thecapability of a field specific search which en-ables users to narrow down the number of re-sults especially useful for collecting sequencesof their specific needs We have also developeda sequence similarity search (SSS) service to findhomologous sequences with various algorithmsincluding BLAST FASTA SSEARCH TRANSand EXONERATE This variety of options isunique among the public services and users canselect an appropriate method to search similarsequences according to their query Because al-gorithms such as TRANS and EXONERATE arehighly time consuming the SSS service is back-ended by the distributed computing environ-ment with the Sun Grid Engine in our supercomputer system HiGet and SSS services areavailable at httphigethgcjp and httpssshgcjp respectively

Publications

Kanehisa M Goto S Furumichi M TanabeM Hirakawa M KEGG for representationand analysis of molecular networks involvingdiseases and drugs Nucleic Acids Research 38D355-D360 2010

Katayama T Nakao M Takagi T TogoWSintegrated SOAP and REST APIs for interop-erable bioinformatics Web services Nucleic Ac-ids Research 38 W706-W711 2010

Katayama T Arakawa K Nakao M Ono KAoki-Kinoshita KF Yamamoto Y Yama-guchi A Kawashima S Chun HW AertsJ Aranda B Barboza LH Bonnal RJBruskiewich R Bryne JC Fernaacutendez JMFunahashi A Gordon PM Goto N Gro-scurth A Gutteridge A Holland R KanoY Kawas EA Kerhornou A Kibukawa EKinjo AR Kuhn M Lapp H LehvaslaihoH Nakamura H Nakamura Y NishizawaT Nobata C Noguchi T Oinn TMOkamoto S Owen S Pafilis E Pocock MPrins P Ranzinger R Reisinger F Salwin-ski L Schreiber M Senger M ShigemotoY Standley DM Sugawara H Tashiro TTrelles O Vos RA Wilkinson MD YorkW Zmasek CM Asai K Takagi T TheDBCLS BioHackathon standardization and in-

teroperability for bioinformatics web servicesand workflows Journal of Biomedical Semantics1 8 2010

Goto N Prins P Nakao M Bonnal R AertsJ Katayama T BioRuby bioinformatics soft-ware for the Ruby programming languageBioinformatics 26 2617-2619 2010

Yamanishi Y Kotera M Kanehisa M GotoS Drug-target interaction prediction fromchemical genomic and pharmacological datain an integrated framework Bioinformatics 26i246-i256 2010

Erguner B Hattori M Goto S Kanehisa MCharacterizing common substructures ofligands for GPCR protein subfamilies GenomeInformatics 24 31-41 2010

Kotera M Kobayashi T Hattori M Toki-matsu T Goto S Mihara H Kanehisa MComprehensive genomic analysis of sulfur-relay pathway genes Genome Informatics 24104-115 2010

Mizutani S Tanaka M Wheelock C Kane-hisa M Goto S Phylogenetic analysis oflipid mediator GPCRs Genome Informatics 24116-126 2010

Nishimura Y Tokimatsu T Kotera M GotoS Kanehisa M Genome-wide analysis of

98

plant UGT family based on sequence and sub-strate information Genome Informatics 24 127-

138 2010

99

The recent advances in biomedical research have been producing large-scaleultra-high dimensional ultra-heterogeneous data Due to these post-genomic re-search progresses our current mission is to create computational strategy for sys-tems biology and medicine towards translational bioinformatics With this missionwe have been developing computational methods for understanding life as systemand applying them to practical issues in medicine and biology

1 Gene Network Analysis

a Inferring dynamic gene networks undervarying conditions for transcriptomic net-work comparison

Teppei Shimamura Seiya Imoto Rui Yama-guchi Masao Nagasaki Satoru Miyano

Elucidating the differences between cellularresponses to various biological conditions or ex-ternal stimuli is an important challenge in sys-tems biology Many approaches have been de-veloped for reverse-engineering a cellular sys-tem called gene network from time series mi-croarray gene expression data in order to under-stand a transcriptomic response under a condi-tion of interest Comparative topological analy-sis has also been applied based on the gene net-

works inferred independently from each of themultiple time series datasets under varying con-ditions to find critical differences between thesenetworks However these comparisons oftenlead to misleading results because each networkcontains considerable noise due to the limitedlength of the time series With this motivationwe developed an integrated approach for infer-ring multiple gene networks from time seriesexpression data under varying conditions Tothe best of our knowledge our approach is thefirst reverse-engineering method that is intendedfor transcriptomic network comparison betweenvarying conditions Furthermore we developeda state-of-the-art parameter estimation methodrelevance-weighted recursive elastic net for pro-viding higher precision and recall than existingreverse-engineering methods We analyze ex-perimental data of MCF-7 human breast cancer

Human Genome Center

Laboratory of DNA Information AnalysisLaboratory of Sequence Data AnalysisDNA情報解析分野シークエンスデータ情報処理分野

Professor Satoru Miyano PhDAssociate Professor Seiya Imoto PhDAssistant Professor Masao Nagasaki PhDProject Assistant Professor Yoshinori Tamada PhDProject Assistant Professor Teppei Shimamura PhDAssociate Professor Tetsuo Shibuya PhDLecturer Rui Yamaguchi PhD

教 授 理学博士 宮 野 悟准教授 博士（数理学） 井 元 清 哉助 教 博士（理学） 長 正 朗特任助教 博士（情報学） 玉 田 嘉 紀特任助教 博士（工学） 島 村 徹 平准教授 博士（理学） 渋 谷 哲 朗講 師 博士（理学） 山 口 類

100

cells stimulated by epidermal growth factor orheregulin with several doses and provide novelbiological hypotheses through network compari-son The software NETCOMP is available athttp bonsai ims u-tokyo ac jp ~shima NETCOMP

b Collocation-based sparse estimation forconstructing dynamic gene networks

Teppei Shimamura Seiya Imoto Masao Na-gasaki Mai Yamauchi13 Rui Yamaguchi An-dreacute Fujita Yoshinori Tamada Noriko Gotoh13Satoru Miyano

One of the open problems in systems biologyis to infer dynamic gene networks describingthe underlying biological process with mathe-matical statistical and computational methodsThe first-order difference equation-based modelssuch as dynamic Bayesian networks and vectorautoregressive models were used to infer time-lagged relationships between genes from time-series microarray data However two primaryproblems greatly reduce the effectiveness of cur-rent approaches The first problem is the tacitassumption that time lag is stationary The sec-ond is the inseparability between measurementnoise and process noise (unmeasured distur-bances that pass through time process) To ad-dress these problems we developed a stochasticdifferential equation model for inferringcontinuous-time dynamic gene networks underthe situation in which both of the process noiseand the observation noise exist We devised acollocation-based sparse estimation for simulta-neous parameter estimation and model selectionin the model The collocation-based approach re-quires considerably less computational effortthan traditional methods in ordinary stochasticdifferential equation models We also incorpo-rated various biological knowledge easily to re-fine the estimation accuracy with this methodThe results using simulated data and real time-series expression data of human primary smallairway epithelial cells demonstrate that this ap-proach outperformed competing approaches andcould provide significant genes influenced byGefitinib

c Gene set-based module discovery de-codes cis-regulatory codes governing di-verse gene expression across human mul-tiple tissues

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Saatoru Miyano

Decoding transcriptional programs governing

transcriptomic diversity across human multipletissues is a major challenge in bioinformatics Toaddress this problem a number of computa-tional methods have focused on cis-regulatorycodes driving overexpression or underexpres-sion in a single tissue as compared to others Onthe other hand we recently proposed a differentapproach to mine cis-regulatory codes startingfrom gene sets sharing common cis-regulatorymotifs the method screens for expression mod-ules based on expression coherence Howeverboth approaches seem to be insufficient to cap-ture transcriptional programs that control geneexpression in a subset of all samples Especiallythis limitation would be serious when analyzingmultiple tissue data To overcome this limita-tion we developed a new module discoverymethod termed BEEM (Biclusering-based Extrac-tion of Expression Modules) in order to discoverexpression modules that are functional in a sub-set of tissues We showed that when applied toexpression profiles of human multiple tissuesBEEM finds expression modules missed by twoexisting approaches that are based on the coher-ent expression and the single tissue-specific dif-ferential expression From the BEEM results weobtained new insights into transcriptional pro-grams controlling transcriptomic diversity acrossvarious types of tissues This study introducesBEEM as a powerful tool for decoding regula-tory programs from a compendium of gene ex-pression profiles

d Model-free unsupervised gene set screen-ing based on information enrichment inexpression profiles

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Andreacute Fujita Teppei Shima-mura Satoru Miyano

A number of unsupervised gene set screeningmethods have recently been developed forsearch of putative functional gene sets based ontheir expression profiles Most of the methodsstatistically evaluate whether the expression pro-files of each gene set are fit to assumed modelseg co-expression across all samples or a sub-group of samples However it is possible thatthey fail to capture informative gene sets whoseexpression profiles are not fit to the assumedmodels To overcome this limitation we devel-oped a model-free unsupervised gene set screen-ing method Matrix Information EnrichmentAnalysis (MIEA) Without assuming any specificmodels MIEA screens gene sets based on infor-mation richness of their expression profiles Weextensively compared the performance of MIEAto those of other unsupervised gene set screen-

101

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

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strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

plant UGT family based on sequence and sub-strate information Genome Informatics 24 127-

138 2010

99

The recent advances in biomedical research have been producing large-scaleultra-high dimensional ultra-heterogeneous data Due to these post-genomic re-search progresses our current mission is to create computational strategy for sys-tems biology and medicine towards translational bioinformatics With this missionwe have been developing computational methods for understanding life as systemand applying them to practical issues in medicine and biology

1 Gene Network Analysis

a Inferring dynamic gene networks undervarying conditions for transcriptomic net-work comparison

Teppei Shimamura Seiya Imoto Rui Yama-guchi Masao Nagasaki Satoru Miyano

Elucidating the differences between cellularresponses to various biological conditions or ex-ternal stimuli is an important challenge in sys-tems biology Many approaches have been de-veloped for reverse-engineering a cellular sys-tem called gene network from time series mi-croarray gene expression data in order to under-stand a transcriptomic response under a condi-tion of interest Comparative topological analy-sis has also been applied based on the gene net-

works inferred independently from each of themultiple time series datasets under varying con-ditions to find critical differences between thesenetworks However these comparisons oftenlead to misleading results because each networkcontains considerable noise due to the limitedlength of the time series With this motivationwe developed an integrated approach for infer-ring multiple gene networks from time seriesexpression data under varying conditions Tothe best of our knowledge our approach is thefirst reverse-engineering method that is intendedfor transcriptomic network comparison betweenvarying conditions Furthermore we developeda state-of-the-art parameter estimation methodrelevance-weighted recursive elastic net for pro-viding higher precision and recall than existingreverse-engineering methods We analyze ex-perimental data of MCF-7 human breast cancer

Human Genome Center

Laboratory of DNA Information AnalysisLaboratory of Sequence Data AnalysisDNA情報解析分野シークエンスデータ情報処理分野

Professor Satoru Miyano PhDAssociate Professor Seiya Imoto PhDAssistant Professor Masao Nagasaki PhDProject Assistant Professor Yoshinori Tamada PhDProject Assistant Professor Teppei Shimamura PhDAssociate Professor Tetsuo Shibuya PhDLecturer Rui Yamaguchi PhD

教 授 理学博士 宮 野 悟准教授 博士（数理学） 井 元 清 哉助 教 博士（理学） 長 正 朗特任助教 博士（情報学） 玉 田 嘉 紀特任助教 博士（工学） 島 村 徹 平准教授 博士（理学） 渋 谷 哲 朗講 師 博士（理学） 山 口 類

100

cells stimulated by epidermal growth factor orheregulin with several doses and provide novelbiological hypotheses through network compari-son The software NETCOMP is available athttp bonsai ims u-tokyo ac jp ~shima NETCOMP

b Collocation-based sparse estimation forconstructing dynamic gene networks

Teppei Shimamura Seiya Imoto Masao Na-gasaki Mai Yamauchi13 Rui Yamaguchi An-dreacute Fujita Yoshinori Tamada Noriko Gotoh13Satoru Miyano

One of the open problems in systems biologyis to infer dynamic gene networks describingthe underlying biological process with mathe-matical statistical and computational methodsThe first-order difference equation-based modelssuch as dynamic Bayesian networks and vectorautoregressive models were used to infer time-lagged relationships between genes from time-series microarray data However two primaryproblems greatly reduce the effectiveness of cur-rent approaches The first problem is the tacitassumption that time lag is stationary The sec-ond is the inseparability between measurementnoise and process noise (unmeasured distur-bances that pass through time process) To ad-dress these problems we developed a stochasticdifferential equation model for inferringcontinuous-time dynamic gene networks underthe situation in which both of the process noiseand the observation noise exist We devised acollocation-based sparse estimation for simulta-neous parameter estimation and model selectionin the model The collocation-based approach re-quires considerably less computational effortthan traditional methods in ordinary stochasticdifferential equation models We also incorpo-rated various biological knowledge easily to re-fine the estimation accuracy with this methodThe results using simulated data and real time-series expression data of human primary smallairway epithelial cells demonstrate that this ap-proach outperformed competing approaches andcould provide significant genes influenced byGefitinib

c Gene set-based module discovery de-codes cis-regulatory codes governing di-verse gene expression across human mul-tiple tissues

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Saatoru Miyano

Decoding transcriptional programs governing

transcriptomic diversity across human multipletissues is a major challenge in bioinformatics Toaddress this problem a number of computa-tional methods have focused on cis-regulatorycodes driving overexpression or underexpres-sion in a single tissue as compared to others Onthe other hand we recently proposed a differentapproach to mine cis-regulatory codes startingfrom gene sets sharing common cis-regulatorymotifs the method screens for expression mod-ules based on expression coherence Howeverboth approaches seem to be insufficient to cap-ture transcriptional programs that control geneexpression in a subset of all samples Especiallythis limitation would be serious when analyzingmultiple tissue data To overcome this limita-tion we developed a new module discoverymethod termed BEEM (Biclusering-based Extrac-tion of Expression Modules) in order to discoverexpression modules that are functional in a sub-set of tissues We showed that when applied toexpression profiles of human multiple tissuesBEEM finds expression modules missed by twoexisting approaches that are based on the coher-ent expression and the single tissue-specific dif-ferential expression From the BEEM results weobtained new insights into transcriptional pro-grams controlling transcriptomic diversity acrossvarious types of tissues This study introducesBEEM as a powerful tool for decoding regula-tory programs from a compendium of gene ex-pression profiles

d Model-free unsupervised gene set screen-ing based on information enrichment inexpression profiles

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Andreacute Fujita Teppei Shima-mura Satoru Miyano

A number of unsupervised gene set screeningmethods have recently been developed forsearch of putative functional gene sets based ontheir expression profiles Most of the methodsstatistically evaluate whether the expression pro-files of each gene set are fit to assumed modelseg co-expression across all samples or a sub-group of samples However it is possible thatthey fail to capture informative gene sets whoseexpression profiles are not fit to the assumedmodels To overcome this limitation we devel-oped a model-free unsupervised gene set screen-ing method Matrix Information EnrichmentAnalysis (MIEA) Without assuming any specificmodels MIEA screens gene sets based on infor-mation richness of their expression profiles Weextensively compared the performance of MIEAto those of other unsupervised gene set screen-

101

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

The recent advances in biomedical research have been producing large-scaleultra-high dimensional ultra-heterogeneous data Due to these post-genomic re-search progresses our current mission is to create computational strategy for sys-tems biology and medicine towards translational bioinformatics With this missionwe have been developing computational methods for understanding life as systemand applying them to practical issues in medicine and biology

1 Gene Network Analysis

a Inferring dynamic gene networks undervarying conditions for transcriptomic net-work comparison

Teppei Shimamura Seiya Imoto Rui Yama-guchi Masao Nagasaki Satoru Miyano

Elucidating the differences between cellularresponses to various biological conditions or ex-ternal stimuli is an important challenge in sys-tems biology Many approaches have been de-veloped for reverse-engineering a cellular sys-tem called gene network from time series mi-croarray gene expression data in order to under-stand a transcriptomic response under a condi-tion of interest Comparative topological analy-sis has also been applied based on the gene net-

works inferred independently from each of themultiple time series datasets under varying con-ditions to find critical differences between thesenetworks However these comparisons oftenlead to misleading results because each networkcontains considerable noise due to the limitedlength of the time series With this motivationwe developed an integrated approach for infer-ring multiple gene networks from time seriesexpression data under varying conditions Tothe best of our knowledge our approach is thefirst reverse-engineering method that is intendedfor transcriptomic network comparison betweenvarying conditions Furthermore we developeda state-of-the-art parameter estimation methodrelevance-weighted recursive elastic net for pro-viding higher precision and recall than existingreverse-engineering methods We analyze ex-perimental data of MCF-7 human breast cancer

Human Genome Center

Laboratory of DNA Information AnalysisLaboratory of Sequence Data AnalysisDNA情報解析分野シークエンスデータ情報処理分野

Professor Satoru Miyano PhDAssociate Professor Seiya Imoto PhDAssistant Professor Masao Nagasaki PhDProject Assistant Professor Yoshinori Tamada PhDProject Assistant Professor Teppei Shimamura PhDAssociate Professor Tetsuo Shibuya PhDLecturer Rui Yamaguchi PhD

教 授 理学博士 宮 野 悟准教授 博士（数理学） 井 元 清 哉助 教 博士（理学） 長 正 朗特任助教 博士（情報学） 玉 田 嘉 紀特任助教 博士（工学） 島 村 徹 平准教授 博士（理学） 渋 谷 哲 朗講 師 博士（理学） 山 口 類

100

cells stimulated by epidermal growth factor orheregulin with several doses and provide novelbiological hypotheses through network compari-son The software NETCOMP is available athttp bonsai ims u-tokyo ac jp ~shima NETCOMP

b Collocation-based sparse estimation forconstructing dynamic gene networks

Teppei Shimamura Seiya Imoto Masao Na-gasaki Mai Yamauchi13 Rui Yamaguchi An-dreacute Fujita Yoshinori Tamada Noriko Gotoh13Satoru Miyano

One of the open problems in systems biologyis to infer dynamic gene networks describingthe underlying biological process with mathe-matical statistical and computational methodsThe first-order difference equation-based modelssuch as dynamic Bayesian networks and vectorautoregressive models were used to infer time-lagged relationships between genes from time-series microarray data However two primaryproblems greatly reduce the effectiveness of cur-rent approaches The first problem is the tacitassumption that time lag is stationary The sec-ond is the inseparability between measurementnoise and process noise (unmeasured distur-bances that pass through time process) To ad-dress these problems we developed a stochasticdifferential equation model for inferringcontinuous-time dynamic gene networks underthe situation in which both of the process noiseand the observation noise exist We devised acollocation-based sparse estimation for simulta-neous parameter estimation and model selectionin the model The collocation-based approach re-quires considerably less computational effortthan traditional methods in ordinary stochasticdifferential equation models We also incorpo-rated various biological knowledge easily to re-fine the estimation accuracy with this methodThe results using simulated data and real time-series expression data of human primary smallairway epithelial cells demonstrate that this ap-proach outperformed competing approaches andcould provide significant genes influenced byGefitinib

c Gene set-based module discovery de-codes cis-regulatory codes governing di-verse gene expression across human mul-tiple tissues

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Saatoru Miyano

Decoding transcriptional programs governing

transcriptomic diversity across human multipletissues is a major challenge in bioinformatics Toaddress this problem a number of computa-tional methods have focused on cis-regulatorycodes driving overexpression or underexpres-sion in a single tissue as compared to others Onthe other hand we recently proposed a differentapproach to mine cis-regulatory codes startingfrom gene sets sharing common cis-regulatorymotifs the method screens for expression mod-ules based on expression coherence Howeverboth approaches seem to be insufficient to cap-ture transcriptional programs that control geneexpression in a subset of all samples Especiallythis limitation would be serious when analyzingmultiple tissue data To overcome this limita-tion we developed a new module discoverymethod termed BEEM (Biclusering-based Extrac-tion of Expression Modules) in order to discoverexpression modules that are functional in a sub-set of tissues We showed that when applied toexpression profiles of human multiple tissuesBEEM finds expression modules missed by twoexisting approaches that are based on the coher-ent expression and the single tissue-specific dif-ferential expression From the BEEM results weobtained new insights into transcriptional pro-grams controlling transcriptomic diversity acrossvarious types of tissues This study introducesBEEM as a powerful tool for decoding regula-tory programs from a compendium of gene ex-pression profiles

d Model-free unsupervised gene set screen-ing based on information enrichment inexpression profiles

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Andreacute Fujita Teppei Shima-mura Satoru Miyano

A number of unsupervised gene set screeningmethods have recently been developed forsearch of putative functional gene sets based ontheir expression profiles Most of the methodsstatistically evaluate whether the expression pro-files of each gene set are fit to assumed modelseg co-expression across all samples or a sub-group of samples However it is possible thatthey fail to capture informative gene sets whoseexpression profiles are not fit to the assumedmodels To overcome this limitation we devel-oped a model-free unsupervised gene set screen-ing method Matrix Information EnrichmentAnalysis (MIEA) Without assuming any specificmodels MIEA screens gene sets based on infor-mation richness of their expression profiles Weextensively compared the performance of MIEAto those of other unsupervised gene set screen-

101

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

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(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

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Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

cells stimulated by epidermal growth factor orheregulin with several doses and provide novelbiological hypotheses through network compari-son The software NETCOMP is available athttp bonsai ims u-tokyo ac jp ~shima NETCOMP

b Collocation-based sparse estimation forconstructing dynamic gene networks

Teppei Shimamura Seiya Imoto Masao Na-gasaki Mai Yamauchi13 Rui Yamaguchi An-dreacute Fujita Yoshinori Tamada Noriko Gotoh13Satoru Miyano

One of the open problems in systems biologyis to infer dynamic gene networks describingthe underlying biological process with mathe-matical statistical and computational methodsThe first-order difference equation-based modelssuch as dynamic Bayesian networks and vectorautoregressive models were used to infer time-lagged relationships between genes from time-series microarray data However two primaryproblems greatly reduce the effectiveness of cur-rent approaches The first problem is the tacitassumption that time lag is stationary The sec-ond is the inseparability between measurementnoise and process noise (unmeasured distur-bances that pass through time process) To ad-dress these problems we developed a stochasticdifferential equation model for inferringcontinuous-time dynamic gene networks underthe situation in which both of the process noiseand the observation noise exist We devised acollocation-based sparse estimation for simulta-neous parameter estimation and model selectionin the model The collocation-based approach re-quires considerably less computational effortthan traditional methods in ordinary stochasticdifferential equation models We also incorpo-rated various biological knowledge easily to re-fine the estimation accuracy with this methodThe results using simulated data and real time-series expression data of human primary smallairway epithelial cells demonstrate that this ap-proach outperformed competing approaches andcould provide significant genes influenced byGefitinib

c Gene set-based module discovery de-codes cis-regulatory codes governing di-verse gene expression across human mul-tiple tissues

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Saatoru Miyano

Decoding transcriptional programs governing

transcriptomic diversity across human multipletissues is a major challenge in bioinformatics Toaddress this problem a number of computa-tional methods have focused on cis-regulatorycodes driving overexpression or underexpres-sion in a single tissue as compared to others Onthe other hand we recently proposed a differentapproach to mine cis-regulatory codes startingfrom gene sets sharing common cis-regulatorymotifs the method screens for expression mod-ules based on expression coherence Howeverboth approaches seem to be insufficient to cap-ture transcriptional programs that control geneexpression in a subset of all samples Especiallythis limitation would be serious when analyzingmultiple tissue data To overcome this limita-tion we developed a new module discoverymethod termed BEEM (Biclusering-based Extrac-tion of Expression Modules) in order to discoverexpression modules that are functional in a sub-set of tissues We showed that when applied toexpression profiles of human multiple tissuesBEEM finds expression modules missed by twoexisting approaches that are based on the coher-ent expression and the single tissue-specific dif-ferential expression From the BEEM results weobtained new insights into transcriptional pro-grams controlling transcriptomic diversity acrossvarious types of tissues This study introducesBEEM as a powerful tool for decoding regula-tory programs from a compendium of gene ex-pression profiles

d Model-free unsupervised gene set screen-ing based on information enrichment inexpression profiles

Atsushi Niida Seiya Imoto Rui YamaguchiMasao Nagasaki Andreacute Fujita Teppei Shima-mura Satoru Miyano

A number of unsupervised gene set screeningmethods have recently been developed forsearch of putative functional gene sets based ontheir expression profiles Most of the methodsstatistically evaluate whether the expression pro-files of each gene set are fit to assumed modelseg co-expression across all samples or a sub-group of samples However it is possible thatthey fail to capture informative gene sets whoseexpression profiles are not fit to the assumedmodels To overcome this limitation we devel-oped a model-free unsupervised gene set screen-ing method Matrix Information EnrichmentAnalysis (MIEA) Without assuming any specificmodels MIEA screens gene sets based on infor-mation richness of their expression profiles Weextensively compared the performance of MIEAto those of other unsupervised gene set screen-

101

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

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Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

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Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

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The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

ing methods using various types of simulatedand real data The benchmark tests demon-strated that MIEA can detect singular expressionprofiles that the other methods fail to find andperforms broadly well for various types of inputdata Taken together this study introducesMIEA as a broadly applicable gene set screeningtool for mining regulatory programs from tran-scriptome data

e Gene regulatory network clustering forgraph layout based on microarray geneexpression data

Kaname Kojima Seiya Imoto Masao Na-gasaki Satoru Miyano

We developed a statistical model realizing si-multaneous estimation of gene regulatory net-work and gene module identification from timeseries gene expression data from microarray ex-periments Under the assumption that genes inthe same module are densely connected thismethod detects gene modules based on the vari-ational Bayesian technique The model can alsoincorporate existing biological prior knowledgesuch as protein subcellular localization We ap-plied our model to the time series data from asynthetically generated network and verified theeffectiveness of the proposed model This modelis also applied to the time series microarray datafrom HeLa cell Detected gene module informa-tion gave the great help on drawing the esti-mated gene network

f Optimal search on clustered structuralconstraint for learning Bayesian networkstructure

Kaname Kojima Eric Perrier Seiya Imoto Sa-toru Miyano

We studied the problem of learning an opti-mal Bayesian network in a constrained searchspace skeletons are compelled to be subgraphsof a given undirected graph called the super-structure The previously derived constrainedoptimal search (COS) remains limited even forsparse super-structures To extend its feasibilitywe developed a method to divide the super-structure into several clusters and perform anoptimal search on each of them Further to en-sure acyclicity we introduced the concept of an-cestral constraints (ACs) and derive an optimalalgorithm satisfying a given set of ACs Finallywe theoretically derived the necessary and suffi-cient sets of ACs to be considered for finding anoptimal constrained graph Empirical evalu-ations demonstrated that our algorithm can

learn optimal Bayesian networks for somegraphs containing several hundreds of verticesand even for super-structures having a high av-erage degree (up to four) which is a drastic im-provement in feasibility over the previous opti-mal algorithm Learnt networks were shown tolargely outperform state-of-the-art heuristic al-gorithms both in terms of score and structuralhamming distance

g A fast and robust statistical test based onlikelihood ratio with Bartlett correction toidentify Granger causality between genesets

Andreacute Fujita Kaname Kojima Alexandre GPatriota1 Joatildeo Ricardo Sato2 PatriciaSeverino3 Satoru Miyano 1University of SatildeoPaulo 2Universidade Federal do ABC 3AlbertEinstein Research and Education Institute

We developed a likelihood ratio test (LRT)with Bartlett correction in order to identifyGranger causality between sets of time seriesgene expression data The performance of theproposed test is compared to a previously pub-lished bootstrap-based approach LRT is shownto be significantly faster and statistically power-ful even within non-Normal distributions An Rpackage named gGranger containing an imple-mentation for both Granger causality identifica-tion tests is also provided httpdnagardenims u-tokyo ac jp afujita en doku php id =ggranger

h Comparison of gene expression profilesproduced by CAGE Illumina microarrayand Real Time RT-PCR

Andreacute Fujita Masao Nagasaki Seiya ImotoAyumu Saito Emi Ikeda Teppei ShimamuraRui Yamaguchi Yoshihide Hayashizaki4 Sa-toru Miyano 4RIKEN Yokohama Institute

Several technologies are currently used forgene expression profiling such as Real Time RT-PCR microarray and CAGE (Cap Analysis ofGene Expression) CAGE is a recently developedmethod for constructing transcriptome mapsand it has been successfully applied to analyz-ing gene expressions in diverse biological stud-ies The principle of CAGE has been developedto address specific issues such as determinationof transcriptional starting sites the study of pro-moter regions and identification of new tran-scripts We made both quantitative and qualita-tive comparisons among three major gene ex-pression quantification techniques namelyCAGE illumina microarray and Real Time RT-

102

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

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(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

PCR by showing that the quantitative values ofeach method are not interchangeable howevereach of them has unique characteristics whichrender all of them essential and complementaryUnderstanding the advantages and disadvan-tages of each technology will be useful in select-ing the most appropriate technique for a deter-mined purpose

i Identification of Granger causality betweengene sets

Andreacute Fujita Joatildeo Ricardo Sato2 Kaname Ko-jima Luciana Rodrigues Gomes1 LR MariCleide Sogayar1 Satoru Miyano

Wiener and Granger have introduced an in-tuitive concept of causality (Granger causality)between two variables which is based on theidea that an effect never occurs before its causeLater Geweke generalized this concept to amultivariate Granger causality ie n variablesGranger-cause another variable AlthoughGranger causality is not ldquoeffective causalityrdquo inthe Aristothelic sense this concept is useful toinfer directionality and information flow in ob-servational data Granger causality is usuallyidentified by using VAR (Vector Autoregressive)models due to their simplicity In the last fewyears several VAR-based models were pre-sented in order to model gene regulatory net-works We generalized the multivariate Grangercausality concept in order to identify Grangercausalities between sets of gene expressions iewhether a set of n genes Granger-causes anotherset of m genes aiming at identifying the flow ofinformation between gene networks (or path-ways) The concept of Granger causality for setsof variables is presented Moreover a methodfor its identification with a bootstrap test is pro-posed This method is applied in simulated andalso in actual biological gene expression data inorder to model regulatory networks This con-cept may be useful for the understanding of thecomplete information flow from one network orpathway to the other mainly in regulatory net-works Linking this concept to graph theorysink and source can be generalized to node setsMoreover hub and centrality for sets of genescan be defined based on total information flowAnother application is in annotation when thefunctionality of a set of genes is unknown butthis set is Granger-caused by another set ofgenes which is well studied Therefore this in-formation may be useful to infer or constructsome hypothesis about the unknown set ofgenes

j Granger causality in systems biologymodeling gene networks in time series mi-croarray data using vector autoregressivemodels

Andreacute Fujita Patricia Severino3 Joatildeo RicardoSato2 Miyano S

Understanding the molecular biological proc-esses underlying disease onset requires a de-tailed description of which genes are expressedat which time points and how their products in-teract in so-called cellular networks High-throughput technologies such as gene expres-sion analysis using DNA microarrays have beenextensively used with this purpose As a conse-quence mathematical methods aiming to inferthe structure of gene networks have been pro-posed in the last few years Granger causality-based models are among them presenting wellestablished mathematical interpretations to di-rectionality at the edges of the regulatory net-work Here we describe the concept of Grangercausality and explore recent advances and appli-cations in gene expression regulatory networksby using extensions of Vector Autoregressivemodels

k Discovering functional gene pathways as-sociated with cancer heterogeneity viasparse supervised learning

Shuichi Kawano Teppei Shimamura AtsuhiNiida Seiya Imoto Rui Yamaguchi MasaoNagasaki Ryo Yoshida5 Cristin Print6 SatoruMiyano 5Institute of Statistical Mathematics6University of Auckland

We developed a statistical method for uncov-ering gene pathways that characterize cancerheterogeneity To incorporate knowledge of thepathways into the model we define a set of ac-tivities of pathways from microarray gene ex-pression data based on the sparse probabilisticprincipal component analysis A pathway activ-ity logistic regression model is then formulatedfor cancer phenotype To select pathway activi-ties related to binary cancer phenotypes we usethe elastic net for the parameter estimation andderive a model selection criterion for selectingtuning parameters included in the model esti-mation Our method can also reverse-engineergene networks based on the identified multiplepathways that enables us to discover novelgene-gene associations relating with the cancerphenotypes We illustrated the whole process ofthe proposed method through the analysis ofbreast cancer gene expression data

103

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

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Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

l Identifying hidden confounders in genenetworks by Bayesian networks

Tomoya Higashigaki7 Kaname Kojima RuiYamaguchi Masato Inoue7 Seiya Imoto Sa-toru Miyano 7Waseda University

For estimating gene networks from microar-ray gene expression data we developed a statis-tical method for quantification of the hiddenconfounders in gene networks which were pos-sibly removed from the set of genes on the genenetworks or are novel biological elements thatare not measured by microarrays Due to highcomputational cost of the structural learning ofBayesian networks and the limited source of themicroarray data it is usual to perform gene se-lection prior to the estimation of gene networksTherefore there exist missing genes that de-crease accuracy and interpretability of the esti-mated gene networks The proposed methodcan identify hidden confounders based on theconflicts of the estimated local Bayesian networkstructures and estimate their ideal profiles basedon the proposed Bayesian networks with hiddenvariables with an EM algorithm From the esti-mated ideal profiles we can identify geneswhich are missing in the network or suggest theexistence of the novel biological elements if theideal profiles are not significantly correlatedwith any expression profiles of genes To thebest of our knowledge this research is the firststudy to theoretically characterize missing genesin gene networks and practically utilize this in-formation to refine network estimation

2 Pathway Modeling Simulation and Analy-sis

a Cell Illustrator 40 A computational plat-form for systems biology

Masao Nagasaki Ayumu Saito Euna JeongChen Li Kaname Kojima Emi Ikeda SatoruMiyano

Cell Illustrator is a software platform for Sys-tems Biology that uses the concept of Petri netfor modeling and simulating biopathways It isintended for biological scientists working atbench The latest version of Cell Illustrator 40uses Java Web Start technology and is enhancedwith new capabilities including automaticgraph grid layout algorithms using ontology in-formation tools using Cell System Markup Lan-guage (CSML) 30 and Cell System Ontology30 parameter search module high-performancesimulation module CSML database manage-ment system conversion from CSML model to

programming languages (FORTRAN C C++Java Python and Perl) import from SBML

CellML and BioPAX and export to SVG andHTML Cell Illustrator employs an extension ofhybrid Petri net in an object-oriented style sothat biopathway models can include objectssuch as DNA sequence molecular density 3Dlocalization information transcription withframe-shift translation with codon table as wellas biochemical reactions

b Time-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram

Chen Li Masao Nagasaki Ayumu Saito Sa-toru Miyano

Investigating the dynamic features of currentcomputational models promises a deeper under-standing of complex cellular processes Thisleads us to develop a method that utilizes struc-tural properties of the model over all simulationtime steps Further user-friendly overviews ofdynamic behaviors can be considered to providea great help in understanding the variations ofsystem mechanisms We developed a novelmethod for constructing and analyzing a so-called active state transition diagram (ASTD) byusing time-course simulation data of a high-level Petri net Our method includes two newalgorithms The first algorithm extracts a seriesof subnets (called temporal subnets) reflectingbiological components contributing to the dy-namics while retaining positive mathematicalqualities The second one creates an ASTD com-posed of unique temporal subnets ASTD pro-vides users with concise information allowingthem to grasp and trace how a key regulatorysubnet andor a network changes with timeThe applicability of our method is demonstratedby the analysis of the underlying model for cir-cadian rhythms in Drosophila Building ASTD isa useful means to convert a hybrid model deal-ing with discrete continuous and more compli-cated events to finite time-dependent statesBased on ASTD various analytical approachescan be applied to obtain new insights into notonly systematic mechanisms but also dynamics

c On determining delay time of transitionsfor Petri net based signaling pathways byintroducing stochastic decision rules

Yoshimasa Miwa8 Chen Li Qi-Wei Ge8 Hiro-shi Matsuno8 Satoru Miyano 8Yamaguchi Uni-versity

Parameter determination is important in mod-

104

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

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Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

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Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

eling and simulating biological pathways includ-ing signaling pathways Parameters are deter-mined according to biological facts obtainedfrom biological experiments and scientific publi-cations However such reliable data describingdetailed reactions are not reported in mostcases This prompted us to develop a generalmethodology of determining the parameters of amodel in the case of that no information of theunderlying biological facts is provided In thisstudy we used the Petri net approach for mod-eling signaling pathways and developed amethod to determine firing delay times of tran-sitions for Petri net models of signaling path-ways by introducing stochastic decision rulesPetri net technology provides a powerful ap-proach to modeling and simulating various con-current systems and recently has been widelyaccepted as a description method for biologicalpathways Our method enables to determine therange of firing delay time which realizes smoothtoken flows in the Petri net model of a signalingpathway The availability of this method hasbeen confirmed by the results of an applicationto the interleukin-1 induced signaling pathway

d An efficient biological pathway layout al-gorithm combining grid-layout and springembedder for complicated cellular locationinformation

Kaname Kojima Masao Nagasaki Satoru Miy-ano

We developed a new grid-layout algorithmbased on the spring embedder algorithm thatcan handle location information and providelayouts with harmonized appearance In grid-layout algorithms the mapping of nodes to gridpoints that minimizes a cost function issearched By imposing positional constraints ongrid points location information including com-plex shapes can be easily considered Our layoutalgorithm includes the spring embedder cost asa component of the cost function We further ex-tended the layout algorithm to enable dynamicupdate of the positions and sizes of compart-ments at each step The new spring embedder-based grid-layout algorithm and a spring em-bedder algorithm were applied to three biologi-cal pathways endothelial cell model Fas-induced apoptosis model and C elegans cell fatesimulation model From the positional con-straints all the results of our algorithm satisfylocation information and hence more compre-hensible layouts were obtained as compared tothe spring embedder algorithm From the com-parison of the number of crossings the resultsof the grid-layout-based algorithm tend to con-

tain more crossings than those of the spring em-bedder algorithm due to the positional con-straints

3 Data Assimilation for Systems Biology

e DA 10 parameter estimation of biologicalpathways using data assimilation ap-proach

Chuan Hock Koh9 Masao Nagasaki AyumuSaito Limsoon Wong10 Satoru Miyano 9Na-tional University of Singapore and HumanGenome Center Institute of Medical ScienceUniversity of Tokyo 10National University ofSingapore

Data assimilation (DA) is a computational ap-proach that estimates unknown parameters in apathway model using time-course informationParticle filtering the underlying method used isa well-established statistical method that ap-proximates the joint posterior distributions ofparameters by using sequentially generatedMonte Carlo samples We released the Java-based software (DA 10) with an intuitive anduser-friendly interface to allow users to carryout parameters estimation using DA DA 10was developed using Java and thus would beexecutable on any platform installed with JDK60 (not JRE 60) or later DA 10 is freely avail-able for academic users and can be launched ordownloaded from httpdacsmlorg

f Phosphoproteomics-based modeling de-fines the regulatory mechanism underlyingaberrant EGFR signaling

Shinya Tasaki11 Masao Nagasaki M HirokoKozuka-Hata11 Kentaro Semba12 Noriko Go-toh13 Seisuke Hattori14 Jun-ichiro Inoue15Tadashi Yamamoto15 Satoru Miyano SumioSugano16 Masaaki Oyama 11Medical Proteom-ics Laboratory Institute of Medical ScienceUniversity of Tokyo 12Department of Life Sci-ence and Medical Bio-Science Waseda Univer-sity 13Division of Systems Biomedical Technol-ogy Institute of Medical Science University ofTokyo 14Department of Biochemistry School ofPharmaceutical Sciences Kitasato University15Department of Cancer Biology Institute ofMedical Science University of Tokyo 16Depart-ment of Medical Genome Sciences GraduateSchool of Frontier Sciences University of To-kyo

Mutation of the epidermal growth factor re-ceptor (EGFR) results in a discordant cell signal-ing leading to the development of various dis-

105

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

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(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

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Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

eases However the mechanism underlying thealteration of downstream signaling due to suchmutation has not yet been completely under-stood at the system level Here we report aphosphoproteomics-based methodology forcharacterizing the regulatory mechanism under-lying aberrant EGFR signaling using computa-tional network modeling Our phosphopro-teomic analysis of the mutation at tyrosine 992(Y992) one of the multifunctional docking sitesof EGFR revealed network-wide effects of themutation on EGF signaling in a time-resolvedmanner Computational modeling based on thetemporal activation profiles enabled us to notonly rediscover already-known protein interac-tions with Y992 and internalization property ofmutated EGFR but also further gain model-driven insights into the effect of cellular contentand the regulation of EGFR degradation Our ki-netic model also suggested critical reactions fa-cilitating the reconstruction of the diverse effectsof the mutation on phosphoproteome dynamicsOur integrative approach provided a mechanis-tic description of the disorders of mutated EGFRsignaling networks which could facilitate thedevelopment of a systematic strategy towardcontrolling disease-related cell signaling

4 Next-Generation Sequencer Data Analysis

a International network of cancer genomeprojects

International Cancer Genome Consortium

The International Cancer Genome Consortium(ICGC) was launched to coordinate large-scalecancer genome studies in tumours from 50 dif-ferent cancer types andor subtypes that are ofclinical and societal importance across the globeSystematic studies of more than 25000 cancergenomes at the genomic epigenomic and tran-scriptomic levels will reveal the repertoire of on-cogenic mutations uncover traces of themutagenic influences define clinically relevantsubtypes for prognosis and therapeutic manage-ment and enable the development of new can-cer therapies In this project we developed anext-generation sequence data analysis pipelinefor the supercomputer system of HumanGenome Center

b Whole-genome sequencing and compre-hensive variant analysis of a Japanese in-dividual using massively parallel sequenc-ing

Akihiro Fujimoto17 Hidewaki Nakagawa17Naoya Hosono17 Kaoru Nakano17 Tetsuo Abe17

Keith A Boroevich17 Masao Nagasaki RuiYamaguchi Tetsuo Shibuya Michiaki Kubo17Satoru Miyano Yusuke Nakamura TatsuhikoTsunoda17 17Center for Genomic MedicineRIKEN

We report the analysis of a Japanese male us-ing high-throughput sequencing totimes40 cover-age More than 99 of the sequence reads weremapped to the reference human genome Usinga Bayesian decision method we identified3132608 single nucleotide variations (SNVs)Comparison with six previously reportedgenomes revealed an excess of singleton non-sense and nonsynonymous SNVs as well as sin-gleton SNVs in conserved non-coding regionsWe also identified 5319 deletions smaller than10 kb with high accuracy in addition to copynumber variations and rearrangements De novoassembly of the unmapped sequence reads gen-erated around 3 Mb of novel sequence whichshowed high similarity to non-reference humangenomes and the human herpesvirus 4 genomeOur analysis suggests that considerable vari-ation remains undiscovered in the humangenome and that whole-genome sequencing isan invaluable tool for obtaining a complete un-derstanding of human genetic variation In thisresearch we developed a next-generation se-quence data analysis pipeline for the supercom-puter system of Human Genome Center

5 Algorithms for Protein Structures

a Geometric suffix tree Indexing protein 3-Dstructures

Tetsuo Shibuya

Protein structure analysis is one of the mostimportant research issues in the post-genomicera and faster and more accurate index datastructures for such 3-D structures are highly de-sired for research on proteins This article pro-poses a new data structure for indexing protein3-D structures For strings there are many effi-cient indexing structures such as suffix trees butit has been considered very difficult to designsuch sophisticated data structures against 3-Dstructures like proteins Our index structure isbased on the suffix tree and is called the geo-metric suffix tree By using the geometric suffixtree for a set of protein structures we can ex-actly search for all of their substructures whoseRMSDs (root mean square deviations) orURMSDs (unit-vector root mean square devia-tions) to a given query 3-D structure are notlarger than a given bound Though there are O(N 2) substructures in a structure of size N our

106

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

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(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

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Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

data structure requires only O (N ) space for in-dexing all the substructures We propose an O(N 2) construction algorithm for it while a naivealgorithm would require O (N 3) time to con-struct it Moreover we propose an efficientsearch algorithm Experiments show that we cansearch for similar structures much faster thanprevious algorithms if the RMSD threshold isnot larger than 1Å The experiments also showthat the construction time of the geometric suffixtree is practically almost linear to the size of thedatabase when applied to a protein structuredatabase

b Searching protein 3-D structures in fasterthan linear time

Tetsuo Shibuya

Searching for similar structures from a three-dimensional (3-D) structure database of proteinsis one of the most important problems in post-genomic computational biology To comparetwo structures we ordinarily use a measurecalled the root mean square deviation (RMSD)as the similarity measure We consider a veryfundamental problem of finding all the sub-structures whose RMSDs to the query are withinsome given threshold from a 3-D structure da-tabase The problem also appears in many otherfields such as computer vision and robotics Inthis article we propose the first algorithm thatruns in faster than linear time on average Our

new algorithm runs in average-case O (m＋N m(1-ε)) where N is the database size m is thequery length and epsilon is an arbitrary smallconstant such that 0＜ε＜1 It is a significant im-provement over previous algorithms on theproblem considering that the best known worst-case time complexity of the problem is O (N logm) and the best known average-case (expected)time complexity of the problem was O (N )

6 Pandemic Control Simulation

a When should we intervene to control the2009 influenza A(H1N1) pandemic

Hiroki Sato18 Haruka Nakada19 Rui Yama-guchi Seiya Imoto Satoru Miyano MasahiroKami19 18Department of Medical InformaticsNational Defense Medical College Hospital19Division of Social Communication System forAdvanced Clinical Research Institute of Medi-cal Science University of Tokyo

We simulated the early phase of the 2009 in-fluenza A(H1N1) pandemic and assessed the ef-fectiveness of public health interventions in Ja-pan We show that the detection rate of borderquarantine was low and the timing of the inter-vention was the most important factor involvedin the control of the pandemic with the maxi-mum reduction in daily cases obtained after in-terventions started on day 6 or 11 Early inter-ventions were not always effective

Publications

1 Do JH Nagasaki M Miyano S The sys-tems approach to the prespore-specific acti-vation of sigma factor SigF in Bacillus sub-tilis Biosystems 100 178-184 2010

2 Ferreira CE Miyano S Stadler PF (Eds)Advances in Bioinformatics and Computa-tional Biology Lecture Notes in ComputerScience Vol 6268 Springer 2010

3 Fujimoto A Nakagawa H Hosono NNakano K Abe G Boroevich KA Na-gasaki M Yamaguchi R Shibuya TKubo M Miyano S Nakamura YTsunoda T Whole-genome sequencing andcomprehensive variant analysis of a Japa-nese individual using massively parallel se-quencing Nature Genetics 42 931-936 2010

4 Fujita A Kojima K Patriota AG Sato JR Severino P Miyano S A fast and ro-bust statistical test based on likelihood ratiowith Bartlett correction to identify Grangercausality between gene sets Bioinformatics26(18) 2349-2351 2010

5 Fujita A Nagasaki M Imoto S Saito AIkeda E Shimamura T Yamaguchi RHayashizaki Y Miyano S Comparison ofgene expression profiles produced byCAGE Illumina microarray and Real TimeRT-PCR Genome Informatics 24 56-682010

6 Fujita A Sato JR Demasi MAA Miy-ano S Sogayar MC Ferreira CE An in-troduction to time-varying connectivity esti-mation for gene regulatory networksldquoMedical Biostatistics for Complex Diseasesrdquo(Frank Emmert-Streib Matthias Dehmer(Eds)) Weinheim Germany Wiley VCHVerlag 205-230 2010

7 Fujita A Sato JR Kojima K Gomes LRSogayar MC Miyano S Identification ofGranger causality between gene sets J Bio-informatics and Computational Biology 8(4)679-701 2010

8 Fujita A Severino P Sato JR Miyano SGranger causality in systems biology mod-

107

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

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Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

eling gene networks in time series microar-ray data using vector autoregressive modelsLecture Notes in Bioinformatics 6268 13-242010

9 HigashigakiT Kojima K Yamaguchi RInoue M Imoto S Miyano S Identifyinghidden confounders in gene networks byBayesian networks Proc 10th IEEE Bioinfor-matics and Bioengineering 168-173 2010

10 International Cancer Genome ConsortiumHudson TJ et al International network ofcancer genome projects Nature 464(7291)993-998 2010

11 Kaufmann K Nagasaki M Jaacuteuregui RModelling the molecular interactions in theflower developmental network of Arabidop-sis thaliana In Silico Biol 10 0008 2010

12 Kawano S Shimamura T Niida AImoto S Yamaguchi R Nagasaki MYoshida R Print C Miyano S Discover-ing functional gene pathways associatedwith cancer heterogeneity via sparse super-vised learning Proc IEEE 10th Interna-tional Symposium on Bioinformatics amp Bio-engineering 253-258 2010

13 Koh CH Nagasaki M Saito A WongL Miyano S DA 10 parameter estimationof biological pathways using data assimila-tion approach Bioinformatics 26(14) 1794-1796 2010

14 Kojima K Imoto S Nagasaki M MiyanoS Gene regulatory network clustering forgraph layout based on microarray gene ex-pression data Genome Informatics 24 84-95 2010

15 Kojima K Nagasaki M Miyano S An ef-ficient biological pathway layout algorithmcombining grid-layout and spring embedderfor complicated cellular location informa-tion BMC Bioinformatics 11 335 2010

16 Kojima K Perrier E Imoto S Miyano SOptimal search on clustered structural con-straint for learning Bayesian network struc-ture J Machine Learning Research11 285-310 2010

17 Li C Nagasaki M Saito A Miyano STime-dependent structural transformationanalysis to high-level Petri net model withactive state transition diagram BMC Sys-tems Biology 4 39 2010

18 Mitou N Matsuno H Miyano S InouyeS Essential role of Ror gene in the interac-tion of feedback loops in mammalian circa-dian clocks ldquoModeling in Systems Biology-The Petri Net Approachrdquo (Koch I ReisigW Schreiber F (Eds)) Springer 281-3062010

19 Miwa Y Li C Ge QW Matsuno H Mi-yano S On determining delay time of tran-

sitions for Petri net based signaling path-ways by introducing stochastic decisionrules In Silico Biol 10 0004 2010

20 Nagasaki M Saito A Jeong E Li C Ko-jima K Ikeda E Miyano S Cell Illustra-tor 40 A computational platform for sys-tems biology In Silico Biol 10 0002 2010

21 Niida A Imoto S Yamaguchi R Na-gasaki M Miyano S Gene set-based mod-ule discovery decodes cis-regulatory codesgoverning diverse gene expression acrosshuman multiple tissues PLoS ONE 5(6) e10910 2010

22 Niida A Imoto S Yamaguchi R Na-gasaki M Fujita A Shimamura T Miy-ano S Model-free unsupervised gene setscreening based on information enrichmentin expression profiles Bioinformatics 26(24)3090-3097 2010

23 Saito A Nagasaki M Miyano S Hybridfunctional Petri net with extension for dy-namic pathway modeling ldquoModeling in Sys-tems Biology-The Petri Net Approachrdquo(Koch I Reisig W Schreiber F (Eds))Springer 101-120 2010

24 Sato H Nakada H Yamaguchi R ImotoS Miyano S Kami M When should weintervene to control the 2009 influenza A(H1N1) pandemic Euro Surveill 7 15(1) pii19455 2010

25 Shibuya T Searching protein 3-D structuresin faster than linear time J Comput Biol 17(4) 593-602 2010

26 Shibuya T Searching protein 3-D structuresin linear time J Comput Biol 17(3) 203-219 2010

27 Shibuya T Geometric suffix tree Indexingprotein 3-D structures J ACM 57(3) 1-172010

28 Shibuya T Fast hinge detection algorithmsfor flexible protein structures IEEEACMTransactions on Computational Biology andBioinformatics 7(2) 333-341 2010

29 Shibuya T Jansson J Sadakane KLinear-time protein 3-D structure searchingwith insertions and deletions BMC Algo-rithms for Molecular Biology 5 7 2010

30 Shimamura T Imoto S Yamaguchi RNagasaki M Miyano S Inferring dynamicgene networks under varying conditions fortranscriptomic network comparison Bioin-formatics 26(8) 1064-1072 2010

31 Shimamura T Imoto S Nagasaki MYamauchi M Yamaguchi R Fujita ATamada Y Gotoh N Miyano SCollocation-based sparse estimation for con-structing dynamic gene networks GenomeInformatics 24 164-178 2010

32 Sogawa Y Shimizu S Hyvarinen A

108

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

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Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

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The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

Washio T Shimamura T Imoto S Discov-ery of exogenous variables in data withmore variables than observations Proc 20thInternational Conference on Artificial NeuralNetworks 67-76 2010

33 Tasaki S Nagasaki M Kozuka-Hata HSemba K Gotoh N Hattori S Inoue JYamamoto T Miyano S Sugano SOyama M Phosphoproteomics-based mod-eling defines the regulatory mechanism un-derlying aberrant EGFR signaling PLoS

ONE 5(11) e13926 201034 Yamaguchi R Imoto S Miyano S

Network-based predictions and simulationsby biological state space models Search fordrug mode of action J Computer Scienceand Technology 25(1) 13-153 2010

35 Yuji K Matsumura T Miyano STsuchiya R Kami M Human papillomavi-rus vaccine coverage Lancet 376(9738) 329-330 2010

109

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

The major goal of our group is to identify genes of medical importance and to de-velop new diagnostic and therapeutic tools We have been attempting to isolategenes involving in carcinogenesis and also those causing or predisposing to vari-ous diseases as well as those related to drug efficacies and adverse reactions Bymeans of technologies developed through the genome project including a high-resolution SNP map a large-scale DNA sequencing and the cDNA microarraymethod we have isolated a number of biologically andor medically importantgenes and are developing novel diagnostic and therapeutic tools

1 Genes playing significant roles in humancancer

Koichi Matsuda Yataro Daigo HidewakiNakagawa Ryuji Hamamoto Hitoshi Zem-butsu Chikako Fukukawa Jae-Hyun ParkYosuke Harada Masahiko Ajiro Jung-WonKim Koji Ueda Nguyen Minh-Hue JunkichiKoinuma Daiki Miki Ken Masuda MasatoAragaki Takashi Fujitomo Hideto OshitaSatoko Uno Yoichiro Kato Su-Youn ChungLianhua Piao Chizu Tanikawa Cui Ri HamdiMbarek Vinod Kumar Osman W Moha-mmed Yuji Urabe Jiaying Lin ZhenzhongDeng Martha Espinosa Motoko Unoki Masa-nori Yoshimatsu Shinya Hayami Hyun-SooCho Goji Toyokawa Tadashi Takawa ReemAbdelrahim Ibrahim Seham Elgazzar Mitsu-ko Nakashima Kang Daechun Cha PeiChieng Low Siew Kee and Yusuke Nakamura

(1) Lung cancer

Dickkopf-1

Dickkopf-1 (DKK1) is an inhibitor of Wntbeta-catenin signaling that is overexpressed inmost lung and esophageal cancers Here weshow its utility as a serum biomarker for a widerange of human cancers and we offer evidencefavoring the potential application of anti-DKK1antibodies for cancer treatment Using an origi-nal ELISA system high levels of DKK1 proteinwere found in serologic samples from 906 pa-tients with cancers of the pancreas stomachliver bile duct breast and cervix which alsoshowed elevated expression levels of DKK1 Ad-ditionally anti-DKK1 antibody inhibited the in-vasive activity and the growth of cancer cells invitro and suppressed the growth of engraftedtumors in vivo Tumor tissues treated with anti-DKK1 displayed significant fibrotic changes and

Human Genome Center

Laboratory of Molecular MedicineLaboratory of Genome Technologyゲノムシークエンス解析分野シークエンス技術開発分野

Professor Yusuke Nakamura MD PhDAssociate Professor Koichi Matsuda MD PhDAssistant Professor Ryuji Hamamoto PhDAssistant Professor Hitoshi Zembutsu MD PhD

教 授 医学博士 中 村 祐 輔准教授 医学博士 松 田 浩 一助 教 理学博士 浜 本 隆 二助 教 医学博士 前 佛 均

110

a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

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Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

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a decrease in viable cancer cells without appar-ent toxicity in mice Our findings suggest DKK1as a serum biomarker for screening against a va-riety of cancers and anti-DKK1 antibodies aspotential theranostic tools for diagnosis andtreatment of cancer

WDHD1 (WD repeat and high-mobility groupbox DNA binding protein 1)

To identify novel biomarkers and therapeutictargets for lung and esophageal cancers wescreened for genes that were overexpressed in alarge proportion of lung and esophageal carci-nomas using a cDNA microarray representing27648 genes or expressed sequence tags A geneencoding WDHD1 a WD repeat and high-mobility group box DNA binding protein 1 wasselected as a candidate Tumor tissue microarrayanalyses covering 267 archival non-small celllung cancers and 283 esophageal squamous cellcarcinomas (ESCC) revealed that positiveWDHD1 immunostaining was associated with apoor prognosis for patients with non-small celllung cancer (P＝00403) as well as ESCC (P＝00426) Multivariate analysis indicated it to bean independent prognostic factor for ESCC (P＝00104) Suppression of WDHD1 expression withsmall interfering RNAs effectively suppressedlung and esophageal cancer cell growth In ad-dition induction of the exogenous expression ofWDHD1 promoted the growth of mammaliancells AKT1 kinase seemed to phosphorylate andstabilize the WDHD1 protein in cancer cellsWDHD1 expression is likely to play an impor-tant role in lung and esophageal carcinogenesisas a cell cycle regulator and a downstreammolecule in the phosphoinositide 3-kinaseAKTpathway and that WDHD1 is a candidatebiomarker and a promising therapeutic targetfor cancer

CDCA5 (cell division cycle associated 5)

We analyzed the gene expression profiles ofclinical lung carcinomas using a cDNA microar-ray containing 27648 genes or expressed se-quence tags and identified CDCA5 (cell divisioncycle associated 5) to be upregulated in the ma-jority of lung cancers Tumor tissue microarrayanalysis of 262 non-small cell lung cancer pa-tients revealed that CDCA5 positivity was an in-dependent prognostic factor for lung cancer pa-tients Suppression of CDCA5 expression withsiRNAs inhibited the growth of lung cancercells concordantly induction of exogenous ex-pression of CDCA5 conferred growth-promotingactivity in mammalian cells We also found thatextracellular signal-regulated kinase (ERK)

kinase phosphorylated CDCA5 at Ser79 and Ser209 in vivo Exogenous expression of phospho-mimicking CDCA5 protein whose Ser209 resi-due was replaced with glutamine acid furtherenhanced the growth of cancer cells In additionfunctional inhibition of the interaction betweenCDCA5 and ERK kinase by a cell-permeablepeptide corresponding to a 20-amino-acid se-quence part of CDCA5 which included the Ser209 phosphorylation site by ERK significantlyreduced phosphorylation of CDCA5 and re-sulted in growth suppression of lung cancercells Our data suggest that transactivation ofCDCA5 and its phosphorylation at Ser209 byERK play an important role in lung cancer pro-liferation and that the selective suppression ofthe ERK-CDCA5 pathway could be a promisingstrategy for cancer therapy

(2) Pancreatic cancer

Involvement of TTLL4 Polyglutamylase inPELP1 Polyglutamylation and Chromatin Re-modeling in Pancreatic Cancer Cells

Polyglutamylation is a new class of post-translational modification in which glutamateside chains are formed on proteins although itsbiological significance is not well knownThrough our genome-wide gene-expression pro-file analysis of pancreatic ductal adenocarci-noma (PDAC) cells we identified overexpres-sion of TTLL4 (tubulin tyrosine ligase-like fam-ily member 4) in PDAC cells Subsequent RT-PCR and northern-blot analyses confirmed itsup-regulation in several PDACs TTLL4 belongsto the TTLL family that was reported to havepolyglutamylase activity Knockdown of TTLL4by shRNA in PDAC cells attenuated the growthof PDAC cells and exogenous introduction ofTTLL4 enhanced the cell growth We also foundthat TTLL4 expression was correlated with poly-glutamylation levels of a glutamate-stretch re-gion of PELP1 (proline glutamate and leucinerich protein 1) that was shown to interact withvarious proteins such as histone H3 and be in-volved in several signaling pathways throughits function as a scaffold protein PELP1 poly-glutamylation could influence to its interactionwith histone H3 and affect histone H3 acetyla-tion We also identified the interaction of PELP1with LAS1L and SENP3 components of theMLL1-WDR5 super-complex involvingchromatin-remodelling Our findings imply thatTTLL4 could play important roles in pancreaticcarcinogenesis through its polyglutamylase ac-tivity and subsequent coordination of chromatinremodeling and might be a good molecularcandidate for development of new therapeutic

111

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

strategies for pancreatic cancer

C12orf48 termed PARP-1 binding protein( PARPBP ) Enhances Poly ( ADP-ribose )Polymerase-1 (PARP-1) Activity and ProtectsPancreatic Cancer Cells from DNA Damage

To identify novel therapeutic targets for ag-gressive and therapy-resistant pancreatic cancerwe had previously performed expression profileanalysis of pancreatic cancers using microarraysand found dozens of genes trans-activated inpancreatic ductal adenocarcinoma (PDAC) cellsAmong them this study focused on the charac-terization of a novel gene C12orf48 whose over-expression in PDAC cells was validated bynorthern blot and immunohistochemical analy-ses Its overexpression was observed in otheraggressive and therapy-resistant malignancies aswell Knockdown of C12orf48 by siRNA inPDAC cells significantly suppressed theirgrowth Importantly we demonstrated that C12orf48 protein could directly interact with Poly(ADP-ribose) Polymerase-1 (PARP-1) one of theessential proteins in the repair of DNA damageand positively regulate the poly(ADP-ribosyl)ation activity of PARP-1 Depletion of C12orf48sensitized PDAC cells to agents causing DNAdamage and also enhanced DNA damage-induced G2M arrest through reduction ofPARP-1 enzymatic activities Hence our find-ings implicate C12orf48 termed PARP-1 bindingprotein (PARPBP) or its interaction with PARP-1 to be a potential molecular target for develop-ment of selective therapy for pancreatic cancer

(3) Prostate cancer

Association of a Novel Long Non-coding RNAin 8q24 with Prostate Cancer Susceptibility

Recent genome-wide association studies re-ported strong and reproducible associations ofmultiple genetic variants in a large ldquogene-desertrdquo region of chromosome 8q24 with suscep-tibility to prostate cancer (PC) However thecausative or functional variants of these 8q24loci and their biological mechanisms associatedwith PC susceptibility remain unclear andshould to be investigated Here focusing on itsmost centromeric region (so-called Region 2 Chr8 12814-12828Mb) among the multiple PC locion 8q24 we performed fine mapping and re-sequencing of this critical region and identifiedSNPs between rs1456315 and rs7463708 (chr8128173119-128173237bp) to be most signifi-cantly associated with PC susceptibility (P＝200times10－24 OR＝174 95 CI＝156-193) Impor-tantly we here show that this region was tran-

scribed as a ~13-kb intron-less long non-codingRNA (ncRNA) termed as PRNCR1 (prostate can-cer non-coding RNA 1) and PRNCR1 expressionwas up-regulated in some of PC cells as well asprecursor lesion PINs Knockdown of PRNCR1by siRNA attenuated the viability of PC cellsand the transactivation activity of androgen re-ceptor which indicates that PRNCR1 could beinvolved in prostate carcinogenesis possiblythrough androgen receptor activity These find-ings could provide a new insight to understandthe pathogenesis of genetic factors for PC sus-ceptibility and prostate carcinogenesis

(4) p53 target genes

XEDAR (X-linked ectodermal dysplasia recep-tor)

We recently identified X-linked ectodermaldysplasia receptor (XEDAR also known asTNFRSF27 or EDA2R) as a direct p53 target thatwas frequently downregulated in colorectal can-cer tissues due to its epigenetic alterations orthrough the p53 gene mutations However therole of the posttranslational regulation ofXEDAR protein in colorectal carcinogenesis wasnot well clarified thus far Here we report thatthe extracellular NH(2) terminus of XEDAR pro-tein was cleaved by a metalloproteinase and re-leased into culture media The remainingCOOH-terminal membrane-anchored fragmentwas rapidly degraded through the ubiquitin-proteasome pathway Interestingly ectopic p53expression also transactivated an XEDARligand EDA-A2 together with XEDAR More-over EDA-A2 blocked the cleavage of XEDARand subsequently inhibited cell growth We alsofound a missense mutation of the XEDAR genein NCI-H716 colorectal cancer cells whichcaused the translocation of XEDAR protein fromcell membrane to cytoplasm This mutation at-tenuated the growth-suppressive effect ofXEDAR indicating that membrane localizationis critical for physiologic XEDAR function Thusour findings clearly revealed the crucial role ofEDA-A2XEDAR interaction in the p53-signaling pathway

2 Pharmacogenetics

Lessons for pharmacogenomics studies as-sociation study between CYP2D6 genotypeand tamoxifen response

We earlier reported a significant associationbetween the cytochrome P450 2D6 (CYP2D6)genotype and the clinical outcome in 282 Japa-nese breast cancer patients receiving tamoxifen

112

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

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(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

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Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

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15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

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McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

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27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

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shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

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Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

monotherapy Although many research groupshave provided evidence indicating the CYP2D6genotype as one of the strongest predictors oftamoxifen response the results still remain con-troversial We hypothesized that concomitanttreatment was one of the causes of these contro-versial results We then studied 167 breast can-cer patients who received tamoxifen-combinedtherapy to evaluate the effects of concomitanttreatment on the association analysis and ob-served no significant association betweenCYP2D6 genotype and recurrence-free survival(P＝044 hazard ratio 064 95 confidential in-terval 020-199 in patients with two variant al-leles vs patients without a variant allele) Whenwe carried out two subgroup analyses for nodalstatus and tumor size we observed a positiveassociation between the CYP2D6 genotype andthe clinical outcome only in patients who re-ceived tamoxifen monotherapy This study ex-plained a part of the discrepancies among thereported results

3 Genome-wide association study

(1) cancer susceptible gene

Variation in TP63 is associated with lung ade-nocarcinoma susceptibility in Japanese andKorean populations

Lung cancer is the most common cause ofdeath from cancer worldwide and its incidenceis increasing in East Asian and Western coun-tries To identify genetic factors that modify therisk of lung adenocarcinoma we conducted agenome-wide association study in a Japanese co-hort with replication in two independent stud-ies in Japanese and Korean individuals in a to-tal of 2098 lung adenocarcinoma cases and11048 controls The combined analyses identi-fied two susceptibility loci for lung adenocarci-noma TERT (rs2736100 combined P＝291times10－11) odds ratio (OR)＝127) and TP63 (rs10937405 combined P＝726times10－12) OR＝131)Fine mapping of the region containing TP63showed that a SNP (rs4488809) in intron 1 ofTP63 showed the most significant associationOur results suggest that genetic variation inTP63 may influence susceptibility to lung adeno-carcinoma in East Asian populations

Genome-wide association study of pancreaticcancer in Japanese population

Pancreatic cancer shows very poor prognosisand is the fifth leading cause of cancer death inJapan Previous studies indicated some geneticfactors contributing to the development and

progression of pancreatic cancer however thereare limited reports for common genetic variantsto be associated with this disease especially inthe Asian population We have conducted agenome-wide association study (GWAS) using991 invasive pancreatic ductal adenocarcinomacases and 5209 controls and identified threeloci showing significant association (P-value＜5times10－7) with susceptibility to pancreatic cancerThe SNPs that showed significant associationcarried estimated odds ratios of 129 132 and373 with 95 confidence intervals of 117-143119-147 and 224-621 P-value of 330times10－7330times10(－7) and 441times10－7 located on chro-mosomes 6p253 12p1121 and 7q362 respec-tively These associated SNPs are located withinlinkage disequilibrium blocks containing genesthat have been implicated some roles in the on-cogenesis of pancreatic cancer

Common variant in 6q26-q27 is associatedwith distal colon cancer in Asian population

Colorectal cancer (CRC) is a multifactorial dis-ease with both environmental and genetic fac-tors contributing to its development The inci-dence of CRC is increasing year by year in Ja-pan Patients with CRC in advanced stages havea poor prognosis but detection of CRC at earlierstages can improve clinical outcome Thereforeidentification of epidemiologic factors that influ-ence development of CRC would facilitate theprevention or early detection of disease

To identify loci associated with CRC risk weperformed a genome-wide association study(GWAS) for CRC and sub-analyses by tumor lo-cation using 1583 Japanese CRC cases and 1898controls Subsequently we conducted replicationanalyses using a total of 4809 CRC cases and2973 controls including 225 Korean subjectswith distal colon cancer and 377 controls

We identified a novel locus on 6q26-q27 re-gion (rs7758229 in SLC22A3 P＝792times10-9Odds ratio of 128) that was significantly associ-ated with distal colon cancer We also replicatedthe association between CRC and SNPs on 8q24(rs6983267 and rs7837328 P＝151times10-8 and744times10-8 Odds ratios of 118 and 117 respec-tively) Moreover we found cumulative effectsof three genetic (rs7758229 rs6983267 and rs4939827 in SMAD7) and one environmental fac-tors (alcohol drinking) which appear to increaseCRC risk approximately twofold

We found a novel susceptible locus in SLC22A3 that contributes to the risk of distal coloncancer in Asian population These findingswould further extend our understanding of therole of common genetic variants in CRC etiol-ogy

113

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

116

McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

(2) other diseases

A genome-wide association study identifiesfour susceptibility loci for keloid in the Japa-nese population

Keloid is a dermal fibroproliferative growththat results from dysfunction of the wound heal-ing processes Through a multistage genome-wide association study using 824 individualswith keloid (cases) and 3205 unaffected controlsin the Japanese population we identified signifi-cant associations of keloid with four SNP loci inthree chromosomal regions 1q41 3q223-23 and15q213 The most significant association withkeloid was observed at rs873549 (combined P＝589times10－23 odds ratio (OR)＝177) on chromo-some 1 Associations on chromosome 3 were ob-served at two separate linkage disequilibrium(LD) blocks rs1511412 in the LD block includingFOXL2 with P＝231times10－13 (OR＝187) and rs940187 in another LD block with P＝180times10－13

(OR＝198) Association of rs8032158 located inNEDD4 on chromosome 15 yielded P＝596times10－13 (OR＝151) Our findings provide new in-sights into the pathophysiology of keloid forma-tion

A genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese

Although the pathogenesis of endometriosis isnot well understood genetic factors have beenconsidered to have critical roles in its etiologyThrough a genome-wide association study and areplication study using a total of 1907 Japaneseindividuals with endometriosis (cases) and 5292controls we identified a significant associationof endometriosis with rs10965235 (P＝557times10－12 odds ratio＝144) which is located inCDKN2BAS on chromosome 9p21 encoding thecyclin-dependent kinase inhibitor 2B antisenseRNA By fine mapping the SNP showing thestrongest association was located in intron 16 ofCDKN2BAS and was implicated in regulatingthe expression of p15 p16 and p14 A SNP rs16826658 in the LD block including WNT4 onchromosome 1p36 which is considered to playan important role in the development of the fe-male genital tract revealed a possible associa-tion with endometriosis (P＝166times10－6 odds ra-tio＝120) Our findings suggest that these re-gions are new susceptibility loci for endometrio-sis

Genome-wide association study of intracra-nial aneurysm identifies three new risk loci

Saccular intracranial aneurysms are balloon-like dilations of the intracranial arterial walltheir hemorrhage commonly results in severeneurologic impairment and death We report asecond genome-wide association study with dis-covery and replication cohorts from Europe andJapan comprising 5891 cases and 14181 controlswith approximately 832000 genotyped and im-puted SNPs across discovery cohorts We identi-fied three new loci showing strong evidence forassociation with intracranial aneurysms in thecombined dataset including intervals near RBBP8 on 18q112 (odds ratio (OR)＝122 P＝11times10－12) STARD13-KL on 13q131 (OR＝120 P＝25times10－9) and a gene-rich region on 10q2432(OR＝129 P＝12times10－9) We also confirmedprior associations near SOX17 (8q1123-q121OR＝128 P＝13times10－12) and CDKN2A-CDKN2B (9p213 OR＝131 P＝15times10－22) It is note-worthy that several putative risk genes play arole in cell-cycle progression potentially affect-ing the proliferation and senescence ofprogenitor-cell populations that are responsiblefor vascular formation and repair

(3) Quantitative trait loci

Genome-wide association study of hemato-logical and biochemical traits in a Japanesepopulation

We report genome-wide association studiesfor hematological and biochemical traits fromapproximately 14700 Japanese individuals Weidentified 60 associations for 8 hematologicaltraits and 29 associations for 12 biochemicaltraits at genome-wide significance levels (P＜5times10(－8)) Of these 46 associations were new tothis study and 43 replicated previous reportsWe compared these associated loci with thosereported in similar GWAS in European popula-tions When the minor allele frequency was＞10 in the Japanese population 32 (941)and 31 (912) of the 34 hematological loci pre-viously reported to be associated in a Europeanpopulation were replicated with P-values lessthan 005 and 001 respectively and 31 (738)and 27 (643) of the 42 European biochemicalloci were replicated

114

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

116

McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

Publications

1 Kiyotani K Mushiroda T Imamura CKHosono N Tsunoda T Kubo M Tani-gawara Y Flockhart DA Desta Z SkaarTC Aki F Hirata K Takatsuka YOkazaki M Ohsumi S Yamakawa TSasa M Nakamura Y and Zembutsu HSignificant effect of polymorphisms in CYP2D6 and ABCC2 on clinical outcomes of adju-vant tamoxifen therapy for breast cancer pa-tients J Clin Oncol 28 1287-1293 2010

2 Sato N Koinuma J Fujita M HosokawaM Ito T Tsuchiya E Kondo S Naka-mura Y and Daigo Y Activation of WDrepeat and high-mobility group box DNAbinding protein 1 in pulmonary and esopha-geal carcinogenesis Clin Cancer Res 16 226-239 2010

3 Wangsomboonsiri W Mahasirimongkol SChantarangsu S Kiertiburanakul S Charoenyingwattana A Komindr S Thongnak C Mushiroda T Nakamura YChantratita W and Sungkanuparph S As-sociation between HLA-B4001 and lipodys-trophy among HIV-infected patients fromThailand who received a stavudine-containing antiretroviral regimen Clin InfectDis 50 597-604 2010

4 Miyazawa M Ohsawa R Tsunoda THirono S Kawai M Tani M NakamuraY and Yamaue H Phase I clinical trial us-ing peptide vaccine for human vascular en-dothelial growth factor receptor 2 in combi-nation with gemcitabine for patients withadvanced pancreatic cancer Cancer Sci 101 433-439 2010

5 Nuinoon M Makarasara W MushirodaT Setianingsih I Wahidiyat PA Sripichai O Kumasaka N Takahashi ASvasti S Munkongdee T Mahasirimong-kol S Peerapittayamongkol C ViprakasitV Kamatani N Winichagoon P KuboM Nakamura Y and Fucharoen S Agenome-wide association identified the com-mon genetic variants influence disease se-verity in beta0-thalassemiahemoglobin EHum Genet 127 303-314 2010

6 Nakahara H Sekiguchi K Hosono NKubo M Takahashi A Nakamura Y andKasai K Criterion values for multiplex SNPgenotyping by the invader assay ForensicSci Int Genet 4 130-136 2010

7 Nakahara H Hosono N Kitayama TSekiguchi K Kubo M Takahashi ANakamura Y Yamano Y and Kai KAutomated SNPs typing system based onthe Invader assay Leg Med (Tokyo) 11Suppl 1 S111-114 2009

8 Sato N Koinuma J Ito T Tsuchiya EKondo S Nakamura Y and Daigo Y Ac-tivation of an oncogenic TBC1D7 (TBC1 do-main family member 7) protein in pulmo-nary carcinogenesis Genes ChromosomesCancer 49 353-367 2010

9 Kamatani Y Matsuda K Okada Y KuboM Hosono N Daigo Y Nakamura Yand Kamatani N Genome-wide associationstudy of hematological and biochemicaltraits in a Japanese population Nat Genet42 210-215 2010

10 Inoue M Senju S Hirata S Ikuta YHayashida Y Irie A Harao M Imai KTomita Y Tsunoda T Furukawa Y ItoT Nakamura Y Baba H and NishimuraY Identification of SPARC as a candidatetarget antigen for immunotherapy of variouscancers Int J Cancer 127 1393-1403 2010

11 Maeda S Kobayashi MA Araki S Baba-zono T Freedman BI Bostrom MACooke JN Toyoda M Umezono T Tar-now L Hansen T Gaede P Jorsal ANg DP Ikeda M Yanagimoto TTsunoda T Unoki H Kawai K ImanishiM Suzuki D Shin HD Park KS Kashi-wagi A Iwamoto Y Kaku K KawamoriR Parving HH Bowden DW PedersenO and Nakamura YA single nucleotidepolymorphism within the acetyl-coenzymeA carboxylase beta gene is associated withproteinuria in patients with type 2 diabetesPLoS Genet 6 e1000842 2010

12 Park JH Nishidate T Kijima K OhashiT Takegawa K Fujikane T Hirata KNakamura Y and Katagiri T Critical rolesof mucin 1 glycosylation by transactivatedpolypeptide N-acetylgalactosaminyltransferase6 in mammary carcinogenesis Cancer Res70 2759-2769 2010

13 Mototani H Iida A Nakamura Y andIkegawa S Identification of sequence poly-morphisms in CALM2 and analysis of asso-ciation with hip osteoarthritis in a Japanesepopulation J Bone Miner Metab 28 547-553 2010

14 Prescott NJ Dominy KM Kubo M Le-wis CM Fisher SA Redon R HuangN Stranger BE Blaszczyk K HudspithB Parkes G Hosono N Yamazaki KOnnie CM Forbes A Dermitzakis ETNakamura Y Mansfield JC Sanderson JHurles ME Roberts RG and Mathew CG Independent and population-specific as-sociation of risk variants at the IRGM locuswith Crohnrsquos disease Hum Mol Genet 19 1828-1839 2010

115

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

116

McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

15 Hayami S Yoshimatsu M Veerakumarasi-vam A Unoki M Iwai Y Tsunoda TField HI Kelly JD Neal DE YamaueH Ponder BA Nakamura Y and Hama-moto R Overexpression of the JmjC histonedemethylase KDM5B in human carcinogene-sis involvement in the proliferation of can-cer cells through the E2FRB pathway MolCancer 9 59 2010

16 Takayama R Nakagawa H Sawaki AMizuno N Kawai H Tajika M YatabeY Matsuo K Uehara R Ono K Naka-mura Y and Yamao K Serum tumor anti-gen REG4 as a diagnostic biomarker in pan-creatic ductal adenocarcinoma J Gastroen-terol 45 52-59 2010

17 Yasuno K Bilguvar K Bijlenga P LowSK Krischek B Auburger G Simon MKrex D Arlier Z Nayak N Ruigrok YM Niemela M Tajima A von und zuFraunberg M Doczi T Wirjatijasa FHata A Blasco J Oszvald A Kasuya HZilani G Schoch B Singh P Stuer CRisselada R Beck J Sola T Ricciardi FAromaa A Illig T Schreiber S vanDuijn CM van den Berg LH Perret CProust C Roder C Ozturk AK Gaal EBerg D Geisen C Friedrich CM Sum-mers P Frangi AF State MW Wich-mann HE Breteler MM Wijmenga CMane S Peltonen L Elio V Sturken-boom MC Lawford P Byrne J MachoJ Sandalcioglu EI Meyer B Raabe ASteinmetz H Rufenacht D Jaaskelainen JE Hernesniemi J Rinkel GJ ZembutsuH Inoue I Palotie A Cambien F Naka-mura Y Lifton RP and Gunel MGenome-wide association study of intracra-nial aneurysm identifies three new risk lociNat Genet 42 420-425 2010

18 Nakajima M Takahashi A Kou IRodriguez-Fontenla C Gomez-Reino JJFuruichi T Dai J Sudo A Uchida AFukui N Kubo M Kamatani NTsunoda T Malizos KN Tsezou A Gon-zalez A Nakamura Y and Ikegawa SNew sequence variants in HLA class IIIIIregion associated with susceptibility to kneeosteoarthritis identified by genome-wide as-sociation study PLoS One 5 e9723 2010

19 Hayami S Kelly JD Cho HS Yoshi-matsu M Unoki M Tsunoda T Field HI Neal DE Yamaue H Ponder BANakamura Y and Hamamoto R Overex-pression of LSD1 contributes to human car-cinogenesis through chromatin regulation invarious cancers Int J Cancer 128 574-5862011

20 Hudson TJ Anderson W Artez A

Barker AD Bell C Bernabe RR BhanMK Calvo F Eerola I Gerhard DSGuttmacher A Guyer M Hemsley FMJennings JL Kerr D Klatt P Kolar PKusada J Lane DP Laplace F YouyongL Nettekoven G Ozenberger B PetersonJ Rao TS Remacle J Schafer AJ Shiba-ta T Stratton MR Vockley JG Wata-nabe K Yang H Yuen MM KnoppersBM Bobrow M Cambon-Thomsen ADressler LG Dyke SO Joly Y Kato KKennedy KL Nicolas P Parker MJ Rial-Sebbag E Romeo-Casabona CM Shaw KM Wallace S Wiesner GL Zeps NLichter P Biankin AV Chabannon CChin L Clement B de Alava E DegosF Ferguson ML Geary P Hayes DNHudson TJ Johns AL Kasprzyk ANakagawa H Penny R Piris MA SarinR Scarpa A Shibata T van de Vijver MFutreal PA Aburatani H Bayes M Bot-well DD Campbell PJ Estivill X Ger-hard DS Grimmond SM Gut I HirstM Lopez-Otin C Majumder P MarraM McPherson JD Nakagawa H NingZ Puente XS Ruan Y Shibata T Strat-ton MR Stunnenberg HG Swerdlow HVelculescu VE Wilson RK Xue HHYang L Spellman PT Bader GD Bou-tros PC Campbell PJ Flicek P Getz GGuigo R Guo G Haussler D Heath SHubbard TJ Jiang T Jones SM Li QLopez-Bigas N Luo R Muthuswamy LOuellette BF Pearson JV Puente XSQuesada V Raphael BJ Sander C Shiba-ta T Speed TP Stein LD Stuart JMTeague JW Totoki Y Tsunoda T Valen-cia A Wheeler DA Wu H Zhao SZhou G Stein LD Guigo R Hubbard TJ Joly Y Jones SM Kasprzyk ALathrop M Lopez-Bigas N Ouellette BFSpellman PT Teague JW Thomas GValencia A Yoshida T Kennedy KL Ax-ton M Dyke SO Futreal PA GerhardDS Gunter C Guyer M Hudson TJMcPherson JD Miller LJ Ozenberger BShaw KM Kasprzyk A Stein LDZhang J Haider SA Wang J Yung CKCross A Liang Y Gnaneshan S Guber-man J Hsu J Bobrow M Chalmers DRHasel KW Joly Y Kaan TS KennedyKL Knoppers BM Lowrance WWMasui T Nicolas P Rial-Sebbag E Ro-driguez LL Vergely C Yoshida T Grim-mond SM Biankin AV Bowtell DDCloonan N deFazio A Eshleman JREtemadmoghadam D Gardiner BAKench JG Scarpa A Sutherland RLTempero MA Waddell NJ Wilson PJ

116

McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

McPherson JD Gallinger S Tsao MSShaw PA Petersen GM MukhopadhyayD Chin L DePinho RA Thayer SMuthuswamy L Shazand K Beck TSam M Timms L Ballin V Lu Y Ji JZhang X Chen F Hu X Zhou G YangQ Tian G Zhang L Xing X Li X ZhuZ Yu Y Yu J Yang H Lathrop MTost J Brennan P Holcatova I ZaridzeD Brazma A Egevard L ProkhortchoukE Banks RE Uhlen M Cambon-Thomsen A Viksna J Ponten F Skry-abin K Stratton MR Futreal PA BirneyE Borg A Borresen-Dale AL Caldas CFoekens JA Martin S Reis-Filho JSRichardson AL Sotiriou C StunnenbergHG Thoms G van de Vijver M vanrsquotVeer L Calvo F Birnbaum D BlancheH Boucher P Boyault S Chabannon CGut I Masson-Jacquemier JD LathropM Pauporte I Pivot X Vincent-SalomonA Tabone E Theillet C Thomas G TostJ Treilleux I Calvo F Bioulac-Sage PClement B Decaens T Degos F FrancoD Gut I Gut M Heath S Lathrop MSamuel D Thomas G Zucman-Rossi JLichter P Eils R Brors B Korbel JOKorshunov A Landgraf P Lehrach HPfister S Radlwimmer B Reifenberger GTaylor MD von Kalle C Majumder PPSarin R Rao TS Bhan MK Scarpa APederzoli P Lawlor RA Delledonne MBardelli A Biankin AV Grimmond SMGress T Klimstra D Zamboni G ShibataT Nakamura Y Nakagawa H Kusada JTsunoda T Miyano S Aburatani HKato K Fujimoto A Yoshida T CampoE Lopez-Otin C Estivill X Guigo R deSanjose S Piris MA Montserrat EGonzalez-Diaz M Puente XS Jares PValencia A Himmelbaue H Quesada VBea S Stratton MR Futreal PA Camp-bell PJ Vincent-Salomon A RichardsonAL Reis-Filho JS van de Vijver M Tho-mas G Masson-Jacquemier JD AparicioS Borg A Borresen-Dale AL Caldas CFoekens JA Stunnenberg HG vanrsquot VeerL Easton DF Spellman PT Martin SBarker AD Chin L Collins FS Comp-ton CC Ferguson ML Gerhard DSGetz G Gunter C Guttmacher A GuyerM Hayes DN Lander ES OzenbergerB Penny R Peterson J Sander C ShawKM Speed TP Spellman PT Vockley JG Wheeler DA Wilson RK Hudson TJ Chin L Knoppers BM Lander ESLichter P Stein LD Stratton MR An-derson W Barker AD Bell C BobrowM Burke W Collins FS Compton CC

DePinho RA Easton DF Futreal PAGerhard DS Green AR Guyer MHamilton SR Hubbard TJ KallioniemiOP Kennedy KL Ley TJ Liu ET LuY Majumder P Marra M Ozenberger BPeterson J Schafer AJ Spellman PTStunnenberg HG Wainwright BJ WilsonRK and Yang H International network ofcancer genome projects Nature 464 993-998 2010

21 Yamaguchi K Sakai M Shimokawa TYamada Y Nakamura Y and FurukawaY C20orf20 (MRG-binding protein) as a po-tential therapeutic target for colorectal can-cer Br J Cancer 102 325-331 2010

22 Kashiwaya K Nakagawa H HosokawaM Mochizuki Y Ueda K Piao LChung S Hamamoto R Eguchi HOhigashi H Ishikawa O Janke C Shino-mura Y and Nakamura Y Involvement ofthe tubulin tyrosine ligase-like family mem-ber 4 polyglutamylase in PELP1 polygluta-mylation and chromatin remodeling in pan-creatic cancer cells Cancer Res 70 4024-4033 2010

23 Akuta N Suzuki F Hirakawa M Kawa-mura Y Yatsuji H Sezaki H Suzuki YHosaka T Kobayashi M Kobayashi MSaitoh S Arase Y Ikeda K Chayama KNakamura Y and Kumada H Amino acidsubstitution in hepatitis C virus core regionand genetic variation near the interleukin 28B gene predict viral response to telaprevirwith peginterferon and ribavirin Hepatol-ogy 52 421-429 2010

24 Yoshimatsu M Toyokawa G Hayami SUnoki M Tsunoda T Field HI Kelly JD Neal DE Maehara Y Ponder BANakamura Y and Hamamoto R Dysregu-lation of PRMT1 and PRMT6 Type I ar-ginine methyltransferases is involved invarious types of human cancers Int J Can-cer 128 562-573 2011

25 Phasukkijwatana N Kunhapan B Stank-ovich J Chuenkongkaew WL ThomsonR Thornton T Bahlo M Mushiroda TNakamura Y Mahasirimongkol S Tun AW Srisawat C Limwongse C Peerapitta-yamongkol C Sura T Suthammarak Wand Lertrit P Genome-wide linkage scanand association study of PARL to the ex-pression of LHON families in ThailandHum Genet 128 39-49 2010

26 Ramamoorthy A Flockhart DA HosonoN Kubo M Nakamura Y and Skaar TCDifferential quantification of CYP2D6 genecopy number by four different quantitativereal-time PCR assays PharmacogenetGenomics 20 451-454 2010

117

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

27 Kochi Y Okada Y Suzuki A Ikari KTerao C Takahashi A Yamazaki KHosono N Myouzen K Tsunoda TKamatani N Furuichi T Ikegawa S Oh-mura K Mimori T Matsuda F IwamotoT Momohara S Yamanaka H YamadaR Kubo M Nakamura Y and YamamotoK A regulatory variant in CCR6 is associ-ated with rheumatoid arthritis susceptibilityNat Genet 42 515-519 2010

28 Kiyotani K Mushiroda T Hosono NTsunoda T Kubo M Aki F Okazaki YHirata K Takatsuka Y Okazaki M Oh-sumi S Yamakawa T Sasa M Naka-mura Y and Zembutsu H Lessons forpharmacogenomics studies associationstudy between CYP2D6 genotype and ta-moxifen response Pharmacogenet Genom-ics 20 565-568 2010

29 Abe H Ochi H Maekawa T Hayes CN Tsuge M Miki D Mitsui F HiragaN Imamura M Takahashi S Ohishi WArihiro K Kubo M Nakamura Y andChayama K Common variation of IL28 af-fects gamma-GTP levels and inflammationof the liver in chronically infected hepatitisC virus patients J Hepatol 53 439-4432010

30 Tanikawa C Ri C Kumar V NakamuraY and Matsuda K Crosstalk of EDA-A2XEDAR in the p53 signaling pathway MolCancer Res 8 855-863 2010

31 Onouchi Y Ozaki K Buns JC ShimizuC Hamada H Honda T Terai MHonda A Takeuchi T Shibuta SSuenaga T Suzuki H Higashi KYasukawa K Suzuki Y Sasago K Kem-motsu Y Takatsuki S Saji T YoshikawaT Nagai T Hamamoto K Kishi FOuchi K Sato Y Newburger JW BakerAL Shulman ST Rowley AH YashiroM Nakamura Y Wakui K FukushimaY Fujino A Tsunoda T Kawasaki THata A Nakamura Y and Tanaka TCommon variants in CASP3 confer suscepti-bility to Kawasaki disease Hum Mol Genet19 2898-2906 2010

32 Unoki M Kelly JD Neal DE Ponder BA Nakamura Y and Hamamoto R UHRF1 is a novel molecular marker for diagnosisand the prognosis of bladder cancer Br JCancer 101 98-105 2009

33 Nguyen MH Koinuma J Ueda K ItoT Tsuchiya E Nakamura Y and DaigoY Phosphorylation and activation of cell di-vision cycle associated 5 by mitogen-activated protein kinase play a crucial rolein human lung carcinogenesis Cancer Res70 5337-5347 2010

34 Fukukawa C Ueda K Nishidate TKatagiri T and Nakamura Y Critical rolesof LGNGPSM2 phosphorylation by PBKTOPK in cell division of breast cancer cellsGenes Chromosomes Cancer 49 861-8722010

35 Sato N Yamabuki T Takano AKoinuma J Aragaki M Masuda KIshikawa N Kohno N Ito H MiyamotoM Nakayama H Miyagi Y Tsuchiya EKondo S Nakamura Y and Daigo Y Wntinhibitor Dickkopf-1 as a target for passivecancer immunotherapy Cancer Res 70 5326-5336 2010

36 Harada Y Kanehira M Fujisawa YTakata R Shuin T Miki T Fujioka TNakamura Y and Katagiri T Cell-permeable peptide DEPDC1-ZNF224 inter-feres with transcriptional repression and on-cogenicity in bladder cancer cells CancerRes 70 5829-5839 2010

37 Uno S Zembutsu H Hirasawa A Taka-hashi A Kubo M Akahane T Aoki DKamatani N Hirata K and Nakamura YA genome-wide association study identifiesgenetic variants in the CDKN2BAS locus as-sociated with endometriosis in Japanese NatGenet 42 707-710 2010

38 Uemura M Honma S Chung S TakataR Furihata M Nishimura K NonomuraN Nasu Y Miki T Shuin T Fujioka TOkuyama A Nakamura Y and Naka-gawa H 5alphaDH-DOC (5alpha-dihydro-deoxycorticosterone) activates androgen re-ceptor in castration-resistant prostate cancerCancer Sci 101 1897-1904 2010

39 Akaza H Kawai K Tsukamoto T Fu-jioka T Tomita Y Kitamura T Ozono SMiki T Naito S Zembutsu H and Naka-mura Y Successful outcomes using combi-nation therapy of interleukin-2 andinterferon-alpha for renal cell carcinoma pa-tients with lung metastasis Jpn J Clin Oncol40 684-689 2010

40 Ueda K Takami S Saichi N Daigo YIshikawa N Kohno N Katsumata MYamane A Ota M Sato TA NakamuraY and Nakagawa H Development of se-rum glycoproteomic profiling technique si-multaneous identification of glycosylationsites and site-specific quantification of gly-can structure changes Mol Cell Proteomics9 1819-1828 2010

41 Ingle JN Schaid DJ Goss PE Liu MMushiroda T Chapman JA Kubo MJenkins GD Batzler A Shepherd L Pa-ter J Wang L Ellis MJ Stearns V Ro-hrer DC Goetz MP Pritchard KIFlockhart DA Nakamura Y and Wein-

118

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

shilboum RM Genome-wide associationsand functional genomic studies of muscu-loskeletal adverse events in women receiv-ing aromatase inhibitors J Clin Oncol 28 4674-4682 2010

42 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N Common vari-ations in PSMD3-CSF3 and PLCB4 are asso-ciated with neutrophil count Hum MolGenet 19 2079-2085 2010

43 Okada Y Kamatani Y Takahashi AMatsuda K Hosono N Ohmiya HDaigo Y Yamamoto K Kubo M Naka-mura Y and Kamatani N A genome-wideassociation study in 19 633 Japanese subjectsidentified LHX3-QSOX2 and IGF1 as adultheight loci Hum Mol Genet 19 2303-23122010

44 Takata R Akamatsu S Kubo M Taka-hashi A Hosono N Kawaguchi TTsunoda T Inazawa J Kamatani NOgawa O Fujioka T Nakamura Y andNakagawa H Genome-wide associationstudy identifies five new susceptibility locifor prostate cancer in the Japanese popula-tion Nat Genet 42 751-754 2010

45 Kim JW Fukukawa C Ueda K Nishi-date T Katagiri T and Nakamura Y In-volvement of C12orf32 overexpression inbreast carcinogenesis Int J Oncol 37 861-867 2010

46 Nakashima M Chung S Takahashi AKamatani N Kawaguchi T Tsunoda THosono N Kubo M Nakamura Y andZembutsu H A genome-wide associationstudy identifies four susceptibility loci forkeloid in the Japanese population NatGenet 42 768-771 2010

47 Iida A Kamei T Sano M Oshima STokuda T Nakamura Y and Ikegawa SLarge-scale screening of TARDBP mutationin amyotrophic lateral sclerosis in JapaneseNeurobiol Aging 2010

48 Low SK Kuchiba A Zembutsu H SaitoA Takahashi A Kubo M Daigo Y Ka-matani N Chiku S Totsuka H OhnamiS Hirose H Shimada K Okusaka TYoshida T Nakamura Y and SakamotoH Genome-wide association study of pan-creatic cancer in Japanese population PLoSOne 5 e11824 2010

49 Kawaoka T Hayes C N Ohishi W OchiH Maekawa T Abe H Tsuge M MitsuiF Hiraga N Imamura M Takahashi SKubo M Tsunoda T Nakamura YKumada H and Chayama K Predictivevalue of the IL28B polymorphism on the ef-

fect of interferon therapy in chronic hepatitisC patients with genotypes 2a and 2b J He-patol 2010

50 Ochi H Maekawa T Abe H HayashidaY Nakano R Kubo M Tsunoda THayes CN Kumada H Nakamura Yand Chayama K ITPA polymorphism af-fects ribavirin-induced anemia and outcomesof therapy--a genome-wide study of Japa-nese HCV virus patients Gastroenterology139 1190-1197 2010

51 Ajiro M Nishidate T Katagiri T andNakamura Y Critical involvement of RQCD1 in the EGFR-Akt pathway in mammarycarcinogenesis Int J Oncol 37 1085-10932010

52 Miki D Kubo M Takahashi A Yoon KA Kim J Lee GK Zo JI Lee JSHosono N Morizono T Tsunoda T Ka-matani N Chayama K Takahashi TInazawa J Nakamura Y and Daigo YVariation in TP63 is associated with lungadenocarcinoma susceptibility in Japaneseand Korean populations Nat Genet 42 893-896 2010

53 Myouzen K Kochi Y Shimane K FujioK Okamura T Okada Y Suzuki A At-sumi T Ito S Takada K Mimori AIkegawa S Yamada R Nakamura Y andYamamoto K Regulatory polymorphisms inEGR2 are associated with susceptibility tosystemic lupus erythematosus Hum MolGenet 19 2313-2320 2010

54 Yamauchi T Hara K Maeda S YasudaK Takahashi A Horikoshi M NakamuraM Fujita H Grarup N Cauchi S Ng DP Ma RC Tsunoda T Kubo M WatadaH Maegawa H Okada-Iwabu M IwabuM Shojima N Shin HD Andersen GWitte DR Jorgensen T Lauritzen TSandbaek A Hansen T Ohshige TOmori S Saito I Kaku K Hirose H SoWY Beury D Chan JC Park KS TaiES Ito C Tanaka Y Kashiwagi AKawamori R Kasuga M Froguel P Ped-ersen O Kamatani N Nakamura Y andKadowaki T A genome-wide associationstudy in the Japanese population identifiessusceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B Nat Genet 42 864-868 2010

55 Akamatsu S Takata R Ashikawa KHosono N Kamatani N Fujioka TOgawa O Kubo M Nakamura Y andNakagawa H A functional variant in NKX31 associated with prostate cancer suscepti-bility down-regulates NKX31 expressionHum Mol Genet 19 4265-4272 2010

56 Okada Y Suzuki A Yamada R Kochi

119

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

Y Shimane K Myouzen K Kubo MNakamura Y and Yamamoto K HLA-DRB10901 lowers anti-cyclic citrullinated peptideantibody levels in Japanese patients withrheumatoid arthritis Ann Rheum Dis 69 1569-1570 2010

57 Cha PC Mushiroda T Takahashi AKubo M Minami S Kamatani N andNakamura Y Genome-wide associationstudy identifies genetic determinants of war-farin responsiveness for Japanese Hum MolGenet 19 4735-4744 2010

58 Chung S Nakagawa H Uemura M PiaoL Ashikawa K Hosono N Takata RAkamatsu S Kawaguchi T Morizono TTsunoda T Daigo Y Matsuda K Kama-tani N Nakamura Y and Kubo M Asso-ciation of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility Can-cer Sci 102 245-252 2011

59 Kumasaka N Yamaguchi-Kabata Y Taka-hashi A Kubo M Nakamura Y and Ka-matani N Establishment of a standardizedsystem to perform population structureanalyses with limited sample size or withdifferent sets of SNP genotypes J HumGenet 55 525-533 2010

60 Piao L Nakagawa H Ueda K Chung SKashiwaya K Eguchi H Ohigashi HIshikawa O Daigo Y Matsuda K andNakamura Y C12orf48 termed PARP-1binding protein enhances poly(ADP-ribose)polymerase-1 (PARP-1) activity and protectspancreatic cancer cells from DNA damageGenes Chromosomes Cancer 50 13-242011

61 Stefanou N Papanikolaou V FurukawaY Nakamura Y and Tsezou A Leptin asa critical regulator of hepatocellular carci-noma development through modulation ofhuman telomerase reverse transcriptaseBMC Cancer 10 442 2010

62 Yamaguchi-Kabata Y Tsunoda T Taka-hashi A Hosono N Kubo M NakamuraY and Kamatani N Making a haplotypecatalog with estimated frequencies based onSNP homozygotes J Hum Genet 55 500-506 2010

63 Hayes CN Kobayashi M Akuta NSuzuki F Kumada H Abe H Miki DImamura M Ochi H Kamatani N Naka-mura Y and Chayama K HCV substitu-tions and IL28B polymorphisms on outcomeof peg-interferon plus ribavirin combinationtherapy Gut 60 261-267 2011

64 Fujimoto A Nakagawa H Hosono NNakano K Abe T Boroevich KA Naga-saki M Yamaguchi R Shibuya T KuboM Miyano S Nakamura Y and Tsunoda

T Whole-genome sequencing and compre-hensive variant analysis of a Japanese indi-vidual using massively parallel sequencingNat Genet 42 931-936 2010

65 Aoki A Ozaki K Sato H Takahashi AKubo M Sakata Y Onouchi YKawaguchi T Lin TH Takano H Yasu-take M Hsu PC Ikegawa S KamataniN Tsunoda T Juo SH Hori MKomuro I Mizuno K Nakamura Y andTanaka T SNPs on chromosome 5p153 as-sociated with myocardial infarction in Japa-nese population J Hum Genet 2010

66 Fujimoto Y Ochi H Maekawa T AbeH Hayes CN Kumada H Nakamura Yand Chayama K A single nucleotide poly-morphism in activated cdc42 associated ty-rosine kinase 1 influences the interferontherapy in hepatitis C patients J Hepatol2010

67 Cho HS Suzuki T Dohmae N HayamiS Unoki M Yoshimatsu M ToyokawaG Takawa M Chen T Kurash JK FieldH Ponder BA Nakamura Y and Hama-moto R Demethylation of RB regulatorMYPT1 by histone demethylase LSD1 pro-motes cell cycle progression in cancer cellsCancer Res 2010

68 Maeda S Araki S Babazono T ToyodaM Umezono T Kawai K Imanishi MUzu T Watada H Suzuki D KashiwagiA Iwamoto Y Kaku K Kawamori Rand Nakamura Y Replication study for theassociation between four Loci identified by agenome-wide association study on EuropeanAmerican subjects with type 1 diabetes andsusceptibility to diabetic nephropathy inJapanese subjects with type 2 diabetes Dia-betes 59 2075-2079 2010

69 Iida A Hosono N Sano M Kamei TOshima S Tokuda T Kubo M Naka-mura Y and Ikegawa S Optineurin muta-tions in Japanese amyotrophic lateral sclero-sis J Neurol Neurosurg Psychiatry 2011

70 Saetre P Vares M Werge T AndreassenOA Arinami T Ishiguro H Nanko STan EC Han DH Roffman JLMuntjewerff J W Jagodzinski P P Kempisty B Hauser J Vilella EBetcheva E Nakamura Y Regland BAgartz I Hall H Terenius L and Jons-son EG Methylenetetrahydrofolate reduc-tase (MTHFR) C677T and A1298C polymor-phisms and age of onset in schizophrenia Acombined analysis of independent samplesAm J Med Genet B Neuropsychiatr Genet2011

71 Ozeki T Mushiroda T Yowang A Taka-hashi A Kubo M Shirakata Y Ikezawa

120

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

Z Iijima M Shiohara T Hashimoto KKamatani N and Nakamura Y Genome-wide association study identifies HLA-A

3101 allele as a genetic risk factor forcarbamazepine-induced cutaneous adversedrug reactions in Japanese population HumMol Genet 2010

72 Yoon KA Park JH Han J Park S LeeGK Han JY Zo JI Kim J Lee JETakahashi A Kubo M Nakamura Y andLee JS A genome-wide association studyreveals susceptibility variants for non-smallcell lung cancer in the Korean populationHum Mol Genet 19 4948-4954 2010

73 Peerbooms OL van Os J Drukker MKenis G Hoogveld L de Hert MDelespaul P van Winkel R and Rutten BP Meta-analysis of MTHFR gene variants inschizophrenia bipolar disorder and unipolardepressive disorder Evidence for a commongenetic vulnerability Brain Behav Immun2010

74 Imai K Hirata S Irie A Senju S IkutaY Yokomine K Harao M Inoue MTomita Y Tsunoda T Nakagawa HNakamura Y Baba H and Nishimura YIdentification of HLA-A2-restricted CTL epi-topes of a novel tumour-associated antigenKIF20A overexpressed in pancreatic cancerBr J Cancer 2010

75 Mizumori O H Zembutsu Y Kato TTsunoda F Miya T Morizono T Tsuka-moto T Fujioka Y Tomita T Kitamura SOzono T Miki S Naito H Akaza and YNakamura Identification of a set of genesassociated with response to interleukin-2and interferon-α combination therapy for re-nal cell carcinoma through genome-widegene expression profiling Experimental andTherapeutic Medicine 1 955-9612010

76 Kato Y H Zembutsu R Takata F Miya

T Tsunoda W Obara T Fujioka and YNakamura Predicting response of bladdercancers to gemcitabine and carboplatinneoadjuvant chemotherapy through genome-wide gene expression profiling Experimen-tal and Therapeutic Medicine In press

77 Hashimoto Y H Ochi H Abe Y Hayashi-da M Tsuge F Mitsui N Hiraga M Ima-mura S Takahashi CN Hayes W OhishiM Kubo T Tsunoda N Kamatani YNakamura and K Chayama Prediction ofresponse to peginterferon-alfa-2 b plusribavirin therapy in Japanese patients in-fected with hepatitis C virus genotype 1b JMed Virol In press

78 Suzuki F Y Suzuki N Akuta H SezakiM Hirakawa Y Kawamura T Hosaka MKobayashi S Saito Y Arase K Ikeda MKobayashi K Chayama N Kamatani YNakamura Y Miyakawa and H KumadaInfluence of ITPA polymorphism on de-creases of hemoglobin during treatmentwith pegylated IFN ribavirin and telaprevirHepatology In press

79 Cui R Y Okada SG Jang JL Ku JGPark Y Kamatani N Hosono T TsunodaV Kumar C Tanikawa N Kamatani RYamada M Kubo Y Nakamura and KMatsuda Common variant in 6q26-q27 is as-sociated with distal colon cancer in Asianpopulation GUT In press

80 Akukta N F Suzuki M Hirakawa YKawamura H Yatsuji H Sezaki Y SuzukiT Hosaka M Kobayashi M Kobayashi SSaitoh Y Arase K Ikeda K Chayama YNakamura and H Kumada Amino acidsubstitution in HCV core region and geneticvariation near IL28B gene affect viral dy-namics during telaprevir peginterferon andribavirin Intervirology In press

121

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

The mission of our laboratory is to conduct computational (ldquoin silicordquo) studies onthe functional aspects of genome information Roughly speaking genome informa-tion represents what kind of proteinsRNAs are synthesized in what conditionsThus our study includes the structural analysis of molecular function of each geneproduct as well as the analysis of its regulatory information which will lead us tothe understanding of its cellular role represented by the networks of inter-gene in-teraction

1 A regression analysis of gene expressionin ES cells reveals two gene classes thatare significantly different in epigenetic pat-terns

Sung-Joon Park and Kenta Nakai

To understand the gene regulatory systemthat governs the pluripotency of embryonicstem (ES) cells is an important step for promot-ing regenerative medicine Although the role ofseveral transcription factors (TFs) has been in-tensively investigated details of their involve-ment in the regulation are still not well clarifiedHere we constructed a predictive model of thegenome-wide gene expression in mouse ES cellsWe firstly reanalyzed ChIP-seq data publiclyavailable Then we estimated TF-binding den-sity profiles from the data The density profilesand the data of several epigenetic states of pro-moters are used as predictors in a simple linearregression model that predicts absolute gene ex-pression We also exhaustively analyzed the ef-fects of predictors and their higher-order inter-actions by statistical tests Through this studywe confirmed that our linear regression modelhas better predictive power than an ordinarylinear regression model Using the proposed

model we identified two gene classes that areeither well explained or inefficiently explainedby the model Since the promoters of these geneclasses have apparently distinct patterns of epi-genetics we inspected the effects of epigeneticmodifications in explaining the gene expressionThe result supports the general idea of relativeimportance of epigenetic effects in ES cellsMoreover it has been found that unknownregulatory mechanisms control approximatelyhalf of ES-specific genes rather than direct regu-lation by the TFs To elucidate such mechanismsis one of further works

2 Transcriptional regulation and networks ofimmune systems

Naoki Osato and Kenta Nakai

Our immune responses involve highly organ-ized activities of many types of genes and cellsUnderstanding the mechanisms of immune re-sponses is important to reveal the causes of dis-eases allergies and immunological rejectionsAlthough these mechanisms have been exam-ined by experimental analyses they are still un-clear Nowadays genome-wide gene expressiondata protein-protein and protein-DNA interac-

Human Genome Center

Laboratory of Functional Analysis In Silico機能解析インシリコ分野

Professor Kenta Nakai PhDAssistant Professor Ashwini Patil PhD

教 授 理学博士 中 井 謙 太助 教 理学博士 パティルアシュウィニ

122

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

tion data and epigenetic data are being pro-duced Analyzing genome sequences and thesedata would contribute to reveal the mechanismsand regulatory networks of immune responsesand the differentiation of immune cells effec-tively For these purposes we plan to developmethods to predict transcription factor bindingsites (TFBS) from human genome sequences andgene expression data and reveal conserved sig-natures of TFBS in each immune cell type or re-sponse by computational analyses We will pre-dict transcriptional regulatory networks of im-mune cells and responses by combining variousgenome-scale data such as known TFBS non-coding RNAs and known pathways Collaborat-ing with experimental researchers we will vali-date our predictions These methods and ap-proaches would also be useful to examine othertranscriptional regulatory mechanisms and net-works

3 Classification and characterization of bi-directional promoters

Riu Yamashita1 Yutaka Suzuki2 SumioSugano2 Kenta Nakai 1Frontier Research In-itiative IMSUT 2Graduate School of FrontierSciences

We have constructed the DataBase of Tran-scription Start Sites (DBTSS httpdbtsshgcjp) which contains the information of accuratetranscription start sites (TSSs) based on experi-mentally determined 5prime-end clones Recently wehave updated the database based on the 5primeendof oligo-cap selected cDNAs in humans andmice Using this database we focused on bi-directional promoters which have TSSs on bothplus and minus strands closely In DLD-1 celllines the distribution of frequency of the dis-tance between a transcriptrsquos TSS and the closestanti-transcript TSS showed two significantpeaks The first peak corresponded to 707 TSSson －160－100 (upstream anti-sense transcriptpromoters upASTPs) and the second corre-sponded to 237 TSSs 0＋40 (downstream anti-sense transcript promoters downASTPs) Wealso defined 2166 TSSs which did not have anyanti-transcript within 10 kb as no anti-sensetranscript promoters (noASTPs) Around TSS re-gion noASTPs and upASTPs had pyrimidine-purine bases on －1＋1 which can be widelyobserved on TSSs However the downASTPsshowed lsquoCTGGrsquo at －4－1 region We also ob-served significant difference of characteristics inthe downASTPs namely GC poor CpG islandspoor and disordered nucleosome structures In-terestingly even though we observed highly or-dered nucleosome structures in both

downASTPs and noASTPs the noASTPsshowed more asymmetrical nucleosome struc-tures These phenomena could be observed notonly in other human cell lines (Hek293 MCF7TIG) but also in a mouse cell line (3T3) Theseresults indicate that we could classify promotersinto three classes based on their anti-transcriptand these classes showed biologically differentfeatures

4 The effect of Alu elements on global nu-cleosome positioning in the humangenome using paired-end MNase-Seq

Yoshiaki Tanaka Riu Yamashita1 YutakaSuzuki2 and Kenta Nakai

Understanding the genome sequence-specificpositioning of nucleosomes is essential to under-stand various cellular processes such as tran-scriptional regulation and replication As a typi-cal example the 10-bp periodicity of AATTand GC dinucleotides has been reported in sev-eral species but it is still unclear whether thisfeature can be observed in the whole genomesof all eukaryotes With Fourier analysis wefound that this is not the case 84-bp and 167-bpperiodicities are prevalent in primates The 167-bp periodicity is intriguing because it is almostequal to the sum of the lengths of a nucleosomalunit and its linker region After masking Aluelements these periodicities were greatly dimin-ished Next using paired-end sequencing of nu-cleosomal DNAs (MNase-Seq) we analyzed thedistribution of nucleosomes in the vicinity ofAlu elements and showed that (1) there are oneor two fixed slot(s) for nucleosome positioningwithin the Alu element and (2) the positioningof neighboring nucleosomes seems to be inphase more or less with the presence of Aluelements The paired-end data makes it possibleto reduce the number of multiple hits Further-more (3) these effects of Alu elements on nu-cleosome positioning are consistent with inacti-vation of promoter activity in Alu elements Ourdiscoveries suggest that the principle governingnucleosome positioning differs greatly acrossspecies and that the Alu family is an importantfactor in primate genomes

5 Prediction of subcellular locations of pro-teins where to proceed

Kenichiro Imai3 and Kenta Nakai 3Computa-tional Biology Research Center AIST

Since the proposal of the signal hypothesis onprotein subcellular sorting a number of compu-tational analyses have been performed in this

123

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

field A typical example is the development ofprediction algorithms for the subcellular local-ization sites of input protein sequences In thisreview we mainly focus on the biologicalgrounds of the prediction methods rather thanthe algorithmic issues because we believe theformer will be more fruitful for future develop-ment Recent advances on the study of proteinsorting signals will hopefully be incorporatedinto future prediction methods Unfortunatelymany of the state-of-the-art methods are pub-lished without sufficiently objective tests In facta simple test employed in this article shows thatthe performance of specifically developed pre-dictors is not significantly better than that of ahomology search We suspect this is a generalproblem associated with the interpretation ofgenome sequences which have evolved throughgene duplication and speciation

6 Computational prediction of mitochondrialinner membrane proteins

Toshiyuki Tsuji and Kenta Nakai

Proteins are transferred to the correct subcel-lular location to properly perform their func-tions Prediction of the protein subcellular local-ization is very important for exploring the func-tion of proteins in the cell Although many sub-cellular localization prediction methods havebeen developed these systems ignore the mito-chondrial inner membrane proteins without N-terminal targeting signal It is known that theinner membrane proteins have an internal tran-sit noncleavable signal However the detectionof the internal signals is very difficult In thisstudy we analyzed the propensities of aminoacids and various physicochemical properties offive types of proteins which are localized at themitochondrial inner membrane the mitochon-drial matrix cytoplasm the cell membrane orthe extracellular space These properties wereused for developing a prediction method basedon support vector machine (SVM) We analyzedthe amino acid propensities around the cleavagesite of the mitochondria targeting signal at theN-terminus of mitochondrial matrix proteinsand made a position specific score matrix(PSSM) Using the PSSM we searched the po-tential cleavage site of mitochondrial innermembrane proteins The distributions of physi-cochemical properties around the potentialcleavage site were used as the input of SVMMeanwhile we revealed that the mitochondrialinner membrane proteins tend to dislike thecluster of negative charged residues We alsoused the size of negatively charged cluster as aninput of SVM The performance of our predictor

outperforms previous predictors in the discrimi-nation of the mitochondrial inner membraneproteins

7 Development and maintenance of the data-bases Hintdb and HitPredict - Ashwini Pa-til Kenta Nakai and Haruki Nakamura44Osaka University

Protein-protein interactions (PPIs) are vital forcellular function in organisms and hence theirdetection is of considerable importance The ad-vent of high-throughput technologies has leadto a manifold increase in the PPI information inseveral model organisms through large scaleyeast two hybrid (Y2H) and tandem affinity pu-rification in combination with mass spectrome-try (TAPMS) experiments However this datahas two major drawbacks leading to its limitedusage-(i) the large number of spurious interac-tions detected and (ii) the absence of direct bi-nary interaction information in protein co-complex data obtained from TAPMS experi-ments As a result most studies using PPI infor-mation either use data obtained exclusivelyfrom small-scale experiments or those con-firmed in multiple experiments Both types ofinteraction subsets are considered high confi-dence but constitute only a fraction of theamount of data available and their use can oftenlead to biased results An alternative approachis to utilize the high confidence subsets pro-vided by authors of high-throughput experi-ments However these interaction subsets areassessed using a range of techniques with differ-ing accuracies making comparisons among datasets difficult Frequently such high confidenceinteraction subsets are available only for one ortwo species typically yeast and human As a re-sult a large amount of the PPI information inseveral species though correct and potentiallyuseful is often ignored The major reason forthis lack of information usage is the scarcity ofcomprehensive PPI databases that provide confi-dence scores assessing the quality of the interac-tions To address these issues we created Hit-Predict (httphintdbhgcjphtp) a databaseof quality assessed interactions in nine speciesHitPredict combines interactions from IntAct Bi-oGRID and HPRD and determines the confi-dence level of the interactions based on a reli-ability score calculated using the sequencestructure and functional annotations of the inter-acting proteins HitPredict was first introducedin 2005 as a database of high confidence PPIsfrom high-throughput data sets It has sincebeen updated annually and has now been ex-panded to include small-scale interactions alongwith a more intuitive user interface Similarly

124

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

Hintdb a database of homologous protein-protein interactions was also updated

8 Functional characterization of intrinsicallydisordered regions in mammalian proteins

Ashwini Patil Shunsuke Teraguchi4 DaronStrandley4 and Kenta Nakai

Intrinsically disordered regions in proteins areregions without a stable tertiary structure De-spite the lack of a stable structure these regionsplay an important role in protein function as aresult of their flexibility and adaptability Intrin-sically disordered regions are found in proteinsfunctioning in cell signaling and transcriptionregulation However several such regions arenot associated with any function and are oftenignored during the functional annotation of pro-teins In this project we group similar intrinsi-cally disordered regions in an attempt to iden-tify those that function in a similar manner Wefind that disordered regions can be classifiedinto different groups based on the prevalence ofcharged and hydrophobic residues We also find

that disordered regions in distinct groups areassociated with distinct functions suggesting apossible functional classification of disorderedregions

9 Using gene expression correlations toseparate functionally distinct genes

Ashwini Patil Kenta Nakai and Kengo Ki-noshita5 5Tohoku University

The expression patterns of genes under vari-ous conditions have been extensively studiedHowever the differences in the levels of expres-sions of genes with different functions have notyet been extensively studied In this project wetried to identify if functionally distinct geneshad different expression patterns using humangene expression data and a gene expression sta-bility measure The stability measure indicateshow variable the expression of a gene is acrossmultiple samples We grouped the genes into 4groups based on their stability and average cor-relation coefficient and studied the functionaldifferences between them

Publications

Sathira N Yamashita R Tanimoto K KanaiA Arauchi T Kanematsu S Nakai K Su-zuki Y and Sugano S Characterization oftranscription start sites of putative non-codingRNAs by multifaceted use of massively paral-leled sequencer DNA Res 17(3) 169-1832010

Tanaka Y Yoshimura I and Nakai K Posi-tional variations among heterogeneous nu-cleosome maps give dynamical informationon chromatin Chromosoma 119(4) 391-4042010

Kubo A Suzuki N Yuan X Nakai K SatohN Imai K and Satou Y Genomic cis-regulatory networks in the Ciona intestinalisembryo Development 137(10) 1613-16232010

Patil A Kinoshita K and Nakamura H Hubpromiscuity in protein-protein interaction net-works Int J Mol Sci 11(4) 1930-1943 2010

Tanaka Y Yamashita R Suzuki Y and NakaiK Effects of Alu elements on global nu-cleosome positioning in the human genomeBMC Genomics 11 309 2010

Kawaki H Kubota S Aoyama E Fujita NHanagata H Miyauchi A Nakai K andTakigawa M Design and utility of CCN2 an-chor peptide aptamers Biochemie 92(8) 1010-1015 2010

Patil A Kinoshita K and Nakamura H Do-

main distribution and intrinsic disorder inhubs in the human protein-protein interactionnetwork Protein Sci 19(8) 1461-1468 2010

Schoumlnbach C Nakai K Tan T-W and Ranga-nathan S InCoB2010-9th International Con-ference on Bioinformatics at Tokyo JapanSeptember 26-28 2010 BMC Bioinformatics11(Suppl 7) S1 2010

Okamura K Matsumoto K and Nakai KGradual transition from mosaic to globalDNA methylation patterns during deuteros-tome evolution BMC Bioinformatics 11(Suppl7) S2 2010

Teraguchi S Patil A and Standley DM In-trinsically disordered domains deviate signifi-cantly from random sequences in innate im-mune and generic mammalian proteins BMCBioinformatics 11(Suppl 7) S7 2010 (jointfirst author)

Satoh T Takeuchi O Vandenbon A YasudaK Tanaka Y Kumagai Y Miyake T Ma-tsushita K Okazaki T Saitoh T HonmaK Matsuyama T Yui K Tsujimura TStandley D M Nakanishi K Nakai K andAkira S The JMJD3-IRF4 axis regulates M2macrophage polarization and host responsesagainst helminth infection Nature Immunol11(10) 936-944 2010

Imai K and Nakai K Prediction of subcellularlocation of proteins where to proceed Pro-

125

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

teomics 10(22) 3970-3983 2010Ranganathan S Schoumlnbach C Nakai K and

Tan T-W Challenges of the next decade forthe Asia Pacific region 2010 InternationalConference in Bioinformatics (InCoB 2010)BMC Genomics 11(Suppl 4) S1 2010

Patil A Nakai K and Nakamura H HitPre-dict a database of quality assessed protein-protein interactions in nine species Nucl Ac-ids Res 39 D744-D799 2011 (published on-line on October 14 2010)

Park S-J and Nakai K A regression analysis ofgene expression in ES cells reveals two geneclasses that are significantly different in epige-

netic patterns BMC Bioinformatics 12 (Suppl1) S50 2011

Khare P Mortimer SI Cleto CL OkamuraK Suzuki Y Kusakabe T Nakai KMeedel TH and Hastings KEM Cross-validated methods for promotertranscriptionstart site mapping in SL trans-spliced genesestablished using the Ciona intestinalis tro-ponin I gene Nucleic Acids Res publishedonline on November 24 2010中井謙太ゲノム配列情報解析の課題と未来についてScience Portal China（中国科学技術月報）２０１０

126

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

The Department of Public Policy works to achieve three major missions publicpolicy studies of translational research its application and its impact on societyresearch ethics consultation for scientists to comply with ethical guidelines and tobuild public trust and development of ldquominority-centeredrdquo scientific communicationBy conducting qualitative and quantitative social science study and policy analysiswe facilitate discussion of challenges arising from advances in medical sciencesFurthermore we study specific ethics issues related to construction of a humanbiological substances collection and related to vaccination policy We also held aSciArt Exhibition titled as ldquoOffice Bacteria-the Spacerdquo at the Medical Science Mu-seum as one outreach activity undertaken via art

1 Biobank Japan Project (BBJP) and its ethi-cal legal and social implications

The Biobank Japan Project (BBJP) is a disease-focused biobanking project headed by ProfessorYusuke Nakamura since 2003 Biobank Japanconsists of donated DNA sera and clinical infor-mation from 200000 patients of 66 hospitals inJapan Informed consent which ensures theautonomous decisions of participants is be-lieved to be practically impossible for the bio-banking project in general Consequently theconcept of lsquotrustrsquo which is ldquojudgment and ac-tion in conditions of less than perfect informa-tionrdquo has been suggested to compensate for thislimitation To clarify the role and significance oftrust we conducted a questionnaire survey ofresearch coordinators (n＝157) and of partici-pants (n＝1378) in 2007 We also conducted in-terview studies of research coordinators (n＝50)in 2010

Our latest paper (1) emphasizes the impor-tance of communication with participants after

receiving their consent in the case of the bio-banking project After describing the limitationsof informed consent within the BBJP based on asurvey we conducted we introduced our at-tempts to communicate with participants dis-cussing their implications as a means to com-pensate for the limitations of informed consentin the biobanking project

As a means to maintain the participantsrsquo trustof the project research coordinators who hadbeen specially trained for the BBJP have playedimportant roles We have worked steadily tocomplete analyses of the research coordinatorsof the BBJP At the beginning of the BBJP theirprimary roles were recruitment After the end ofrecruitment their roles shifted to the tracing ofparticipants to extract clinical information andto input it into the database However theirsupport and encouragement of participants com-plemented the contents of the initial consentprocess and reinforced participantsrsquo incentive tocontinue in their role The results of this studywill contribute to improved quality control and

Human Genome Center

Department of Public Policy公共政策研究分野

Associate Professor Kaori Muto PhDAssistant Professor Yusuke Inoue PhDProject Assistant Professor Hyunsoo Hong PhDProject Assistant Professor Ayako Kamisato MA

准教授 博士（保健学） 武 藤 香 織助 教 博士（社会健康医学）井 上 悠 輔特任助教 学術博士 洪 賢 秀特任助教 法学修士 神 里 彩 子

127

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

better communication between administrators oflong-term research projects and the project par-ticipants

2 Rethinking academic freedom

How should we regulate scientific researchespecially life science research which is devel-oping rapidly To find a clue to answer thisquestion Kamisatorsquos paper (6) returns to article23 of the Constitution ldquoAcademic FreedomrdquoShe described the necessity of reinterpreting thisarticle in response to the demands of the timesbecause it traditionally has not been providedand discussed that Academic Freedom includesthe freedom of scientific research Then she dis-cussed whether freedom of scientific research isprotected by this article and considered the bestways to regulate scientific research along withnew issues that emerged from the freedom topublish the research results

3 Research ethics consultation

Public interest in research ethics has grownSociety increasingly makes demands in thisarea Provision of a system that can supportldquoon-siterdquo researchers to avail themselves of im-mediate consultation when concerns and issuesarise related to research ethics and other mattersis also among those demands Based on thesedemands in recent years the universities andresearch institutes providing ldquoresearch ethicsconsultationrdquo have become increasingly numer-ous in the United States Several papers fromthe USA explaining ldquoresearch ethics consulta-tionrdquo reveal that the contents and methods ofldquoresearch ethics consultationrdquo differ among in-stitutions and also show that pre-screening ofethical review applications is excluded from thecontents of ldquoresearch ethics consultationrdquo in theUS Our paper (7) presented analyses of allconsulted cases (n＝234) from April to Decem-ber 2009 to the Office of Research Ethics (ORE)of the IMSUT from researchers We extracted 20categories of their consultation needs andshowed that 12 were related to ldquohow to surviveethical reviewrdquo and pre-screening of documentsfor ethical review What is ldquoresearch ethics con-sultationrdquo and what creates these differencesWe studied the answers to these questions andfound that the extent of academic and social un-derstanding of research ethicsrsquo importance iscritical information for considering these ques-tions

4 Science and Art

We have been organizing a series of artwork

exhibitions related to scientific knowledge espe-cially that related to biomedical science at theMuseum of Modern Medical Sciences twice ayear since 2009 The ldquoIMSUT Science Art Exhibi-tionsrdquo are intended to provide audiences the op-portunity to encounter the field of science fromthe perspectives of artists and to present thepossibility of subjective reflection on what isconsidered to be the most objective form ofknowledge through the artworks themselvesand through talks given by the artists duringthe exhibition

This year we have organized two exhibitionsldquoBoundary Face lsaquo-rsaquo界面空間rdquo (24 February 2010-18 March 2011) and ldquo宇宙(Universe)rdquo(6 January2011-30 January 2011) The former exhibition ofinstalled works by Hideo Iwasaki and EmikoInoue developed in the laboratory of Iwasakiwho is also a molecular biologist received ap-proximately 500 visitors The latter exhibition ofOFFICE BACTERIA is still on view includingoil paintings by Teppei Ikehira and accessoriesdesigned by Kanae Briandet inspired by micro-scopic pictures taken by Roman Briandet who isa molecular biologist Additionally we intro-duced our activities as an effective form of sci-ence communication by reflecting on the firstexhibition we organized in 2008 at the AnnualMeeting of the Society for Social Studies of Sci-ence (August 25-29 2010)

As the principle for promotion of dialogueswith the public on science and technology asrecently published by the minister in charge ofthe governance of science and technology ex-plaining the implications of scientific studies tothe public is now regarded as an important re-sponsibility of scientists Various means of com-municating science have been introduced asways to fulfill this responsibility With our ac-tivities of exhibiting science art we are propos-ing another mode of communicating science thatcovers the limitations of the orthodox mode ofscience communication based on the dialoguebetween experts and non-experts

5 Living liver organ donation in Japan

The global criticism of organ trafficking andtransplant tourism requires many countries topursue legal protection of living organ donorsfor organ transplantation Japan is one suchcriticized country more than 26000 people havebecome living organ donors Mutorsquos paper (4)presents an exploration of living liver transplan-tation in Japan from legal social and ethical per-spectives Since the first living liver transplanta-tion in 1989 the cases have increased with ex-tremely high dependency in spite of a fewdeaths and cases of severe disability Govern-

128

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

ment and professional guidelines stipulate thatliving donors be ldquorelativesrdquo so that living organtransplantation can be privatized and regardedas a family issue although it is strictly limitedto altruistic cases in some countries Based onresults of the Living Liver Donor Survey con-ducted in 2004 Japanese liver donors have hadvaried experiences Most male donors were em-ployed felt some obligation and harbored con-cerns about financial effects and employmentduring decision-making In contrast only aquarter of female donors were employed feltguilty about the health conditions of their chil-dren and did not have opportunities for regularhealth checkups after donation Severe tensionsand family dissolution occurred in adult-to-adult cases although donors were satisfied withdonation overall The author suggests that weshould rethink privatization of living organ do-nation and that independent advocates shouldsupport potential donors Further research isnecessary to explore the reasons why organ do-nation is privatized even in some forms of ca-daver cases in Japan

6 Ethical issues in human tissue and databanking

Banking human tissue samples and data forfuture use (biobanking) is a fundamental com-ponent of the infrastructure supporting biomedi-cal research activities For research activities col-lecting these resources has been important formedical research activities but research ethics inbiobanking has some unique characteristics thatdiffer from traditional notions of human sub-jectsrsquo protection in clinical research First wehave studied consent and monitoring processesrelated to biobanking activities to explore theideal relation between society and biobankingAs some results we presented some identifiedethical issues related to the large scale clinicaldatabase in summer (Japanese College of Cardi-ology September 2010) Second we investigatedethical issues in cadaveric research Primarilytwo theories have prevailed one regards a body(or a part of it) as a kind of object which can bea property and the other maintains that a deadbody should be respected as a remnant of an in-dividualrsquos personality or identity Additionallysome explanations suggest that a dead body it-self deserves respect The role of the bereavedfamily and moral status of the dead body variesdepending on these different standpoints Wehave just started questionnaire surveys of hu-man tissue collections in forensic medicine labo-ratories in Japan to elucidate the status of a hu-man body and to evaluate socially expected re-quirements for research usage

7 Vaccination Policy

Striking a balance between the rapid availabil-ity of a novel vaccine while ensuring its safetyquality and efficacy is a major challenge duringa pandemic We elucidated physiciansrsquo attitudesrelated to novel vaccines during the influenza AH1N1 pandemic of 2009 and to determine fac-tors that affected their vaccination recommenda-tions to patients (2) Of a random sample of1000 general practitioners (GPs) in Japan 515participated in a cross-sectional anonymous sur-vey conducted immediately before the novelvaccine became available (between 28 Septemberand 18 October 2009) In all 453 GPs (883) re-plied that they intended to receive the new vac-cine themselves However only 177 GPs (346)intended to recommend it proactively to theirpatients The anticipated cost of the vaccinenegatively influenced the intention to vaccinatethemselves and their recommendations to pa-tients (P＜0001 χ2test) Results of multivariatelogistic regression analysis showed that physi-cians with experience in influenza AH1N1 pa-tient contacts [1-20 contacts odds ratio (OR)＝749 (95 confidence interval [CI] 173-3236) P＝0007 ＞20 contacts OR＝803 (95 CI 177-3650) P＝0007 compared with no contacts]were more likely to recommend the vaccine topatients although those with knowledge of thefear of a causal association between Guillain-Barre syndrome (GBS) cases and the 1976 swineflu vaccination in the USA were less likely torecommend the vaccine [OR＝066 (95 CI045-097) P＝0036] Results of our survey indi-cate that physicians experience a moral conflictrelated to the recommendation of the novel vac-cine to patients which might result from theirown experience with the disease knowledge ofvaccine side-effects and cost

8 Research in progress

We have been conducting other studies as de-scribed below- Ethical legal and social implications of com-

mercial geneticgenomic testing services ineastern Asia

- Development and evaluation of communica-tion methods with participants of Biobank Ja-pan and other long-term studies

- Analysis of roles of research coordinators forbetter recruitment and for building trust fromparticipants

- Ethical legal and social implications of stemcell studies including animal-human chimericembryos and iPS cell banking

- Bench-side research ethics consultation andquality assurance of research ethics committees

129

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130

- Science communication through art and ethicalchallenges of biomaterial art

- Ethics issues in collecting human biological

substances for constructing a research infra-structure

- Vaccination policy

Publications

1 Watanabe M Inoue Y Chang C Hong HKobayashi I Suzuki S Muto K For what amI participating-The need for communicationafter receiving consent form biobanking pro-ject participants experience in Japan J Hu-man Genetics in press 2011

2 Inoue Y Matsui K Physiciansrsquo recommenda-tions to their patients concerning a novelvaccine a cross-sectional survey on 2009 AH1N1 vaccination in Japan EnvironmentalHealth and Preventive Medicine in press2011

3 Inoue Y Wada Y Motohashi Y Koizumi AHistory of blood transfusion before 1990 in-creases cancer mortality risk independent ofliver diseases prospective long-term follow-up Environmental Health and PreventiveMedicine 15 180-187 2010

4 Muto K Organ transplantation as a familyissue living liver donors in Japan Interna-tional Journal of Japanese Sociology 19(1)

35-48 20105 Semba Y Chang C Hong H Kamisato A

Kokado M Muto K Surrogacy donor con-ception regulation in Japan Bioethics 24(7)348-57 2010

6 神里彩子科学研究規制をめぐる「学問の自由」の現代的意義と課題社会技術研究論文集７２１１―２２１２０１０

7 神里彩子武藤香織「研究倫理コンサルテーション」の現状と今後の課題―東京大学医科学研究所研究倫理支援室の経験より生命倫理２１１８３―１９３２０１０

8 井上悠輔赤林朗発生学の展開と幹細胞研究の諸問題Biophilia６６６―７０２０１０

9 井上悠輔人体要素を研究資源として利用する際の研究倫理上の諸問題医療生命と倫理社会９１―２２２０１１

10 玉腰暁子武藤香織『医療現場における調査研究倫理ハンドブック』東京医学書院２０１１

130