french academic strengths in epigenetics …...- innovative therapies (epigenetics; hadrontherapy)...

Innovative Projects for International Business Opportunities

and R&D Collaborations

Projects Book 2nd EditionFebruary 2016

Strategic Tech Transfer Field: Therapeutic Innovation in Oncology

Yoann Schumacher, Ph.D., Project Manager [email protected]

Melina Gaffré, Ph.D., Coordinator, Inserm Transfert [email protected]

FREnCh aCaDEMIC STREnGThS In

EPIGEnETICS anD CanCER

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InTRODuCTIOn

The Thematic Tech Transfer Consortium (aka Consortium de Valorisation Thématique or CVT in French) from the national alliance in life sciences, aviesan, aims to coordinate the policies, strengths and expertises of its stakeholders* in the fields of life science

and health. This is developed through several Strategic Tech Transfer Fields (aka Domaine de Valorisation Stratégique or DVS in French) whose goal is to provide national analyses and actions for their scientific and industrial communities, and to promote partnering opportunities.

The DVS “Therapeutic Innovation in Oncology”, in particular, is supported by Inserm Transfert and Institut Curie and is dedicated to facilitate the transfer of academic innovations in onco-logy to the Industry. For this purpose, the DVS has focused its actions on two axis: the identi-fication of novel and innovative epigenetic targets and the development of focalized therapies for treating cancer.

Concerning the epigenetic targets, the mains objectives of the DVS are:

1. Stimulate and facilitate the setting up of partnerships between industrials and academics by: > Mapping and gathering the French academic expertises in epigenetics > Mapping both academic and industrial French Intellectual Property in epigenetic target validation > analyzing industrial needs > Identifying potential collaborative R&D projects > Contributing to build, develop and maintain a trusted relation between academics and industry > Boosting the development of novel therapeutic approaches

2. Identify main technology transfer hurdles in this axis

3. Contribute to maintain the visibility of France in this innovative theme.

Directly in line with these objectives, the DVS “Therapeutic Innovation in Oncology” has gathered in this book innovative projects to highlight French academic strengths in epigenetics and to: > Enhance the visibility of French research in epigenetics > Trigger collaborations between researchers > Facilitate Industry-academia Partnerships

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SOMMaIRE

•> 4 Geneviève ALMOUZNI & Zachary GURARD-LEVIN Chromatin Dynamics

•> 7 Paola B. ARIMONDO Epigenetic Targeting of Cancer

•> 10 Catherine BAUGÉ Chondrosarcomas: Physiopathology and Innovative Therapies

•> 13 Olivier BERNARD normal and malignant hematopoises

•> 15 Philippe BERTRAND hDaC inhibitors and their delivery

•> 17 Pierre-François CARTRON Design of a new generation of epidrugs targeting certains selective interactions between an epigenetic protein and one of its partner

•> 20 Jean CAVARELLI Structural Biology of Epigenetic Targets

•> 21 Hervé CHNEIWEISS Plasticity and Development of human Brain Tumor

•> 24 Françoise DANTZER & Valérie SCHREIBER Poly(aDP-ribosyl)ation and genome integrity

•> 27 Estelle DUPREZ Epigenetic control of normal and pathological hematopoiesis

•> 30 Reini FERNANDEZ DE LUCO Epigenetic and alternative Splicing

•> 33 Pierre FERRIER Deciphering functional activity of TLX homeodomain oncogenes in T-cell acute Leukemia (T-aLL): Epigenetic analysis

•> 34 Hinrich GRONEMEYER Systems biology of cell fate decisions in normal and tumor cells

•> 39 Christophe François GROSSET Regulation of Genes by microRnas in Cancer and Development

•> 42 Dominique GUENOT Impact of hypoxia and microenvironment in tumor progression and response to treatment. Translational approaches and epidemiology

•> 45 Christel GUILLOUF Pu.1 transcription factor in epigenetic and splicing regulation

•> 48 Zdenko HERCEG Epigenome deregulation and cancer : mechanisms and biomarkers

•> 51 Eric JULIEN Functions of lysine methylation pathways

•> 54 Saadi KHOCHBIN Epigenetic and Cell Signaling

•> 57 José Arturo LONDO ñO-VALLEJO Chromosome instability, epigenetics and microRnas

•> 60 Jérôme MOREAUX Epigenetic and genomic instability mining in Multiple Myeloma to define precision medicine

•> 63 Antonin MORILLON lncRna and cancer

•> 66 Jean MOSSER Integrated Functional Genomic and Biomarkers

•> 69 Christian MUCHARDT Transcription and Splicing in the Context of Chromatin

•> 72 Peter MULLIGAN Epigenetics and Cancer

•> 75 Françoise OCHSENBEIN Molecular assemblies and genome integrity

•> 78 Benjamin ORY Genetic and Epigenetic aspects of primary bone tumors development and bone mineralization

•>82 Yves RENAUDINEAU B cell diseases and epigenetics

•>85 Claire ROUGEULLE non-coding Rnas in development and disease

•>88 Jörg TOST Laboratory for Epigenetics & Environment

•> 91 Michèle TRABUCCHI Control of Gene Expression

•> 94 Isabelle VAN SEUNINGEN Epigenetics and epithelial stemness, differentiation and carcinogenesis

•> 97 André VERDEL Rna and Epigenetics

•> 99 Thierry VIROLLE Molecular basis of glioma cancer stem cells properties and functional intra tumor heterogeneity

•> 102 Bohdan WASYLYK Molecular and Cellular Biology of hnSCC and Prostate Cancer

•> 105 Michael WEBER Laboratory « Epigenetic Regulation of Cell Identity » headed by Michael Weber

•> 108 Jonathan WEITZMAN Epigenetics and Cell Fate

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Chromatin Dynamics

Grants • Various research / clinical grants, including 2 european research grants,• Industrial collaboration,• ERC grant.

Major publications over the past four years• Montes de Oca R. et al. (2014) hJuRP, a CEnP-a chaperone as a new prognostic factor in luminal a breast carcinoma. Mol. Oncol., in press.Müller S. et al. (2014). Phosphorylation and Dna-binding of hJuRP deter-mine its centromeric recruitment and function in Cenh3CEnP-a loading. Cell Rep., 8, 190-203.Lacoste n. et al. (2014). Mislocalization of the centromeric histone variant Cenh3/CEnP-a in human cells depends on the chaperone DaXX. Mol. Cell, 53, 631-644.

adam S. et al. (2013). Transcription recovery after Dna damage requires chromatin priming by the h3.3 histone chaperone hIRa. Cell, 155, 94-106.Casanova M. et al. (2013). heterochromatin reorganization during early mouse development requires a single-strand non-coding transcript. Cell Rep., 4, 1156-1167.

Patents • 4 patients available for licencing.

Geneviève ALMOUZNI & Zachary GURARD-LEVIN

> Research Center; Town: Institut Curie, Paris

> Administrative affiliations: Institut Curie - CnRS uMR 3664

> Tech Transfer Office: Institut Curie www.curie.fr

Keywords:

• Chromatin dynamics

• Chaperones

• Genome stability

• Centromeres

• Epigenetics

Ph.D.Contact: [email protected]

Synopsis:Our team is interested in understanding how chromatin organization is established, propagated, maintained, and changed during development and in response to environmental cues. Errors in these processes can lead to mis-regulation of genome functions and pathological outcomes, such as cancer.

Abstract:We study how chromatin organization is established, propagated, maintained, and changed during development and in response to environmental cues. Errors in these processes can lead to mis-regulation of genome function and pathological outcomes, such as cancer. We have dissected the mechanisms of chromatin assembly, from the basic structural unit, the nucleosome, to higher-order nuclear structures. We revealed the importance of key chaperones involved in nucleosome assembly including histone management and their specific marks typical of particular chromatin domains. We integrate these findings with dynamic changes during cell cycle/repair and differentiation and their consequences for nuclear organization and pathologies.

SELECTED REFERENCES

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Business Development opportunities

Objectives:• We study how chromatin organization is established, propagated, maintained, and changed during development and in response to environmental cues. Errors in these processes can lead to mis-regulation of genome function and pathological outcomes, such as cancer.

Tools:• SnaP-tagging and imaging • ChIP and ChIP-seq• Rna interference in cultured cells• Protein complexes purification from cells stably expressing tagged-factors• Micro-injection / manipulation of Xenopus and mouse early embryos (2 cell stage) and

follow-up of development• advance 3D and time-lapse fluorescence microscopy• Transgenic / KO mouse models• Bio-computing analysis of high-throuput sequencing / expression data• analysis of the dynamics of factors in vivo by SnaP-Tag and imaging including FRaP,

local damage• annotated samples, tumor library• Cohort of patients with their follow-up Unique selling points:• Our team has over 20 years of expertise in chromatin, nuclear organization, replication

repair and development. • We have dissected the mechanisms of chromatin assembly, from the basic structural

unit, the nucleosome, to higher-order nuclear structures. We revealed the importance of key chaperones involved in nucleosome assembly including histone management and their specific marks typical of particular chromatin domains. We integrate these findings with dynamic changes during cell cycle/repair and differentiation and their consequences for nuclear organization and pathologies.

Chromatin Dynamics

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project / expertise

Results• Design of specific inhibitor of a histone cha-perone and its applications in breast cancer therapy

Perspectives• Extend the approach for other applications to new challenging new target in the epigenetic area

CHAPTAR

Chromatin Dynamics

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Epigenetic Targeting of Cancer

Paola B. ARIMONDO

Grants • PlanCancer 2014-2017, EpiChemSeq• Fondation InnaBioSanté 2013-2015, Epigenetic aggressivity of Mela-

noma• aTiP CnRS (2010-2012) and Equipe d’Excellence Midi Pyrenées 2011-

2013, Targeing Dna methylation

Major publications over the past four years• Ceccaldi a, et al.aCS Chem Biol. 2013 8(3):543-8 • Moison C, e et al.. FaSEB J. 2013 27(4):1468-78 • Erdmann a, et al. J Med Chem. 2015 58(6):2569-83 • Gros C, et al. J Biol Chem 2015 290(10):6293-302. • Vispé S, et al. OncoTarget 2015 6(17):15265-82.

Patents • Ceccaldi a., Sénamaud-Beaufort C., Jurkowska R., Gagey n., Dauzonne

D., Jeltsch a., Guianvarc’h D., arimondo P.B. n° Dépôt °09305840.2, Sep-tember 14, 2009.

• halby, L.; Guianvarc’h, D.; Sénamaud-Beaufort, C.; Ferroud, C.; Grellier, P.; arimondo, P.B., n° Dépôt: 10306004, 20/09/2010.

• halby, L.; arimondo, P.B., n° Dépôt: EP13306073. 24/07/2013. WO2015040169

Keywords:

• Dna methylation

• histone methylation

• Medicinal chemistry

• Pharmacology

• Chemical Biology

Synopsis:We carry out pluridisciplinary approaches spanning from chemistry to biology in the field of epigenetics to identify new therapeutical agents and targets to fight cancer.

Abstract:Epigenetics defines when and where genes are expressed. Epigenetic marks are reversible and inheritable, integrate the impact of the environment and provide cellular plasticity. aberrant epigenetic patterns are involved in tumor formation and maintenance. notably, epigenetic modifications can be modified by chemical agents. Recently, several epigenetic chemical agents entered clinical trials to treat hematological tumors.Our research projects combine exploratory aspects (as the research of new biological mechanisms and targets) and applied ones (drug candidates discovery) in the field of Cancer Epigenetics. More specifically, our projects are focused on innovation in terms of 1) Chemistry with the synthesis of novel oriented chemical libraries to target Dna and histone

methyltransferases in cell; 2) Chemical Biology to identify the target of the bioactive molecules in cancer cells upon use of chemical

probes and 3) pharmacological strategy to reprogram epigenetically the cancer cells to a less aggressive state and more

sensitive to chemotherapy and immunotherapy.

SELECTED REFERENCES


> Research Center; Town: Centre de recherche et de développement Pierre Fabre (CRDPF), Toulouse

> Administrative affiliations: CnRS - Pierre Fabre uSR 3388

> Tech Transfer Office: Toulouse Tech Transfert www.toulouse-tech-transfer.com

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Paola B. ARIMONDO



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project / expertise

Study of the epigenetics of Leukemia Initiating Cells (LIC) in the context of the microenvironment and their interplay in AML and CLL chemoresistance.

Aims:• The short-term application of the project is the development of HCS technology for epigenetic impact characterisa-tion resulting in a standardized methodology/kit/service for patients stratification in AML and CLL for epidrug treatment

• Long-term applications are to find new treatments to fight leukaemia, in particular to eradicate LICs causing relapse and improvement of the safety of the treatments.

Partners:

Paola B. ARIMONDO


Epigenetic Reprogramming of Leukemia

Dr François ICHAS, Fluofarma, Pessac

Dr. Anne QUILLET-MARY, Dr. Jean-Emmanuel SARRYCRCT, Toulouse

Prof. Louis CASTEILLASTROMALab, Toulouse

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Chondrosarcomas: Physiopathology and Innovative Therapies

Keywords:• hypoxia• Genetics/epigenetics• in vitro and in vivo models

Ph.D. Contact: [email protected]

Laboratory research areaCartilage and associated diseasesChondrosarcomas: - mechanism of resistance to treatments (chemotherapy and radiotherapy)- innovative therapies (epigenetics; hadrontherapy)

AbstractChondrosarcomas (ChS) are malignant tumors of bone that produce hyaline cartilage matrix. Primary ChS is the second most frequently primary malignant tumor of bone after osteosarcoma, and represents about 25% of bone sarcomas. ChS is considered as highly resistant to both chemotherapy and radiations, making surgical resection the only curative treatment. however, mechanisms of resistance are not well understood. Our first project aims to investigate resistance mechanism to radiotherapy and chemotherapy. We compared the response of five different chondrosarcoma cell lines to X-ray radiation and cisplatin. We showed that chondrosarcoma lines respond differently to treatments. In addition, our study is the first one which extensively characterizes commonly used human ChS cell lines by exome sequencing. These genetic data provide essential information on resistance mechanisms. Environmental factors such as hypoxia are also studied.Our second project aims to identify new strategies to treat chondrosarcomas. In particular, we focus on epigenetic therapy. We showed that high grade chondrosarcomas highly express the histone methylase EZh2, when compared to enchondromas or chondrocytes. In addition, we showed that DZnep inhibits EZh2 protein expression and reduces h3K27me3 in some ChS, leading to cell death by apoptosis in vitro and in vivo. These results indicate that DZnep may be an interesting molecule to treat chondrosarcomas. however, its mechanism action is still under investigation.

Grants • Fhu “SuRFaCE” (2015-2020)• PhRC “Exorhum” (2014 – 2020)• Emerging Programme “CaEn” (Region Basse-normandie : 2014-2016)• FP6 “Genostem”

Major publications over the past four years• Manna et al. histone h3 Lysine 27 demethylases Jmjd3 and utx are requi-red for T cell differentiation. nature Commun 2015 (accepted)• Baugé, Boumediene. use of adult stem cells for cartilage tissue enginee-ring: current status and future developments. Stem cells Int 2015 (in press)

• Baugé et al. histone methylases as novel drug targets: developing inhibi-tors of EZh2. Future Med Chem 2014; 6(17), 1927-1948 • Girard et al.. 3-deazaneplanocin a (DZnep), an inhibitor of the histone methyltransferase EZh2, induces apoptosis and reduces cell migration in chondrosarcoma cells. Plos One 2014 May;9(5): e98176. • Duval et al. Molecular mechanism of hypoxia induced chondrogenesis and its application in in vivo cartilage tissue engineering. Biomaterials 2012 Sep;33(26):6042-51.

SELECTED REFERENCES

Catherine BAUGÉ

> Research Center; Town: Caen

> Administrative affiliations: université de Caen Ea4652

> Tech Transfer Office: université de Caen www. recherche.unicaen.fr

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Catherine BAUGÉ


Objectives:• Identification of new therapeutic targets for cartilage associated-diseases (chondrosarcomas and osteoarthritis)• understanding the role of h3K27 methylation in cartilage during development, ageing and diseases.

Tools:• Cellular and molecular biology• Biochemistry• animal models• Transcriptomics, nGS, bioinformatics

Unique selling points:• Team nationally and internationally recognized for its expertise in cartilage biology and tissue engineering (Eu, anR, Fhu…)• Multidisciplinary team (cell biology, physiology, genetics, bioinformatics scientists; pathologists, anatomists, rheumatologists, orthopaedic surgeons…)• Original models for study

- chondrogenesis without interference with serum or growth factor - Oa chondrocytes (primary culture) - chondrosarcomas (cell lines and primary cells) with complete molecular characterizations (full exome sequencing)

• access to conditional KO mice for histone demethylases

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project / expertise

H3K27me3 in cartilage tumoral cells (chondrosarcomas)

Results• The histone methylase EZH2 is highly expressed in high grade chondrosarcomas. Its inhibition by DZNep induced chondrosarcoma death in vitro and in vivo.

Perspectives• Validate results with more chondrosarcomas• Confirm data with additional animal models• Identify molecular mechanism involved• Role of histone demethylases ?

Results• DZNep reduces inflammation in OA cartilage

Perspectives• Identify all target pathways of DZNep in chondrocytes• Validate data in OA animal models• Improve cartilage tissue engineering, and/or pharmaceutical treatment of OA

• Study role of the histone methylase EZH2, and demetylase JMJD3 and UTX in chon-drogenesis, aging and OA process.

H3K27me3 in osteoarthritis (OA) cartilage

Catherine BAUGÉ

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Normal and malignant hematopoises

Major publications over the past four years• TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis. Quivoron et al. Cancer Cell. 2011 Jul 12;20(1):25-38. • Mutation in TET2 in myeloid cancers. Delhommeau et al. n Engl J Med. 2009 May 28;360(22):2289-301• Targeted inhibition of mutant IDh2 in leukemia cells induces cellular diffe-rentiation. Wanget al. Science. 2013 May 3;340(6132):622-6

• Serum 2-hydroxyglutarate production in IDh1- and IDh2-mutated de novo acute myeloid leukemia: a study by the acute Leukemia French asso-ciation group. Janin et al. J Clin Oncol 2014;32:297-305.• Characterization of novel genomic alterations and therapeutic approaches using acute megakaryoblastic leukemia xenograft models. Thiollier et al. J Exp Med. J Exp Med 2012;209:2017-31.

Olivier BERNARD

Keywords:

• Stem cell biology

• Megakaryocytic differentiation

• Erythroid differentiation

• acute leukemia

• Lymphoproliferative disorders

• Lymphoma

• Genetics and epigenetics

• Transcription control

• Modeling

• Mutant IDh proteins

• TET proteins

• Clinical trials


SynopsisThe unit is conducting an integrated approach of malignant and benign hematology, including clinical trials, thorough analyses of primary samples and modelling in human and mouse contexts, using cutting edge technologies.

Abstract:We are investigating the mutations landscape in human malignancies, including non-malignant megakaryocytosis, acute myeloblastic leukemia, chronic myelomonocytic leukemia, myeloproliferative neoplams, lymphoproliferative disorders and lymphomas. This includes both acquired and germinal variant and lead to the identification of «druggable» targets that are tested in early phase clinical trials. The genomic results lead to modeling in mouse and human cells for functional analyses and pre-clinical trials

SELECTED REFERENCES

> Research Center; Town: Institut Gustave Roussy, Villejuif

> Administrative affiliations: Institut Gustave Roussy, Inserm, université Paris Saclay

> Tech Transfer Office: Gustave Roussy Transfert www.gustaveroussy.fr/en/content/technology-transfer-overview

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Olivier BERNARD


Objectives:• We are investigating the mutations landscape in human malignancies, including non-malignant megakaryocytosis, acute myeloblastic leukemia, chronic myelomonocytic leukemia, myeloproliferative neoplams, lymphoproliferative disorders and lymphomas. This includes both acquired and germinal variant and lead to the identification of «druggable» targets that are tested in early phase clinical trials. The genomic results lead to modeling in mouse and human cells for functional analyses and pre-clinical trials

Tools:• Exceptional continuum between clinics and research• Clinical structure dedicated to clinical trials• 17 ongoing clinical trials (single agents and combinations)• all aspect of cellular and molecular murine and human hematology• next generation sequencing (exome, Rna-seq,ChIP-Seq)• FaCS analyses• Cell sorting• Xenografts

Normal and malignant hematopoises

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HDAC inhibitors and their delivery

Grants • anR 2009-2011, Ligue, Region Poitou-Charentes

Major publications over the past four years• Biomacromolecules 2013, 14, 2396−2402• Biomacromolecules 2014, 15, 4534−4543• Oncotarget, 2014, 5, 4504• Eur. J. Pharm. Biopharm. 85 (2013) 862–872• Eur. J. Med. Chem. 95 (2015) 369

Patents • uS2014/0219925 a1

Philippe BERTRAND

Keywords:

• Chemical biology of epigenetics

• Epigenetic target inhibitor synthesis

• Drug delivery, prodrugs

Ph.D, associate professorContact: [email protected]

Attractive synopsisOur original research focus on synthesis of epigenetic targets inhibitors by means of superacid chemistry and green processes, coupled to simplified strategies for ph-mediated delivery

AbstractThe work is applied in oncology (mesothelioma and myeloma). The expertise of the team is organic synthesis in general, asymmetric and total synthesis in particular, using all available methods in the field (micro waves, superacid, chiral resolution, greener catalytic transformation of building blocks….). The research strategy is currently focusing on acetylation dynamics in cellular environments as the major mechanism of action of our compounds, major data include successful application of selective delivery of histone deacetylase inhibitors in mesothelioma in vivo. Developing this current knowledge to develop more specific histone deacetylases inhibitors and novel ways for delivery connected to diagnostics

SELECTED REFERENCES

> Research Center; Town: Institut de Chimie de Milieux et Matériaux de Poitiers (IC2MP), Poitiers

> Administrative affiliations: IC2MP team 5 organic synthesis, université de Poitiers, CnRS

> Tech Transfer Office: SaTT Grand Centre www.sattgc.com

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Philippe BERTRAND


Objectives:• Synthesis of epigenetic targets inhibitors • Chemistry for delivery

Tools:• all tools needed for organic synthetic chemistry including chiral molecules

HDAC inhibitors and their delivery

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Design of a new generation of epidrugs targeting certains selective interactions between an epigenetic protein and one of its partner

Grants • “Canceropole Grand Ouest”• “Ligue contre le Cancer”

Major publications over the past four years• Cheray M, Pacaud R, nadaradjane a, Oliver L, Vallette FM and Cartron PF. Specific inhibition of DnMT3a/ISGF3g interaction increases temozolomide efficency by reducing tumor growth. Theranostics. In press.• Pacaud R, Cheray M, nadaradjane a, Vallette FM, Cartron PF. histone h3 phosphorylation in GBM: a new rational to guide the use of kinase inhibitors in anti-GBM therapy. Theranostics. 2015 Jan 1;5(1):12-22. • Cheray M, nadaradjane a, Bonnet P, Routier S, Vallette FM, Cartron PF. Specific inhibition of DnMT1/CFP1 reduces cancer phenotypes and en-hances chemotherapy effectiveness. Epigenomics. 2014 Jun;6(3):267-75. • Pacaud R, Sery Q, Oliver L, Vallette FM, Tost J, Cartron PF. DnMT3L in-teracts with transcription factors to target DnMT3L/DnMT3B to specific

Dna sequences: role of the DnMT3L/DnMT3B/p65-nFkB complex in the (de-)methylation of TRaF1. Biochimie. 2014 Sep;104:36-49. • Pacaud R, Brocard E, Lalier L, hervouet E, Vallette FM, Cartron PF. The DnMT1/PCna/uhRF1 disruption induces tumorigenesis characterized by similar genetic and epigenetic signatures. Sci Rep. 2014 Mar 18;4:4230. • Cartron PF, nadaradjane a, Lepape F, Lalier L, Gardie B, Vallette FM. Iden-tification of TET1 Partners That Control Its Dna-Demethylating Function. Genes Cancer. 2013 May;4(5-6):235-41. • Cheray M, Pacaud R, nadaradjane a, Vallette FM, Cartron PF. Specific inhibition of one DnMT1-including complex influences tumor initiation and progression. Clin Epigenetics. 2013 Jun 28;5(1):9. doi: 10.1186/1868-7083-5-9.

Patents • new method for treating and prognosing cancer (EP15305314.5).

Pierre-François CARTRON

Keywords:

• Dna methylation / demethylation

• histone post-translational modifications :

phosphorylation

• apoptosis

• Glioma, lung and brest cancers


Laboratory research areaEstablishment of an epigenetic therapy targeting the writers of epigenetics signatures associated with a phenotype of apopto-resistance to standard anticancer therapies in order to restore efficiency of this anticancer treatment.

SynopsisDesign of a new generation of epidrugs targeting certains selective interactions between an epigenetic protein and one of its partner.

SELECTED REFERENCES

> Research Center; Town: Centre de recherche en cancérologie nantes-angers (CRCna) nantes

> Administrative affiliations: Inserm uMRS 892 - CnRS 6299

> Tech Transfer Office: Inserm Transfert www.inserm-transfert.fr

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Objectives:• Identification, in cohort of cancer-patients of epigenetic actor-including complexes (EpaICs) whose presence is associated with poor prognosis. • Identification of peptides, compounds and/or design of small molecules able to specifically disrupt EpaICs of interest (named Selective Epigenetic Drug, SED).• Validation of SEDs in cellular and in vivo models and identification of the role played by the EpaICs of interest during development.

Tools:• Biobank of tumors (Glioma, prostate, breast,…)• Expertise on several epigenetic actors: DnMTs, hDaCs, histone kinases, Brd proteins.• Expertise on the identification, characterization, monitoring of protein-protein interactions via mastery of a large panel of methods (immunoprecipitation, pull down, competitive pull down, Biacore, P-LISa, BRET, epitope mapping, nuclear micro-injection).• Expertise on devleopment of peptide inhibiting protein-protein interaction. Unique selling points:• Bank of peptide inhibiting specific protein-protein interactions such as DnMT1/PCna, DnMT/uhRF1, DnMT1/CFP1…• Expertise on protein-protein interaction: epitope mapping method.• Expertise on cellular microinjection.


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project / expertise

Results• The 1081-1097DNMT1 pep-tide, a peptide down-regulating the formation of the DNMT1/CFP1 interaction, enhances the antitumor effect of a TMZ treat-ment.

Perspectives• Development of peptide or molecule disrupting selective DNMT1/CFP1 interaction

Results• By focusing on interactions existing between DNMT3A and DNMT3A-binding protein (D3A-BP), our work identifies the DNMT3A/ISGF3γ interaction such as a biomarker whose the pres-ence level is associated with a poor survival pro-gnosis and with a poor prognosis of response to the conventional chemotherapeutic treatment of glioblastoma multiforme (radiation plus temo-zolomide). Our data also demonstrates that the disruption of DNMT3A/ISGF3γ interactions increases the efficiency of chemotherapeutic treatment on established tumors in mice.

Perspectives• Development of peptide or molecule disrupting selective DNMT3A/ISGF3γ interaction


After the induction of tumor (volume = 100mm3) by the subcutaneous injection of U251 cells, mice were treated 5 days per week during6 weeks with the indicated treatment.The asterisk (*) indicates the presence of significant modulations in the tumor weight between the considered conditions according to the realization of the t-test (p < 0.05). Graphs illustrate the average ± standard deviation of tumor weight obtained by considering the treatment of five mice per condition.

Source: Cheray M, Nadaradjane A, Bonnet P, Routier S, Vallette FM, Cartron PF. Specific inhibition of DNMT1/CFP1 reduces cancer phenotypes and enhances chemotherapy effectiveness.Epigenomics. 2014 Jun;6(3):267-75. PMID: 25111481.


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Structural biology of epigenetic targets

Major publications over the past four years• Functional insights from high resolution structures of mouse protein argi-nine methyltransferase 6.Bonnefond L, Stojko J, Mailliot J, Troffer-Charlier n, Cura V, Wurtz JM, Cian-férani S, Cavarelli J.J Struct Biol aug 2015 ; 191:175-83.

• Structure of the Elongator cofactor complex Kti11/Kti13 provides insight into the role of Kti13 in Elongator-dependent tRna modification.Kolaj-Robin O, McEwen aG, Cavarelli J, Séraphin B.FEBS J Mar 2015 ; 282:819-33.

• Structural insight into arginine methylation by the mouse protein arginine methyltransferase 7: a zinc finger freezes the mimic of the dimeric state into a single active site.Cura V, Troffer-Charlier n, Wurtz JM, Bonnefond L, Cavarelli J.acta Crystallogr D Biol Crystallogr 1 septembre 2014 ; 70:2401-12.

• Molecular Basis for the antiparasitic activity of a Mercaptoacetamide Derivative That Inhibits histone Deacetylase 8 (hDaC8) from the human Pathogen Schistosoma mansoni.Stolfa Da, Marek M, Lancelot J, hauser aT, Walter a, Leproult E, Melesina J, Rumpf T, Wurtz JM, Cavarelli J, Sippl W, Pierce RJ, Romier C, Jung M.J Mol Biol 9 octobre 2014 ; 426:3442-53.

• Cloning, expression, purification and preliminary X-ray crystallographic analysis of mouse protein arginine methyltransferase 7.Cura V, Troffer-Charlier n, Lambert Ma, Bonnefond L, Cavarelli J.acta Crystallogr F Struct Biol Commun Jan 2014.

• Structural Basis for the Inhibition of histone Deacetylase 8 (hDaC8), a Key Epigenetic Player in the Blood Fluke Schistosoma mansoni.Marek M, Kannan S, hauser aT, Moraes Mourão M, Caby S, Cura V, Stolfa Da, Schmidtkunz K, Lancelot J, andrade L, Renaud JP, Oliveira G, Sippl W, Jung M, Cavarelli J, Pierce RJ, Romier C.PLoS Pathog Sep 2013 ; 9:e1003645.

Jean CAVARELLI

Keywords:

• arginine methylation

• Structure-based drug design

• Crystallography

Ph.D, Pr.Contact: [email protected]

SELECTED REFERENCES

> Research Center; Town: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Strasbourg

> Administrative affiliations: CnRS uMR 7104 - Inserm u 964 - université de Strasbourg

> Tech Transfer Office: Conectus www.conectus.fr

SynopsisOur team has a solid background in structural biology and develops within the ChemStrappPRMTs consortium chemical tools to understand Protein aginine Methyl Transferase substrate recognition specificity, selectivity and molecular mechanism providing lead compounds for epigenetic inhibitor discovery.

AbstractOur team research is focusing on the understanding of the structure/function relationships of epigenetic targets at the atomic level. The goals are to decipher at the molecular level the mechanisms governing epigenetic processes mainly (but not only) by using information provided at the atomic level by X-ray crystallography. Our team gathers expertise covering several aspects of modern structural biology, including the reconstitution of macromolecular complexes by multi-expression, the characterization of protein and macromolecular complexes by biophysical and structural means, and the modeling and design of lead targets. We are developing structure-based rational approaches to characterize small molecule modulators of the biological activities of our targets since they are frequently involved in human diseases. Our team also participates in collaborative research on the structural studies of complexes involving cancer-related targets.

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Plasticity and development of human brain tumor

Grants • InCa PLBIO 2013-15 (>200k€)• aRC Fundation 2013-2014 and 2007-2008 (>50k€)• La Ligue 2013-2015 and 2007-2009 (>200k€)

Major publications over the past four years• Metabolic reprogramming: Bentaib, et al., 2015. J Proteomics• Orthotopic xenografts in mice: Jeitany, et al., 2015. Int J. Cancer• Epigenetic regulation: Sayd, et al., 2014. Stem Cell Rev.• Roles of miRnas in stemness: Fareh, et al., 2012. Cell Death Differ.• Secretome analysis: Thirant, et al., 2012. Stem Cells• Glioma Stem Cell model: Thirant, et al., 2011. Plos One

Patents • WO2014/202776: GhB derivatives for use in the treatment of cancer • WO2012/168885: Bisacodyl as drugs for treating cancer• WO2012/0110768: use miRna 302-367 cluster to treat cancer

Hervé CHNEIWEISS

Keywords:

• Glial plasticity

• Brain tumor development

• Cancer stem cells

• Epigenetics

• Proteomics

MD, Ph.D.Contact: [email protected]

SynopsisThe team relies on an integrated approach comprising the analysis of epigenetic marks regulation, paracrine dialogue and metabolic pathways in cells derived from patients in order to understand the mechanism of brain tumor development.

AbstractGlioblastomas are the most common form of primary brain tumors, and the most aggressive: they resist to current therapies and the median survival of the patients is shorter than 18 months. The team contributed to build the model of cancer stem cells, and focuses now its effort on understanding the mechanisms underlying stemness regulation in this context. using cells derived from patients, the team explored the interplay between epigenetic marks and metabolic pathway. noteworthy, the researchers i) firstly involved TGF-α in the dedifferentiation of astroctytes; ii) highlighted the importance of environment secretome in the maintenance of the stemness and iii) identified a cluster of miRna governing the epigenetic fingerprint of cancer stem cells. In his ambition to find new therapeutic approaches against glioma, hervé Chneiweiss is strongly dedicated to transfer technology.

SELECTED REFERENCES

> Research Center; Town: Institut de Biologie Paris Seine (IBPS) Paris

> Administrative affiliations: CnRS uMR 8246 - Inserm u1130 - université Pierre et Marie Curie

> Tech Transfer Office: SaTT Lutech www.sattlutech.com

22

Hervé CHNEIWEISS


Objectives:• understanding the role glial plasticity in glioma development• Characterizing tumor leaders: Glioma Stem Cell (GSC) • Identifying compounds toxic for GSC or restricting their aggressive properties

Tools:• Collection of glioma stem cells derived from adult and pediatric patients• animal model: mice with orthotopic xenografts• Optical imagery tools to monitor cultured cells• Flow cytometry to selected subpopulations of GSC• Quantitative Proteomics: 2D-DIGE followed by mass spectrometry• Metabolic analysis. Epigenetic analysis.

Unique selling points:• Privileged access to cancer cells derived from adult and pediatric glioma• Expertise at the molecular and functional level on Glioma Stem Cells (GSC)• Integrated approaches via multiple collaborations: transcriptome and metabolome

profiling, epigenetic regulations, and proteomics• International acknowledgement for the GSC model (4 reviews)• Editorial boards: Progress in neurobiology, Médecine/Sciences (ed. in chief)• Involvement in administration and regulation:

Sit at the Ethic committee of Inserm, and at the national advisory board for bioethics Sit at the Office Parlementaire d’évaluation des choix scientifiques et technologiques


23

Hervé CHNEIWEISS

project / expertise

Development and plasticity of glioma: The Glioma Stem Cell (GSC) model

Dissecting the molecular mechanisms governing stem properties of GSC

Results• Cells derived from pediatric glioma show self-renewal properties• Tumor cells with prolonged self-renewal proper-ties are associated with poor patient outcome, and resistance• Pediatric derived oncospheres have the ability to form highly invasive tumors when xenografted in mice brain

Perspectives• Pediatric and adult glioma show similar root causes• Therapeutic anti-cancer strategies should take cell plasticity into account

Results• Identification of the miR-302-367 cluster: its expression is sufficient to suppress the stemness signature of Glioma Stem Cells (GSC)• Epigenetic alterations of the expression of miR-302-367: dif-ferential expression (down- or up-regulation of >300 genes)• Metabolic alterations of the expression of miR-302-367: GHB production is increased

Perspectives• miR-302-367 appears as an interesting target for therapies aiming to suppress GSC stem properties• Therapeutic potential of GHB: treatment with GHB can reca-pitulate the loss of stemness in GSC


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Poly(ADP-ribosyl)ation and genome integrity

Grants • LabEX Medalis (2011-2020)• Equipe labellisée Ligue (2011-2015)• anR (2014-2017)• FRM (2015-2017)• Ligue (2016), aRC (2016-2017), EDF (2016)

Major publications over the past four years• Schreiber V, Illuzzi G, héberlé E and Dantzer F (2015) De la découverte du poly(aDP-ribose) aux inhibiteurs PaRP en thérapie du cancer. Bull Cancer, 102, 863-73• Robert I, Gaudot L, Rogier M, heyer V, noll a, Dantzer F, Reina-San-Martin B. (2015). Parp3 negatively regulates immunoglobulin class switch recom-bination. PLoS Genet, 22;11(5):e1005240. doi: 10.1371.• Illuzzi G, Fouquerel E, amé JC, noll a, Rehmet K, nasheuer hP, Dantzer F and Schreiber V (2014). PaRG is dispensable for recovery from tran-sient replicative stress but required to prevent detrimental accumulation of poly(aDP-ribose) upon prolonged replicative stress. nucleic acids Res. 42,7776-92

• Beck C, Boehler C, Barbat JG, Bonnet ME, Illuzzi G, Ronde P, Gauthier LR, Magroun n, Rajendran a, Lopez BS, Scully R, Boussin FD, Schreiber V and Dantzer F (2014). PaRP3 affects the relative contribution of homologous recombination and nonhomologous end-joining pathways. nucleic acids Res. 2014;42(9):5616-32• De Vos M, El Ramy R, Quénet D, Wolf P, Spada F, Magroun n, Babbio F, Schreiber V, Leonhardt h, Bonapace IM and Dantzer F (2014) Poly(aDP-ribose) polymerase 1 (PaRP1) associates with E3 ubiquitine-protein li-gase uhRF1 and modulates uhRF1 biological functions. J. Biol. Chem. 289(23):16223-16238 • Beck C, Robert I, Reina San Martin B, Schreiber V and Dantzer F (2014). Poly(aDP-ribose) polymerases in double-strand break repair : focus on PaRP1, PaRP2 and PaRP3. Exp. Cell Res. 329(1):18-25.• Le May n, Iltis I, amé JC, Zhovmer a, Biard D, Egly JM, Schreiber V* and Coin F* (2012) Poly(aDP-ribose) glycohydrolase regulates retinoic acid receptor-mediated gene expression. Mol Cell 48, 785-798.

Françoise DANTZERValérie SCHREIBER

> Research Center; Town: Institut de Recherche de l’Ecole de Biotechnologie de Strasbourg (IREBS), Illkirch

> Administrative affiliations: uMR7242 - CnRS - université de Strasbourg

> Tech Transfer Office: SaTT Conectus alsace [email protected]

Keywords:

• poly(aDP-ribosyl)ation

• Dna repair and genome stability

• cell division and differenciation

• glioblastomas, breast cancers

Ph.D.Contact: [email protected]: [email protected]

Synopsis:The aim of our team is to decipher the complex role of poly(aDP-ribosyl)ation reactions in the mechanisms governing genome stability and tumorigenesis

Abstract:Regulation of poly(aDP-ribose) produced by PaRPs in response to Dna insults and degraded by PaRG is critical for the outcome of the damaged cell. PaRP inhibitors are engaged in clinical trials for their promising potentializing effect in chemo- and radiotherapy and one molecule has been approved for its cytotoxic effect on repair-deficient (BRCa-mutated) advanced ovarian cancers. We have recently revealed an essential role of PaRP-3 and PaRG in the cell recovery from Dna damage or replicative stress and in mitotic progression and cell differentiation. Our goal is to decipher the biological role of PaRP-3 and PaRG in the maintenance of genome integrity and in tumorigenesis, with the aim of determining the value of their pharmacological targeting in cancer therapies. In light with this objective, we also develop strategies to generate specific inhibitors of PaRP-3 and PaRG.

SELECTED REFERENCES

25



Objectives:• Role of PaRPs and PaRG in the maintenance of genome integrity• Role of PaRP3 in cell fate• Defining the interest of targeting PaRP3 and PaRG in cancer therapy• Biochemical characterisation of PaRP-3 enzymatic activity • Deciphering the in vivo regulation of PaRG activity• Generation of PaRP-3 and PaRG specific inhibitors

Tools:• Cellular and animal models (KO, CRISPr-Cas9, shRna)(Parp-1-/-, Parp-2-/-, Parp-3-/-, Parp-9-/-; Parp-1-/-;Parp-2flox; Parp-1-/-;Parp-3-/-…)• PaRPs and PaRG recombinant proteins• Poly(aDP-ribose) biochemistry• Dna repair assays• Cell death, differentiation and proliferation studies• Tumorigenesis assays, xenografts

Unique selling points :• Extensive and worldwide expertise in cellular response to Dna damage and PaRPs biology • Pioneer in the development of human cell lines and mouse models deficient in PaRP family members (Parp-1-/-, Parp-2-/-, Parp-3-/- and Parp-9-/- mice as well as combined mutants)• Production of highly pure PaRPs and PaRG enzymes for biochemical, structural and pharmacological analyses• Driving force in continuously increasing number of stimulating and fruitful collaborations• Co-funder of the Labex MEDaLIS «Drug Discovery Center»: access to drug discovery screening platform and medicinal chemistry optimization processs


26


project / expertise

PARP-3, a key actor in double-strand break repair and mitosis

Critical role of PARG to prevent the detrimental accumulation of PAR following genotoxic insult

ResultsPARP3 :

• is involved in the repair of double-strand breaks (DSB) and controls telomere segregation and microtubule dynamics for faithfull mitosis. Boehler et al (2011) PNAS, 108:2783-2788.

• influences the DSB repair pathway choice and inhibits resection to drive repair towards the non-homologous end-joining route. Beck et al (2014) Nucleic Acids Res. 42: 5616-5632.

Perspectives• to decipher the importance of PARP3 in stem cell

fate and tumorigenesis

• to define the molecular properties of PARP3 in DSB repair

ResultsPARG:

• ifacilitates repair of radioinduced DNA da-mages, and reduced radiotoxicity Amé et al (2009) J Cell Biol 122, 1990-2002

• a novel modulator of replicative stress, to facilitate recovery from prolonged repli-cation stress by preventing the detrimen-tal accumulation of PAR and DSB Illuzzi et al (2014) Nucleic Acids Res 42,7776-92.

Perspectives

• targeting PARG to potentiate cytotoxicity of ge-notoxic and anti-replicative drugs ?

• deciphering how PARG activity is tightly regula-ted in vivo


27

Grants • Inserm Transfert (130 k€) EPILaM• ITMO-cancer, appel d’offre épigénétique (146,3 k€) TransEpiLe• IncaPLBIO, (230 k€)

Major publications over the past four years• andrea Kühnl, Peter Valk, Mathijs Sanders, Robert hills, Ken Mills, Rose-mary E Gale, Martin Kaiser, Richard Dillon, Melanie Joannides, adam Ivey, amanda Gilkes, Torsten haferlach, Susanne Schnittger, Estelle Duprez, David Linch, Ruud Delwel, Bob Löwenberg, Claudia Baldus, Ellen Solomon, alan Burnett, and David Grimwade. Down-regulation of the Wnt inhibi-tor CXXC5 predicts a better prognosis in acute myeloid leukemia. Blood, 7;125(19):2985-94 (2015)• navarro, JM, Touzard, a, Pradel, L, Loosveld, M, Koubi, M, Fenouil, R, Le noir, S, ahmad Maqboo, M, Morgado, E,, Gregoire, C, Jaeger, S, Mamessier, E, Pignon, C, hacein-Bey, S, Malissen, B Gut,M Gut,I, Dombret, h, Macintyre, E, howes, S, Thrasher, a, Ifrah, n, Payet-Bornet, D, Duprez, E*, andrau, JC*, asnafi, V*, and nadel,B*. Site-& allele-specific de-silencing of polycomb re-pressive activity by insertional oncogenesis: a new recurrent mechanism of TaL1 activation in T-aLL. nat Commun, 23;6:6094.(2015). * Equal contri-bution.

• Tiberi, G, Pekowska, a, Oudin, C, Ivey, a, Prebet, T, Koubi, M, Lembo, F, Mozziconacci, MJ, Bidaut, G, autret, a, Chabannon, C, Grimwade, D, Vey, n, Spicuglia, S, Calmels, B, Duprez, E. PcG methylation of the hIST1 cluster defines an epigenetic marker of acute Myeloid Leukemia Leukemia, Epub 2014 Dec 8 29(5):1202-6 (2015)• Spicuglia S, Vincent-Fabert C, Benoukraf T, Tiberi G, Saurin aJ, Zacarias-Cabeza J, Grimwade D, Mills K, Calmels B, Bertucci F, Sieweke M, Ferrier P, Duprez E. Characterization of genome-wide PLZF/RaRa target genes. PLoS OnE ; 6 (9):e24176 (2011).

Patents • EP14305672.9.nEW BIOMaRKER FOR aML

Epigenetic control of normal and pathological hematopoiesis

Estelle DUPREZ

Keywords:

• Leukemia

• Epigenetics

• hematopoietic stem cell

• h3K27me3


SynopsisWe are applying our in vitro and in vivo epigenetic expertise to understand and characterize malignant hematopoiesis.

Abstractacute myeloid leukemia (aML) is the most common acute leukemia diagnosed in adult patient, characterized by its high heterogeneity in terms of biology and clinical outcome. Our team aims to characterize epigenetic and transcription factors and assess their role in the development of leukemia. using epigenetic profiling on patients samples, we recently discovered a new epigenetic alteration that affects Cn-aML and impacts on prognosis. We demonstrated that a specific locus, the hIST1 cluster, was targeted by epigenetic events that leads to high h3K27me3 level and predicted a good prognosis independently of the already known biomarkers. We will further characterize this new epigenetic abnormality by developing its clinical interest in aML and other pathology. We will also explore the underlying mechanisms that lead to this epigenetic deregulation. We hope that our work will allow the discovery of new biomarkers and therapeutic targets.

SELECTED REFERENCES

> Research Center; Town: Centre de Recherche en Cancérologie de Marseille (CRCM) Marseille

> Administrative affiliations: Inserm uMR 1068 - CnRS uMR 7258 - université aix-Marseille


28

Estelle DUPREZ


Objectives:• Characterization of PcG recruitment to chromatin • Identify new molecular targets in aML• Development of a new epigenetic marker in aML

Tools:• Patient samples• Mouse models• Chromatin immunoprecipitation• Bioinformatics

Unique selling points :• Discovery of epigenetic markers• unique expertise in genomewide technologies applied to patient samples• Developing epigenetic approaches with potential in clinic


29

Estelle DUPREZ

project / expertise


IMPACT OF A NEW EPIGENETIC BIOMARKER in AML

Results

• (A) Epigenetic profiling reveals a specific H3K27me3 signature in AML

• (B) High HIST1 H3K27me3 level correlates to good prognosis

• (C) High HIST1 H3K27me3 is an inde-pendent prognosis marker in AML

PerspectivesExtend the impact of the epigenetic signa-ture: • Other malignancies• Treatment response

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Epigenetic and Alternative Splicing

Grants • aTIP / aVEnIR – with the support of the aRC• Inserm Plan Cancer• Epigenesys network of Excellence in Epigenetics and Systems Biology (FP7-RISE1)• Marie Curie Career Integration Grant (FP7-CIG)

Major publications over the past four years• Gonzalez I, Munita R, agirre E, Dittmer Ta, Gysling K, Misteli T and Luco RF.* a long non-coding Rna regulates alternative splicing via establishment of a splicing-specific chromatin signature. nature Structural Molecular Bio-logy 2015, 22(5):370-6.

• Luco RF.* The non-Coding Genome: a universe in expansion for fine-tu-ning the coding world. Genome Biology 2013, 14(11):314. • Luco RF* and Misteli T. More than a splicing code: Integrating the role of Rna, chromatin and non-coding Rna in alternative splicing regulation. Current Opinion in Genetics and Development 2011, 21:1-7. • Luco RF, allo M, Schor IE, Kornblihtt aR, Misteli T. Epigenetics in alterna-tive pre-mRna splicing. Cell 2011, 144 (1): 16-26. • Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith O, Misteli T. Regulation of alternative splicing by histone modifications. Science 2010, 327(5968):996-1000

Reini FERNANDEZ DE LUCO

Keywords:

• alternative splicing

• Epigenetics

• non-coding Rna

• Long non-coding Rna

• EMT


SynopsisOur group aims at the better understanding of the role of epigenetics and long non-coding Rnas in the onset and maintenance of tissue-specific splicing programs using as a cell redifferentiation model system the epithelial-to-mesenchymal transition (EMT).

Abstractalternative splicing is one of the most general and important biological processes in the eukaryotic cell. It affects more than 90% of human genes, it is essential for protein diversity and any misregulation of the highly tissue-specific alternative splicing programs can lead to disease, such as cancer. however the mechanisms of cell-specific alternative splicing regulation are still largely unknown. We have shown that non-coding Rnas and histone marks can talk to the splicing machinery via recruitment of chromatin/splicing-adaptor complexes. The can play a role in the onset and maintenance of tissue-specific splicing programs using as a cell redifferentiation model system the EMT. For that purpose we will use chromatin immunoprecipitation (ChIP) and genome-wide strand-specific RT and ChIP deep-sequencing to depict the molecular mechanisms of regulation of tissue-specific alternative splicing.

SELECTED REFERENCES

> Research Center; Town: Institut de Génétique humaine (IGh) Montpellier

> Administrative affiliations: CnRS uPR 1142

> Tech Transfer Office: aXLR www.axlr.com

31



Objectives:• To uncover the role of histone marks and long non-coding Rnas in the regulation of

EMT-specific alternative splicing programs.• To modulate splicing of key EMT events by modulating chromatin and/or lncRnas

expression levels. • To impair EMT progression and malignancy by using the newly identified splicing

regulators.

Tools:• high-throughput sequencing: ChIP-seq and strand-specific Rna sequencing • CRISPR/Cas9 system for epigenetic editing and knock out of lncRnas• EMT induction of human epithelial MCF10a-Snail-ER cells(EMT: Epithelial-to-mesenchymal transition – involved in cancer and metastasis)

Unique selling points:• unique expertise in a young field in expansion that studies the interplay between

chromatin and alternative splicing regulation.• Innovative approaches to address the direct role of histone marks in splicing regulation

by adapting the CRISPR/Cas9 system to edit the epigenome. • Interdisciplinary project combining genome-wide/computational approaches with gene-

specific analysis to depict novel mechanisms of splicing regulation. • use of a dynamic and physiologically relevant cell reprogramming system, the EMT, to

discover novel tools to revert disease-specific splicing events. • Identification of chromatin signatures as potential biomarkers for detection of early

stages of metastasis.• Development of lncRnas as a more specific and target-orientated therapeutic strategy

(Rana Therapeutics and Isis Pharmaceuticals are uS companies already targeting diseases using this strategy – in clinical trial for myotonic muscular dystrophy).


32

project / expertise

Results• Alternatively spliced exons are enriched in spe-cific subsets of histone marks. These marks play a direct role in splicing regulation by inducing re-cruitment of specific splicing regulators to the pre-mRNA via protein-protein interaction with chroma-tin-binding proteins that act as adaptors.

Perspectives• To predict alternative splicing patterns based on the subset of histone marks enriched along an exon and to modulate the final splicing outcome by modulating these characteristic chromatin signa-tures.

Results• The expression of a lncRNA within FGFR2 locus triggers recruitment of chromatin complexes, amongst Polycomb, that create the chromatin signature necessary for inclu-sion of the epithelial-specific splicing iso-form. In the absence of the lncRNA, there is a chromatin remodeling that favors inclu-sion of the mesenchymal isoform.

Perspectives• To use lncRNAs to induce or revert a spe-cific splicing event as a novel therapeutic strategy to treat splicing-specific diseases.

Chromatin cross-talks to the splicing machinery via chromatin-adaptor complexes

Chromatin cross-talks to the splicing machinery via chromatin-adaptor complexes



33

Deciphering functional activity of TLX homeodomain oncogenes in T-cell Acute Leukemia (T-ALL): Epigenetic analysis

Grants • anR Blanc International 2014-16: ‘Epigenetics and alternative splicing: role in immune T cell differentiation and leukemogenesis’ [P. Ferrier, coordi-nateur - Collaboration: M. Carmo-Fonseca, IMM Lisbonne (Portugal)]• Inserm ITMO aviesan Plan Cancer, Epigénétique & Cancer (2014-16) & InCa ‘Biologie & Sciences du Cancer (2014-16) Deciphering the functional activity of TLX oncoproteins in T-aLL: a stride towards differentiation the-rapy’ [P. Ferrier, coordinateur - Collaboration: I. andré-Schmutz & V. asnafi, Institut necker Paris]

Major publications over the past four years• Long-range control of V(D)J recombination and allelic exclusion: Modeling views. Outters et al.. adv Immunol. 128, vol. Long Range Regulation of V(D)J Recombination. Cornelis Murre, Ed. (In press). • Transcription-dependent generation of a specialized chromatin struc-ture at the TCRbeta locus. Zacarías-Cabeza et al. J Immunol. 2015 apr 1;194(7):3432-43

• TLX homeodomain oncogenes mediate T cell maturation arrest in T-aLL via interaction with ETS1 and suppression of TCRalpha gene expression. Dadi et al. Cancer Cell. 2012 apr 17;21(4):563-76. • h3K4 tri-methylation provides an epigenetic signature of active enhan-cers. Pekowska et al. EMBO J. 2011 aug 16;30(20):4198-210. • Transcription initiation platforms and GTF recruitment at tissue-spe-cific enhancers and promoters. Koch et al. nat Struct Mol Biol. 2011 Jul 17;18(8):956-63.• a unique h3K4me2 profile marks tissue-specific gene regulation. Pe-kowska et al. Genome Res. 2010 nov;20(11):1493-502. doi: 10.1101/gr.109389.110. Epub 2010 Sep 14. PMID: 20841431• TCR beta allelic exclusion in dynamical models of V(D)J recombina-tion based on allele independence. Farcot et al. J Immunol. 2010 aug 1;185(3):1622-32.

Pierre FERRIER

Keywords:

• Epigenetics

• Lymphoid cell differentiation

• Gene expression and Recombination

• Leukemia

MD, PhD / Inserm Research Director / Team Leader Contact: [email protected]

Synopsishttp://www.ciml.univ-mrs.fr/science/lab-pierre-ferrier/home

AbstractWe investigate the molecular mechanisms involved in the control of differentiation events during lymphocyte development including antigen receptor gene expression and recombination. One approach is to characterize cis-regulatory elements and bound factors at lymphoid gene specific loci and to infer their impact on chromatin structure using molecular biology, high-throughput genomics (microarrays, ChIP-Chip, ChIP-seq, Rna-seq, MeDIP, FaIRE) and bio-informatics; as well as transgenic mouse and gene targeting (knockout/knockin) technologies. Mutant animals are being used to study precursor-product relationships along lymphoid cell developmental pathways, assisted and implemented by mathematical simulation [in collaboration with the team ‘non-Linear Dynamics’ at the Center for Theoretical Physics (CPT), Luminy Campus]. We likewise analyze epigenetic events linked to leukemo/lymphomagenesis. hence, we aim to define the (epi)genetic networks sustaining lymphoid cell ontogenesis and oncogenesis.

SELECTED REFERENCES

> Research Center; Town: Centre d’Immunologie de Marseille-Luminy (CIML), Marseilles, France

> Administrative affiliations: Inserm u1104 - CnRS uMR7280 - université aix Marseille


34

Systems biology of cell fate decisions in normal and tumor cells

Grants • ITMO Cancer – aviesan // Ligue Labelisée //anR // World-wide Cancer Research (aICR)

Major publications over the past four years• Portal MM et al (2015) TaRDIS, a Targeted Rna Directional Sequencing method for rare Rna discovery. nat Protoc, in press [IF 13.5] (patent appli-cation)• Chaligné R et al (2015) The inactive X chromosome is epigenetically uns-table and transcriptionally labile in breast cancer. Genome Res 25, 488 [IF 15.6]• Portal M et al (2015) human cells contain natural double-stranded Rnas with potential regulatory functions. nat Struct Mol Biol 22, 89 [IF 13.3] 3x recommended by F1000Prime; 2 patent applications • Shankaranarayanan P et al (2012) Single-tube linear Dna amplification (LinDa) for genome-wide studies using a few thousand cells. nat Protoc 7, 328 [IF 13.5] (patented)

• Mendoza-Parra Ma et al (2011) Dissecting the retinoic acid-induced dif-ferentiation of F9 embryonal carcinoma cells through integrative genomics. Mol Sys Biol 7, 538 [IF 12.1].• Shankaranarayanan, P et al (2011) Single-tube linear Dna amplification (LinDa) for robust ChIP-seq. nature Methods 8, 565 [IF 32.1] (patented)• Ceschin DG et al (2011) Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin. Genes & Dev 25, 1132 [IF 12.3]

Patents & IP • 2014 Method of capturing and identifying novel Rnas (EP14306648) • 2014 Method of sequencing and identifying Rnas (EP14305822)• Method and system for processing data for evaluating a quality level of a dataset (WO/2014/083018) : national phases EP, uS• Linear Dna amplification (WO/2012/150317) : national phases EP, uS• Software and database registered in the agency for the Protection of Programs (aPP)

Hinrich GRONEMEYER

Keywords:

• Gene regulatory programs for retinoic acid receptor-

induced cell differentiation and stepwise tumorigenic

transformation of human primary cells

• Mechanism of selective tumor cell killing by the TRaIL

pathway

• Genesis and function of non-coding Rnas

Ph.D.Contact: hg @ igbmc.fr

(Pa: [email protected])

SynopsisWe perform integrative genome-wide analyses (signalling, transcriptome, epigenome, chromatin architecture), and develop the required technologies and bioinformatics tools, to (i) understand (patho)physiological cell fate acquisitions and (ii) discover novel regulatory principles.

AbstractWe are deciphering the temporal evolution of gene networks that are involved in physiological (cell differentiation, lineages progression) and pathological (tumorigenesis models) cell fates. We generate a comprehensive view of the regulation of corresponding interconnected networks of genes. For this we have developed technologies (LinDa, TaRDIS) and bioinformatics tools (big data QC, normalization and analysis). Our studies of the tumor susceptibility loci-rich RaM region led to the discovery of novel regulatory natural double stranded Rnas (ndsRnas). We will define the biogenesis and biological function of ndsRnas and their role in cell fate acquisition, generating an entirely novel field of research and possibly completely novel types of biomarkers and targets. Our studies of the tumor-selectivity of, and resistance to TRaIL will lead to new cancer-therapeutic tools.

SELECTED REFERENCES

> Town: Strasbourg

> Administrative affiliations: université de Strasbourg Ea3430


35

Hinrich GRONEMEYER


NGS QC GENERATOR• Patent application WO/2014/083018

- priority date : november 28th 2012 - national phases EP, uS

• Software and database registered in the agency for the Protection of Programs (aPP)• Seeking partners for licensing or services• actively looking for an entrepreneur to exploit the technologies, bioinformatics tools and know-how through the creation of a start-up : QC GEnOMICS

LinDA• Patent application WO2012150317

- priority date : May 11th 2011 - national phases EP, uS

• Seeking partners for licensing or services• actively looking for an entrepreneur to exploit the technologies, bioinformatics tools and know-how through the creation of a start-up : QC GEnOMICS

TARDIS• Patent application PCT/EP2015/062179

- priority date : May 30th 2014• Seeking partners for licensing

ndsRNA• Patent application EP14306648

- priority date : October 16th 2014• Seeking partners for the co-conception of a SaTT Conectus Investment program aiming at the maturation of the ndsRna capture technology• Seeking partners for licensing


36

Hinrich GRONEMEYER

project / expertise

• Bioinformatics tool generating both global and local numerically defined quality control (QC) parameters for genome-wide NGS profiling data sets.• This QC system is applicable to all NGS-based profiling and to certifi-cation process of antibodies dedica-ted to genome-wide studies• First quantifiable measurement for the quality of sequencing datasets (ChIP-seq, HiC and related) obtai-ned by massive parallel sequencing and the quality of the reagents used for the profiling• Searchable databases (NGS-QC for ChIP-seq, etc. & LOGIQA for HiC and other long-range chromatin interactions) comprising a 2-dimen-sional representation of the global QC parameters • This approach allows: - The attribution of a quality label to the profiling - The determination of the optimal sequencing depth - The determination of the best method to implement for a given sample

- First QC of antibodies dedicated to genome-wide studies based on quantitative descriptors • Possibility to give insights for the improvement of the quality of NGS data obtained with a given antibody

• www.ngs-qc.org for further infor-mation


QC certification system for genome-wide studies and associated database

37

Hinrich GRONEMEYER

project / expertise

• Versatile and robust DNA am-plification method, for ChIP-seq and re-ChIP-seq with picogram DNA amounts • Single-tube RNA polymerase-based linear DNA amplification technology which facilitates glo-bal chromatin analyses with very limited cell populations, such as stem or cancer initiating cells. • Consecutive steps are perfor-med in the same tube by sequen-tial addition of reagents, thus eliminating the need for column purification and minimizing the risk of sample losses particularly at early steps.

• Unique GC bias-free DNA am-plification technology (PCR-free procedure)• The single tube design of LinDA is ideal for handling ultra-small amounts of DNA (>30pg) and is compatible with automation• The actual hands-on working time is less than 6h with one overnight reaction• Can be coupled to a great number of global profiling tech-nologies• Allows NGS data pre-proces-sing thanks to the tool TrimLinDA • Technology being further de-veloped to improve sensitivity, versatility (bar coding for large sample sizes) and simplicity.


High-throughput sequencing of picogram amounts of DNA

38

Hinrich GRONEMEYER

project / expertise

• Novel technology for comprehensive target discovery by RNA capture followed by strand-specific RNA-seq• Enables the robust identification and reconstruction of any kind of known or unknown RNA species, inde-pendently of the length, level of expression, poly-A pres-ence or function.• Cheapest and at the same time only comprehensive RNA-seq technology• Based on the direct hybridization of DNA traps genera-ted from any DNA library of interest (i.e Bacterial Artificial Chromosomes (BAC) covering a region of interest), with either the natural small RNA fraction or the entire RNA repertoire.• Workflow comprising 5 main steps:1) BAC selection & production of biotinylated traps2) RNA sample purification 3) targeted RNA capture,4) Strand-specific RNA-seq library preparation,5) RNA-seq data analysis.• Experimental workflow is performed within 10 days in a typical research lab setting. • Validated with the discovery and identification of ndsR-NA

• ndsRNA: recent and original discovery of a novel class of non-coding RNAs with regulatory potential for major cell functions• Development of a method for the specific capture and identification of ndsRNAs (under development)• Potential use of ndsRNAs/patterns as a novel type of biomarkers• Potential ndsRNA-based therapeutics interfering with essential cell physiological functions, such as proliferation and epigenetics• ndsRNAs are critically involved in mitosis• ndsRNAs interact with different regulatory, including mitotic complex and epigenetic factors/machineries

Perspectives• ndsRNAs as biomarkers• ndsRNA-based therapeutics• ndsRNAs constitute a novel field of research with enormous innovative potential for translational re-search


TARgeted RNA DIrectional Sequencing method for rare RNA discovery

Capture, identification and use of ndsRNA

39

Regulation of gene by microRNAs in Cancer and Development

Grants • Cancéropôle Grand Sud-Ouest• InCa PLBIO 2012 • InCa TRanSLa 2013• FRM BIOInFO 2013• Ligue nationale contre le Cancer

Major publications over the past four years• Jalvy-Delvaille, S., et al. (2012). Molecular basis of differential target regu-lation by miR-96 and miR-182: the Glypican-3 as a model. nucleic acids Res 40, 1356-1365.

• Maurel, M., et al. (2013a). MicroRna-1291-mediated silencing of IRE1al-pha enhances Glypican-3 expression. Rna 19, 778-788.• Maurel, M., et al. (2013b). a functional screening identifies five micrornas controlling glypican-3: role of mir-1271 down-regulation in hepatocellular carcinoma. hepatology 57, 195-204.

Patents • “use of catenin- beta 1-targeting microRnas for treating liver cancer”- EP patent filling• “use of glypican-3-targeting microRnas for treating liver cancer” - EP patent filling

Christophe GROSSET


SynopsisMy research aims at identifying oncogene-regulating microRnas that constitute clinical biomarkers (for diagnosis, prognosis or treatment response) and/or therapeutic drugs in adult and paediatric liver cancers.

AbstractMy research is focused on the study of the molecular mechanisms involved in two types of liver cancer: hepatocellular carcinoma and hepatoblastoma. My expertise is about the post-transcriptional regulation of oncogenes (Glypican-3, β-catenin …) by microRnas and their role in liver carcinogenesis. My research strategy comprises in cellulo functional screening of microRna libraries, validation of microRna candidates, assessment of their relevance in patients’ tissues and the study of their biological functions using cell-based tests and animal models (chick chorioallantoic membrane, mouse). My team identified several microRnas targeting key oncogenes in liver cancer, presenting antitumoral properties in vitro in association or not with clinical drugs and constituting reliable clinical biomarkers. My future work aims at identifying new microRnas for the treatment and the clinical management of adult and paediatric patients with liver malignancies.

SELECTED REFERENCES

> Research Center; Town: Groupe de Recherche pour l’Etude du Foie (GREF), Bordeaux

> Administrative affiliations: Inserm u1053 - université de Bordeaux

> Tech Transfer Office: aquitaine Science Transfert® is the technology transfer office in charge of our laboratory. Created in July 2012 by the French government, the aims of this TTO are mainly to boost the academic research results and to improve the efficiency of technology transfer to companies and to create economic value. Two European patents have been deposited last July with Christophe Grosset’s team in order to protect microRnas with prognostic and therapeutic properties in liver cancer.

http://ast-innovations.com/

Keywords:

• Liver cancer: hepatocellular carcinoma, hepatoblastoma

• Paediatric and adult patients

• MicroRnas

• Oncogenes: Glypican-3, Beta-catenin

• Clinical biomarkers

• miRna-replacement therapy

40

Christophe GROSSET


Objectives:• Identifying miRnas targeting pathways and genes involved in hepatocarcinogenesis • Evaluating the therapeutic potential of these miRnas in liver cancer (hepatocellular carcinoma and hepatoblastoma) • Identifying miRnas as biomarkers for prognosis and diagnosis in liver cancer• Determining the differential miRnas/genes expression in tumoral versus non tumoral tissue in patients

Tools:• Innovative functional approach to study post-transcriptional regulations (FunREG)• Innovative screening system (Dual Fluorescence-FunREG)• Panels of adult and pediatric tumors and adjacent non-tumoral livers• Chick chorioallantoic membrane model Unique selling points:• The Dual Fluorescence-FunREG screening system. Screening of libraries of miRnas, shRnas, sgRna, chemical components…• The chick chorioallantoic membrane model• MicroRnas with antitumoral properties in liver cancer (potentially in other types of cancer)• MicroRnas for diagnosis and prognosis


41

Christophe GROSSET

project / expertise

Use of Glypican-3-targeting microRNAs for treating liver cancerResults• Identification of 5 Glypican-3-regulating miRNAs with antitumoral properties in hepatocellular carcinoma (HCC) and in hepatoblastoma (HB).

• These miRNAs are down-regulated in tumors and in some case, they act as prognostic biomarkers.

Perspectives• Preclinical studies in mice.• Development of innovative miRNA-replacement therapies in association with Sorafenib or Cisplatin.

Results• Identification of 5 β-catenin-regulating miRNAs with antitumoral properties in hepatoblastoma (HB).• These miRNAs are down-regulated in tumors and in some case, they act as prognostic biomarkers.

Perspectives• Preclinical studies in chick chorioallantoic membrane.• Development of innovative miRNA-replacement thera-pies in association with Cisplatin.

Use of β-catenin 1-targeting microRNAs for treating liver cancer


42

Impact of hypoxia and microenvironment in tumor progression and response to treatment. Translational approaches and epidemiology

Grants • Idex attractivity project• Ligue contre le cancer• Projet de Recherche et Développement Structurant des Pôles de Compé-titivité (PSPC) : Imodi• alsace contre le cancer • Roche : research in personalized medicine• InCa

Major publications over the past four years• neuville a, et al, human Pathology, 2011 • Guérin G et al, Molecular Medicine, 2012 • Marisa L, et al, Plos Medicine, 2013 • Schmitt C, et al, Bio Med Chem, 2013 • Prim n, et al, Eur Respir Rev, 2014• Romain B, et al, Molecular cancer, 2014• Weingertner n, Pathology, 2015

Dominique GUENOT

Keywords:

• Preclinical development

• hypoxia

• Resistance

• Xenografts

• Tumor banking

• Molecular biology, genomics, transcriptomics


SynopsisThe team composition with researchers, clinicians, scientists and doctoral students in medical training as well as collaborations with established hospital services, represent a major strength of this team for achieving a preclinical translational research Cancer.

AbstractThe goal of our project is to specify the molecular mechanisms by which hypoxia, according to its severity and in close interaction with microenvironment, can dependently or independently of hIFs, promote metastatic spread and resistance to cancer therapies (chemotherapy, radiotherapy ...). understanding these mechanisms will lead to the identification of new markers prognostic of dissemination and predictive of response to treatment. Demonstration of the functional role of such markers will optimize current treatments and develop alternative therapeutic strategies, validated by clinical trials. Our expertise relies on the development of research projects that benefit from both fundamental and applied research in order to establish a continuum between the bedside and the research laboratory.

SELECTED REFERENCES

> Center, town: Strasbourg

> Administrative affiliations: université de Strasbourg Ea3430


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Dominique GUENOT


Objectives:• Impact of hypoxia on dissemination and resistance processes • Impact of chemokine axis on dissemination process• Develop translational therapeutic strategies based on drug combinations

Tools:• Proteomics / metabolomics / genomics – nGS)• Radiobiology (cells and small animal)• Xenografts in nude mice• Biobank and biological resource center with important tumor bank (numerous solid cancers (cerebral, lung, colon, VaDS carcinomas, lymphomas, osteosarcomas)

Unique selling points:• Development of translational research within a pole of fundamental cancer teams • Important collection of solid tumors• Epidemiologist and biostatisticians as team members to develop early phase clinical trials • Close interaction between researchers and clinicians (oncologists, surgeons, anatomo-pathologists)


44

project / expertise

CXCLx/CXCRy/CXCRz axis in human colon cancerResultsIn human colon carcinomas: • Loss of CXCLx expression in part of adenomas• No more CXCLx expression • CXCLx promoter acetylation rather than methylation

in APC mutated mice, HDAC inhibitor Valproate :• Diminishes number of spontaneously developped intestinal tumors • Reexpressed CXCLx in tumor intestinal cells

Perspectives• Identify enzymes and their targets that are involved in the regu-lation of methylation and acetylation of CXCLx promoter• Evaluate if loss of CXCLx expression participates to tumor cell dissemination

Results• Increased expression according to the carcinoma clinical stage • Hypoxia-increased expression of CXCRy via the expression of HIFs• CXCRy is maintained at the membrane up to 48 hours after return to normoxia• No impact of hypoxia on CXCRz expression

Perspectives• Receptor expressions in human colon carcinoma - prognostic value• Role of CXCRy and / or CXCRz in metastasis• Translational development: Inhibit metastatic process via HIFs and CXCRy/CXCRz inhibitors

CXCRs membranous expression and hypoxia

Dominique GUENOT


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PU.1 transcription factor in epigenetic and splicing regulation

Grants • ITMO-cancer, appel d’offre épigénétique TransEpiLe 2013• IncaPLBIO 2014• Ligue nationale contre le CancerFondation de France

Major publications over the past four years• Ridinger-Saison et al., 2013, Epigenetic silencing of Bim transcription by Spi-1/Pu.1 promotes apoptosis resistance in leukaemia. Cell Death and Differentiation, 20, 1268-78

• Boeva et al., nebula-a web server for advanced ChIP-seq data analysis. Bioinformatics, 2012, 28, 2517-9. • Ridinger-Saison et al., 2012, Spi-1/Pu.1 activates transcription through clustered Dna occupancy in erythroleukemia. nucleic acid Research, 140, 8927-41.• Rimmelé et al., 2010, Spi-1/Pu.1 oncogene accelerates Dna replication fork elongation and promotes genetic instability in the absence of Dna breakage. Cancer Res., 70, 6757-66.

Christel GUILLOUF

Keywords:

• Pu.1 transcription factor

• alternative Splicing

• Epigenetic regulation

• hematopoeisis

• Leukemia


SynopsisOur work aims at deciphering the impact of transcription factors on chromatin structure, transcription and splicing in leukemia initiation and progression

Abstractacute Myeloid Leukemias (aMLs) are due to the progressive accumulation of mutations in genes coding for proteins participating to signalling networks, for transcription factors (TFs) and for splicing and epigenetic regulators, leading to deep changes in global gene expression. Genetic alteration of a hematopoietic TF determines aML specificity by blocking the differentiation process of a specific lineage. We aim to describe the molecular mechanisms through which TF drives transformation. Because we know that TFs interact physically with epigenetic and splicing factors and that gene expression results from the coordinated control of these three types of factors, we hypothesized that TFs act by modifying the specificity and activity of epigenetic and splicing regulators in leukemia. To validate our hypothesis, we characterize the mechanisms by which the Pu.1 TF, whose a fine-tuning activity is involved in hematopoietic differentiation and leukemia, modifies gene expression in normal and leukemic cells.

SELECTED REFERENCES

> Center, town: Gustave Roussy Institute, Villejuif

> Administrative affiliations: Inserm-u1170 - CnRS


46


Christel GUILLOUF


Objectives:• To define whether high Pu.1 expression controls gene expression by modifying epigenetic marks and regulators. We focus, in particular, on the interplay between Pu.1 TF and PcG complex. • To characterize how Pu.1 modify alternative splicing, ie dependent on Dna or Rna binding or through competitive activity on proteins. • To define how Pu.1 interconnect alternative splicing, epigenetic regulation and transcriptional targets in leukemia

Tools:• Murine model of leukemia: Pu.1 transgenic mice• Cells with graded Pu.1 expression• ChiP-seq • Rna-seq• CLiP-seq

Unique selling points:• Innovative approaches to address the role of Pu.1 in Rna binding, Clip-seq• unique expertise in Pu.1 transcription factor• Study combining genome-wide strategy with gene expression analysis in in vivo and in cellulo model of leukemia • use of a well-defined multistep leukemic model

47


Christel GUILLOUF

project / expertise

Interplay between PU.1 and PcG complex and its role in leukemogenesis

ResultsPU.1 represses apoptosis and the pro-apoptotic Bim gene through binding to Bim promoter. PU.1 interacts with PRC2 complex also bound upstream in the Bim promoter and increases the H3K27me3 mark at this gene, leading to the repression of RNA transcription.

PerspectivesWe will study the functional relationship between PU.1 and PRC2 by analysing the two following hypotheses: PU.1 recruits or modulates the activity of PRC2 at the Bim promoter and at others targets that need to be identify.

ResultsWe know that PU.1 interacts with splicing factors, epigenetic factors, binds to DNA and RNA and modifies alternative splicing.

PerspectivesWe will use genome wide approaches(see the figure) to characterize how PU.1 regulates all these steps of gene expres-sion regulation and define specific targets involved in leukemogenesis. For that, we will compare leukemic cells overexpres-sing PU.1 and normal cells.

Interconnection between PU.1, alternative splicing, epigenetic control and trans-criptional targets

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Epigenome deregulation and cancer : mechanisms and biomarkers

Grants • InCa – Epigenetic precursors of childhood cancer. 2015-18, 576,000 €• Eu FP7 - a randomized phase II study with Metformin in breast cancer. 2014-17, 1,230,320 €• InCa - Cancer cell identity and gene expression layers. 2014-2017, 469,760 €• nIh - MicroRna & Breast Cancer: Functional Characterization.2013-2018, 4,063,604 uSD• Eu FP7 - an integrated approach for epigenetic biomarkers of breast cancer. 2014-17, 1,388,363 €• InCa – Epigénome et risque de cancer du sein. 2012-15, 650,000 Euros• Eu FP7 - EXPOsOMICS. Co-Is: Z. herceg 2012-16, 9,000,000 €• Bill&Melinda Gates Foundation - Identifying biomarkers for aflatoxin expo-sure. 2013-16,. 2,000,000 uSD

Major publications over the past four years• Vaca-Paniagua F et al Targeted deep Dna methylation analysis of circula-ting cell-free Dna in plasma using high-throughput semiconductor sequen-cing. Epigenomics, 2015 in press

• Tapias a et al. Trrap-dependent histone acetylation specifically regulates cell-cycle gene transcription to control neural progenitor fate decisions. Cell Stem Cell. 2014 May 1;14(5):632-43.• Lee hS et. Modulation of Dna methylation states and infant immune system by dietary supplementation with ω-3 PuFa during pregnancy in an intervention study. am J Clin nutr. 2013 aug;98(2):480-7. • Ichim G et al The histone acetyltransferase is targeted for destruction during cell cycle. Oncogene 2014 Jan 9;33(2):181-92. Genevois aL et al Dependence receptor TrkC is a putative colon cancer tumor suppressor. PnaS 2013 ;110(8):3017-22• Paliwal a et al aberrant Dna methylation links cancer susceptibility locus 15q25.1 to apoptotic regulation and lung cancer. Cancer Research 2010; 70:2779-2788.Murr R et al histone acetylation by Trrap-Tip60 modulates loading of re-pair proteins and repair of Dna double-strand breaks. nature Cell Biology 2006; 8:91-99.

Zdenko HERCEG

Keywords:

• Epigenetics

• Cancer

• Mechanisms of carcinogenesis

• Biomarkers

• Environment

Ph.D, Group head, Department headContact: [email protected]

SynopsisOur laboratory exploits new concepts in cancer epigenetics and recent technological advances in epigenomics in conducting both mechanistic studies and epigenetic profiling, aiming to enhance our understanding of mechanisms of carcinogenesis and cancer causation and to discover and validate new epigenetic biomarkers.

AbstractImproving the knowledge of mechanisms of cancer development related to environmental factors provides a foundation for studies of cancer etiology, therapy and prevention. Our group leads a multi-faceted research programme on epigenetic mechanisms of carcinogenesis and identification and validation of epigenetic-based biomarkers of exposure and cancer risk that enables the testing of new etiological hypotheses and provides the basis for preventive and treatment strategies. Our studies are multidisciplinary, and extensive collaborations have been developed with laboratory scientists, epidemiologists, and biostatisticians from around the world. Our mechanistic studies are focused on functionally important epigenetic changes and molecular pathways altered in response to cancer risk agents using in vitro models and state-of-the-art approaches. List of Published Work in MyBibliography: https://scholar.google.com/citations?hl=en&user=T8GCnZkaaaaJ&view_op=list_works

SELECTED REFERENCES

> Center, town: International agency for Research on Cancer (IaRC) Lyon, France

> Administrative affiliations: International agency for Research on Cancer (IaRC) – World health Organisation (WhO)

> Tech Transfer Office: World health Organisation (WhO)

49


Zdenko HERCEG


Unique selling points:• ISuccessful in integrating interdisciplinary skills in laboratory-based research, molecular epidemiology, and bioinformatics into IaRC’s unique international research setting • Development of high-throughput epigenomic methodologies that are applicable to biobanks associated with population-based cohorts • Capacity to generate and analyse genome-wide epigenetic data, enabling a switch from candidate-gene approaches to epigenome-wide characterization• Successful grant applications to funding agencies and reinforced home Institute’s mission by training a large number of early career scientists and catalysed new scientific collaborations

50


Zdenko HERCEG

project / expertise

ResultsTo study the biological function of epigenetic regulators in control of cellular processes and tumorigenesis, we have taken different approaches that allow inducible inactivation of specific genes in mice and human cancer cell lines. Our results reveal that histone acetyltransferases may function as a molecular link between DNA damage signaling, DNA repair and cell cycle, and illustrate cellular strategy to use the same basic mechanism involving histone modifying complexes to regulate and coordinate distinct cellular processes, such as transcription and DNA repair, and to protect genomic stabi-lity.

PerspectivesAdvance knowledge of mechanismsof cancer development involving epigenetic regulationand underpin studies of cancer etiology, therapy and prevention

Results• We have established assays for quantitative and high-throughput analysis of DNA and combined these assays with series of HCC associated with major risk factors and collec-ted from different geographical areas.• Aberrant methylation of a subset of genes was associated with tumour progression and etiological risk factors, such as hepatitis B virus (HBV) or hepatitis C virus (HCV) infection and alcohol consumption.• Hypermethylation of an independent panel of genes was strongly correlated with survival after cancer therapy.

PerspectivesOur findings could be exploited for biomarker discovery in the clinic and molecular epidemiology studies

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Functions of lysine methylation pathways

Grants • Plan Cancer-aviesan-Inserm

Major publications over the past four years• Tardat M., Brustel J., Kirsh O., Lefevbre C., Callanan M., Sardet C. and Julien E (2010). The histone h4-K20 methyltransferase PR-Set7 regulates repli-cation origins in mammalian cells. nature Cell Biology. 11 : 1086-1093. Selected by faculty 1000 as exceptionnal contribution.• Brustel J, Tardat M, Kirsh O, Grimaud C and Julien E. (2011) Coupling mitosis to Dna replication : The emerging role of the lysine methyltransfe-rase PR-Set7 (2011). Trends in Cell Biology. 21 :452-60.6• Rodier G, Kirsh O, Baraibar M, houlès T, Lacroix M, Delpech h, hatchi E, arnould S, Severac D, Duboix E, Cramal J, Julien E, Friguet B, Le Cam L & Sardet C.(2015). Cell reports apr 14;11(2):220-33.

Patents • Ongoing

Eric JULIEN

Keywords:

• Tumor solid models

• Epigenetic drugs

• Methylation

• Cell cycle


SynopsisOur group develops targeted approaches to understand the function of cancer relevant gene families with a particular focus on epigenetic regulators.

AbstractRecent genomic sequencing and transcriptome analysis in a vast variety of cancers have revealed that a large number of chromatin modifiers and chromatin-binding proteins are found mutated or misexpressed in cancer cells. While known to play key roles in the maintenance of genome structure and functions, these largely unanticipated mutation and/or misexpression findings could illuminate newly recognized epigenetic mechanisms potentially central to the genesis of cancer. By developing targeted approaches in both mammalian and Drosophila genetic models, we are studying functions of key factors in chromatin-associated signaling pathways, with a particular focus on the family of lysine methyltransferases that regulate nuclear and epigenetic processes during normal and neoplasic development.

SELECTED REFERENCES

> Research Center; Town: Institut de Recherche en Cancérologie de Montpellier (IRCM), Montpellier

> Administrative affiliations: Inserm u1194, université de Montpellier


52

Eric JULIEN


Objectives:• Identification of new epigenetic targets for cancer treatment • Functional characterization of epigenetic drugs for cancer therapy• Characterization of epigenetic mechanisms in cancer

Tools:• Cellular and Molecular biology• Drosophila genetic models• Bio-computing analysis of ChIP seq/expression data• access to various clinical samples

Unique selling points :• Team nationally and internationally recognized for its expertise in histone methylation and cell cycle regulation• Original insect and mammalian models for epigenetic studies • Connections to clinical studies & hospitals• Strong national and international network of collaborators• Collaborations with engineering chemistry research labs• Strong expertise in regulation and functions of lysine methyltransferases


53

Eric JULIEN

project / expertise

Results• DNA fiber analysis showing defects in replica-tion initiation sites (green) caused by alterations in H4K20(me) methylation signaling pathways. DNA fibers are shown in red.

Perspectives• Identify new epigenetic regulatory mechanisms of the cell-cycle• Development of chemical drugs against H4K20me enzymes to prevent proliferation of cancer cells

Results• Preneoplastic response (hyperplasia) in Droso-phila imaginal dics upon loss of a specific epige-netic regulator.

Perspectives

• Genetic screens to identify evolutionary conser-ved cancer-related genes• Characterization of new regulatory epigenetic mechanisms in cell proliferation

Replication defects caused by alterations in histone H4-K20 methylation signaling pathway

Studying cancer-related phenotypes in Drosophila


54

Epigenetic and Cell Signaling

Grants • ITn European grant FP7• InCa• anR

Major publications over the past four years• Reynoird et al. Embo Journal 2010 29: 2943-2952.• Tan et al. Cell 2011 146: 1015-1027. • Rousseaux et al. Science Transl Med. 2013 May 22;5(186):186ra66• Emadali et al. EMBO Mol Med. 2013 aug;5(8):1180-95• Montellier et al. Genes Dev. 2013 aug 1;27(15):1680-92.• Le Bescont et al. antioxid Redox Signal. 2014 Mar 6. PMID: 24512221.• Wang et al. Oncotarget. 2015 May 12. PubMed PMID: 26001296.

Patents coinventors Pison Rousseaux Sophie, Khochbin Saadi • In vitro diagnostic method for the diagnosis of somatic and ovarian can-cers. uJF oct, 8 2009: wo 2009/121878• use of specific genes for the prognosis of lung cancer and the correspon-ding prognosis method. uJF apr, 26 2012: wo 2012/052524• use of specific genes or their encoded proteins for a prognosis method of classified lung cancer. / uJF apr, 26 2012: wo 2012/052526

Consulting activities• Occasional consulting for Boehringer Ingelheim (BI), GSK, Sanofi, Ono Pharmaceuticals, Pierre Fabre; Research collaborations with BI and GSK; Scientific adviser for CréaCell.

Saadi KHOCHBIN

Keywords:

• Bromodomain

• acetylation

• Chromatin biology

• Epigenome reprogramming

• Cancer Biomarkers

• Therapeutic targets

• Bioinformatics

Ph.D.Contact: khochbin @ujf-grenoble.fr

SynopsisOur research on the epigenetic basis of cell identity crisis in cancer has opened the door to the discovery of hundreds of cancer biomarkers and new oncogenic mechanisms and therapeutic targets.

AbstractWe are developing an original research line on male genome programming, which not only sheds light on the obscure, yet fundamental and conserved process of male epigenome establishment, but also generated important new concepts applicable to epigenetics and chromatin biology in general. This research program also led to unexpected applications in cancer biology. Consequently, a new approach to cancer is in development in our laboratory, revealing novel oncogenic mechanisms, powerful biomarkers, as well as pointing to novel therapeutic targets. all this research activity is led on a highly collaborative basis involving leading international groups in a multidisciplinary approach, including clinicians (France, uSa, China), structural biology, proteomics, genomics and chemical genomics, as illustrated by the publications from our group reporting collaborative efforts of more than ten independent international laboratories.

SELECTED REFERENCES

> Research Center; Town: Institut albert Bonniot (IaB) Grenoble

> Administrative affiliations: Inserm u823 - université Grenoble alpes

> Tech Transfer Office: Floralis www.floralis.fr

55

Saadi KHOCHBIN


Objectives:• Exploit cancer dependent epigenetically driven gene activation to discover diagnosis/prognosis biomarkers and new targets for drugs and immunotherapy• Setup non invasive cancer detection and prognosis tests• Identify original targets for drugs and immunotherapy

Tools:• Knowledge driven genome-scale transcriptomic and epigenetic data analyses.• Tight collaboration with clinicians in lung and breast cancer and in hematological malignancies.• access to tumor banks and direct patient recruitment Unique selling points:• Deep knowledge of epigenetic regulations• unique translational activity in epigenetics in cancer as well as in other chronic diseases • Tight interactions between basic scientists, bio-statisticians and bio-computing, and medical doctors• an original strategy to identify biomarkers and therapeutic targets applicable to all cancer types as well as to other chronic diseases • International network of collaborators, including scientists and clinicians • Successful marker/target discovery strategy demonstrated in the context lung cancer, acute leukemia and lymphoma (see publications)


56

Saadi KHOCHBIN

project / expertise

Lung cancer Pronostic test based on the ectopic activation of male germline genesResults• Discovery of 26 male germline genes whose aberrant expression in lung cancer cells is associated with poor prognostic

• The same strategy can be used to discover markers in all cancers

Perspectives• Routinely predict prognosis of lung tumour patients in order to adapt the therapeutic strategy.

• Develop screening and follow-up non invasive blood tests for cancer patients

Results• Using the same strategy, 6 prognostic marker genes were discovered and a test was developed to predict the response to the induction treatment and survival in ALL children and adult patients

Perspectives• Routinely predict prognosis of ALL patients in order to adapt the therapeutic strategy.

• Find new therapeutic targets based on these genes

Results• BRD4-NUT induces hyperacetylation feed-forward loop, leading to the formation of nuclear foci

New epigenetic drugs can disperse the foci and reverse the oncogenic activity of Brd4-NUT

Perspectives• Find new targetted therapeutic strategies to treat this deadly tumour

Acute Lymphoblastic Leukemia (ALL)Pronostic test based on the ectopic activation of male germline genes

NUT MIDLINE CARCINOMAMolecular basis of the oncogenic activity of BRD4-NUT


57

Chromosome instability, epigenetics and microRNAs

Grants • PaIR prostate 2011-2014• ITMO epigenetic

Major publications over the past four years• Terry, S., El-Sayed, I.Y., Destouches, D., Maille, P., nicolaiew, n., Ploussard, G., Semprez, F., Pimpie, C., Beltran, h., LOnDOnO-VaLLEJO, a., allory, Y., de la Taille, a., Salomon, D.S. and Vacherot, F. (2015) CRIPTO overexpression promotes mesenchymal differentiation in prostate carcinoma cells through parallel regulation of aKT and FGFR activities. Oncotarget, 6, 11994-2008.• Schertzer, M., Jouravleva, K., Perderiset, M., Dingli, F., Loew, D., Le Guen, T., Bardoni, B., de Villartay, J.P., Revy, P. and LOnDOnO-VaLLEJO, a. (2015) human regulator of telomere elongation helicase 1 (RTEL1) is required for the nuclear and cytoplasmic trafficking of pre-u2 Rna. nucleic acids Res, 43, 1834-47.

• Castro-Vega, L.J., Jouravleva, K., Ortiz-Montero, P., Liu, W.Y., Galeano, J.L., Romero, M., Popova, T., Bacchetti, S., Vernot, J.P. and LOnDOnO-VaL-LEJO, a. (2015) The senescent microenvironment promotes the emer-gence of heterogeneous cancer stem-like cells. Carcinogenesis. epub date 2015/07/15.• Episkopou, h., Draskovic, I., Van Beneden, a., Tilman, G., Mattiussi, M., Go-bin, M., arnoult, n., LOnDOnO-VaLLEJO, a. and Decottignies, a. (2014) alternative Lengthening of Telomeres is characterized by reduced compac-tion of telomeric chromatin. nucleic acids Res, 42, 4391-405.• Castro-Vega, L.J., Jouravleva, K., Liu, W.Y., Martinez, C., Gestraud, P., hupe, P., Servant, n., albaud, B., Gentien, D., Gad, S., Richard, S., Bacchetti, S. and LOnDOnO-VaLLEJO, a. (2013) Telomere crisis in kidney epithelial cells promotes the acquisition of a microRna signature retrieved in aggressive renal cell carcinomas. Carcinogenesis, 34, 1173-80.

José Arturo LONDOñO-VALLEJO

Keywords:

• Telomere

• Chromosome instability (CIn)

• Epigenome

• MicroRna

MD-PhDContact: [email protected]

SynopsisWe are interested in understanding the mechanisms by which chromosome instability contributes to cancer

AbstractOur research has shown that chromosome instability due to telomere shortening in human pre-transformed cells is associated to a genetic reprogramming in which massive microRna deregulation plays a central role. The mechanisms responsible for this deregulation are independent of copy number changes and rather involve a genome-wide redistribution of chromatin marks. On the other hand, the presence of a senescent microenvironment contributes to the full transformation of CIn+ cells by promoting the acquisition of stem-like traits through another microRna-depended process also associated to epigenome modifications.

SELECTED REFERENCES

> Research Center; Town: Institut Curie, Paris 75005

> Administrative affiliations: uMR3244, Institut Curie - CnRS - uPMC

> Tech Transfer Office: Institut Curie www.curie.fr

58



Objectives:• To understand how chromosome instability (CIn) contributes to cancer progression• To identify key players responsible for epigenome modifications and microRna deregulation in response to CIn• To identify key players responsible for the cancer-promoting effect of the senescent microenvironment.

Tools:• nGS: ChIP-seq, Rna-seq, WGS in culture cells and tumor material.• Genome/Transcriptome analyses in culture cells and tumor material.• Rna interference, transcriptome and proteomics in culture cells • Fully annotated prostate cancer specimens and patient cohorts.


59



project / expertise

Results• Telomere-driven chromosome instability contribute to the emergence of cancer stem-like cells through epigenetic- and microRNA-dependent mechanisms

Perspectives• Molecular characterization of events responsible for the emergence of cancer stem-like cells

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Epigenetic and genomic instability mining in Multiple Myeloma to define precision medicine

Grants • 2015-2017 : Multiple Myeloma: Epigenetic Mining and Therapeutic Targe-ting. Cancer Plan-ITMO Cancer. Coordinator: J Moreaux. 500 k€. • 2015-2018 : Role of RECQ helicases in Multiple Myeloma. InCa PLBIO. Coordinator: J Moreaux. 575 k€.

Major publications over the past four years• In vivo treatment with epigenetic modulating agents induces transcriptio-nal alterations associated with prognosis and immunomodulation in multiple myeloma. Maes K, De Smedt E, Kassambara a, hose D, Seckinger a, Van Valckenborgh E, Menu E, Klein B, Vanderkerken K, Moreaux J*, De Bruyne E*. Oncotarget. 2014. Dec 26. (* equal contribution) • Bret C, Klein B, Cartron G, Schved JF, Constantinou a, Pasero P, Moreaux J. Dna repair in Diffuse Large B-cell Lymphoma: a molecular portrait. Br J haematol. 2014. nov 05. • Moreaux J, Reme T, Leonard W, Veyrune JL, Requirand G, Goldschmidt h, hose D, Klein B. Gene expression based prediction of myeloma cell sensi-tivity to histone deacetylase inhibitors. British Journal of Cancer. 2013 aug 6;109(3):676-85. • Moreaux J, Reme T, Leonard W, Veyrune JL, Requirand G, Goldschmidt h, hose D, Klein B. Development of gene expression based score to predict sensitivity of multiple myeloma cells to Dna methylation inhibitors. Molecu-lar cancer therapeutics. 2012 Oct 18.

• Bret C, Klein B, Moreaux J. Gene expression-based risk score in diffuse large B-cell lymphoma. Oncotarget. 2012 Dec 31. • Bou Samra E, Klein B, Commes T, Moreaux J. Development of gene ex-pression-based risk score in cytogenetically normal acute myeloid leukemia patients. Oncotarget. 2012 aug 18.

Patents • Method for predicting multiple myeloma treatment response. J Moreaux, B Klein. PCT/EP2013/069736 and WO2014/044848. • Method for predicting hDaCi treatment response in Multiple Myeloma. J Moreaux, B Klein. PCT/EP2013/070964. • Method for predicting DnMTi/hDaCi combination treatment response in Multiple Myeloma. J Moreaux, B Klein. EP14305404.7 • Methods for predicting response to Dna repair pathway inhibitors in dif-fuse large B-cell lymphoma. J Moreaux, C Bret, G Cartron, a Constantinou, P Pasero. EP14306201.6

Jérôme MOREAUX

Keywords:

• hematology

• Multiple Myeloma

• Epigenetics

• Genomic Instability/Dna repair

• haematological malignancies


SynopsisTreatment improvements will come from detailed molecular analyses to develop individualized therapies taking into account the molecular heterogeneity and subclonality evolution.

AbstractMultiple myeloma (MM) is a rarely curable malignant disease of clonal plasma cells that accumulate in the bone marrow. MM is a genetically and clinically heterogeneous disease. Deep genome sequencing studies have recently revealed an even wider heterogeneity and genomic instability with the identification of a complex mutational landscape and a branching pattern of clonal evolution. all patients invariably relapse after multiple lines of treatment, with shortened intervals in between, and finally become resistant to any treatment, resulting in loss of clinical control over the disease, and death within weeks.Treatment improvements will come from detailed molecular analyses to develop individualized therapies taking into account the molecular heterogeneity, subclonality evolution and drug resistance mechanisms. Our aim is to understand the mechanisms of drug resistance, define biomarkers and generate assays to develop precision medicine approach in hematological malignancies (4 patents).

SELECTED REFERENCES

> Research Center; Town: Institut de Génétique humaine (IGh) Montpellier

> Administrative affiliations: CnRS uPR 1142


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Jérôme MOREAUX


Objectives: Multiple myeloma (MM) is a mostly incurable malignant disease of clonal plasma cells that accumulate in the bone marrow. Our vision is that treatment improvements will come from detailed molecular analyses to develop individualized therapies taking into account the molecular heterogeneity and subclonality evolution. • Characterizing the tumor heterogeneity (genomic and epigenomic diversity) and

understanding how treatment influences intraclonal evolution in MM,• understanding the molecular events involved in myelomagenesis and clonal evolution,• Elucidating the mechanisms of resistance, identifying targets in MM cells to overcome

drug resistance and develop personalized treatments. Tools:• unique collection of human Myeloma Cell Lines.• Gene expression profiles of tumor cells from 300 patients at diagnosis, with a careful

patients’ follow-up. • In vitro model to recapitulate the various steps of human plasma cell. generation. Unique selling points:• Expertise in the field of Multiple Myeloma biology. • unique collection of human Myeloma Cell Lines with molecular (Rna seq, Exome seq,

ChIP seq, Methylome, SnP, miRna, WGS) and drug response characterization.• unique in vitro model to recapitulate the various steps of human plasma cell. generation.• Identification of biomarkers to predict MM cells sensitivity or resistance to treatments (3

patents).


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Jérôme MOREAUX

project / expertise

Results• We recently reported gene expression(GEP)-based scores to predict the sensitivity of myeloma cells to different treatments including DNMTi (Mo-reaux et al. BJH, 2014; Moreaux et al. MCT, 2012) (Figure 1A&B), HDACi (Moreaux et al. BJC, 2013) or combination. These scores allow the identifica-tion of MM patients who could benefit from HDACi, DNMTi or DNMTi/HDACi treatment (3 patents).

Perspectives• Our method could be extended to other drugs and to other cancers. We are currently expanding our approach to other treatments used in MM with the support of the technology transfer acceleration company SATT AxLR and LR region.

Results• We identified RECQ1 among the genes downre-gulated by DNMT inhibitor. RECQ helicase are DNA unwinding enzymes involved in the mainte-nance of chromosome stability. RECQ1 is signi-ficantly overexpressed in primary myeloma cells compared to normal plasma cells. High RECQ1 expression is associated with a poor prognosis in two independent cohorts of patients. RECQ1 knock down inhibits growth of myeloma cells and induces apoptosis. RECQ1 depletion induced spontaneous accumulation of DNA double strand breaks (DSBs). RECQ1 overexpression signifi-cantly protects myeloma cell lines from melphalan and bortezomib-induced apoptosis. Using immu-noprecipitation, RECQ1 was shown to interact with PARP1. An increased association of the two proteins was found upon DNA damages induced by melphalan. In agreement, RECQ1 depletion sensitizes myeloma cell lines to PARP inhibitor.

Perspectives• RECQ1 represent a biomarker of drug resistance in MM, which is targeted by DNMT inhibitors. This suggests association of alkylating agents and/or PARP inhibitors with DNMT inhibitor may represent a therapeutic approach in RECQ1high patients associated with a poor prognosis.

Predict response to epigenetic therapy in MM

Identification of genes regulated by an epigenetic program and associated with the pathophysiology of MM : illustration with RECQ1


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lncRNA and cancer

Grants • aTIP (2006-09)• ERC starting grant (2009-14) • ERC consolidator grant (2015-20)• anR (2015-18)

Major publications over the past four years• Li et al. (2015). a Dual Model for Prioritizing Cancer Mutations in the non-coding Genome Based on Germline and Somatic Events. PLoS Comput Biol 11(11).• Descrimes M et al (2015). VInG: a software for visualization of deep sequencing signals. BMC Res notes. Sep 7;8:419• Kwapisz et al. (2015) Expression of subtelomeric lncRnas links telomeres maintenance to Rna decay in S. cerevisiae. non-Coding Rna 2015, 1(2), 94-126

• Wery M et al. (2013). Zinc-mediated Rna fragmentation allows robust transcript reassembly upon whole transcriptome Rna-Seq. Methods. 2013 Sep 1;63(1):25-31. • Tisseur et al. (2011). Pervasive transcription - Lessons from yeast. Biochi-mie. 2011 nov;93(11):1889-96.• van Dijk et al. (2011). XuTs are a class of Xrn1-sensitive antisense regu-latory non-coding Rna in yeast. nature. 2011 Jun 22;475(7354):114-7.

Patents • Prostate cancer diagnostic tool (under deposition)

Antonin MORILLON

Keywords:

• lncRna...

• epigenetics...

• chromatin...

• transcription


SynopsisMy group is interested in understanding how Long non coding (lnc)Rna (now representing more than 60 000 genes in humans) control genome expression and maintenance in response to environmental signals or differentiation programs leading to aggressive cancer forms.

AbstractWe study how lncRna are expressed and processed and which cellular factors they bind to in response to environmental signals and differentiation processes. Errors in their expression/localization/functions can lead to pathological outcomes, such as aggressive cancer. We characterized several lncRna families from yeast to human cells in particular those antisense to mRna. We revealed their wide-spread expression but also their specificity for different tissues and lineage indicating a key role in cellular identity. We integrated these findings at the genome-wide level using up to date sequencing technologies and compare their patterns of expression with epigenetic marks and nuclear configuration. Distinct signatures were defined among several cancers giving fundamental indications concerning their stage of progression opening new avenues for diagnostic/prognostic tools.

SELECTED REFERENCES

> Research Center; Town: Institut Curie, Paris

> Administrative affiliations: CnRS/PSL-uPMC/Curie institute

> Tech Transfer Office: Institut Curie

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Antonin MORILLON


Objectives: • to uncover the role of lncRna in the regulation of cancer progression• to modulate gene expression and epigenome landscape by controling lncRna

expression level• to limit cancer progression through the control of specific key lncRna Tools:• genome wide approaches (Rna-seq, ChIP-seq, nET-seq) and bioinfo analyses• access to the curie tumors library• human genome editing• unique cell culture approaches mimicking cancer EMT Unique selling points:• expertise in cryptic lncRna characterization (genetics and nGS Rna analyses)• innovative approaches in transcriptomic analyses• functional characterization of lncRna candidates• unique signature profiling of lncRna for diagnostic and prognostic purposes• access to tumors library via a variety of cancer tissues• International visibility and several international collaborations

lncRNA and cancer

65

Antonin MORILLON

lncRNA and cancer

project / expertise

Results• A. Schematic view of the processAfter RNA extraction and genome-wide compari-son, novel lncRNA are characterized. Differential analyses allowed the identification of a specific signature that could be used for cancer diagnostic.• B. Expression clustering of a novel lncRNA si-gnature in prostate cancer by comparing normal and cancer tissues. Colors represent expression intensities.• C. PCA analysis of patients using the novel lncR-NA signature. Prostate cancer patient are specifi-cally isolated via the signature.

Perspectives• Developing rapid and cost effective diagnostic tools for cancer progression and therapeutic tar-gets.

Profiling LncRNA expression in cancer

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Integrated Functional Genomic and Biomarkers

Grants • aO Canceropole Grand Ouest 2014

Major publications over the past four years• Barlesi et al., Lancet 2015 (in press)• de Tayrac, aubry et al., Oncotarget 2015• Etcheverry, aubry et al., Plos One 2014• De Tayrc, aubry et al., Clinical Cancer Research 2011• Etcheverry et al., BMC Genomics 2010• hervouet et al., Genes Cancer 2010

Patents • uS patent application n°14/006023

Jean MOSSER

Keywords:

• Epigenetic mechanism

• Somatic or constitutional genetic disease

• Sporadic cancer (e.g. glioblastoma)

• nGS Technology

Pu-Ph - Ph.D.Contact: [email protected]

SynopsisWe look for the molecular elements associated with tumour heterogeneity (in term of aggressiveness and therapeutic response) in order to improve patients’ molecular stratification.

AbstractThe research interests of the «Integrative Functional Genomics & Biomarkers» team (uMR 6290 IGDR) revolve around two themes, both focusing on the understanding of the genetic and epigenetic mechanisms linked to the development of somatic or constitutional genetic diseases. In sporadic cancers (e.g., glioblastoma), we look for the molecular elements associated with tumour heterogeneity (in term of aggressiveness and therapeutic response) in order to improve patients’ molecular stratification. In the case of cancer arising as a complication of a genetic disease like hemochromatosis, we look for the genetic factors modifying the hemochromatosis-hFE penetrance (GWaS approach, penetrance is considered as a complex genetic trait). For these two projects, we benefit (i) from regional, national and European cohorts, and (ii) from the functional genomics approaches made available by the Biogenouest health Genomic platform (uMS 3480 Biosit ). We use Dna microarrays to identify genes losses and gains and to measure the Dna methylome that we subsequently correlate with transcriptome data. We complete our study by meta-analyses using publicly available omic data. We are also developing nGS technology (next Generation Sequencing) to identify rare genetic variants of susceptibility for cancers with inappropriate occurring (young age; exome approach). ultimately, we use in vitro or in vivo models to validate and decipher the molecular mechanisms involving some of the genes identified through the genomic discovery process.

SELECTED REFERENCES

> Research Center; Town: Institut de Génétique et Développement de Rennes (IGDR) Rennes

> Administrative affiliations: CnRS uMR 6290

> Tech Transfer Office: Ouest Valorisation www.ouest-valorisation.fr

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Jean MOSSER


Targeted populationhigh Grade Glioblastoma (grade IV astrocytoma).• Prognosis, response to treatment• Recruitment in clinical trial• Evaluation tool for new treatment of GBM

Unique selling points• Improvement in patient molecular stratification (nomogram)• higher prediction/pronostication compared to MGMT test

Intellectual propertyPrognosis marker • uS patent application n°14/006023nGS technology• Dry part - Software filed in aPP on 2014• Wet part - Know-how on FFPE samples preparation

Tools• Cohort of 399 GBMs homogeneously treated• algorithm included 7 parameters (age, KPS, Surgery, IDh1, MGMT, DGKI, TERTp)• Pyrosequencing technology


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project / expertise

epdruGBDevelopment of an «epidrug» able to sensitize GBM patients to standard treat-ment (ST)

Jean MOSSER


69

Transcription and splicing in the context of chromatin

Grants • Carnot initiative GLOBaL CaRE

Major publications over the past four years• Shigella flexneri targets the hP1γ subcode through the phosphothreo-nine lyase OspF. harouz h, Rachez C, Meijer BM, Marteyn B, Donnadieu F, Cammas F, Muchardt C, Sansonetti P, arbibe L. EMBO J. 2014 nov 18;33(22):2606-22• DYRK1a phoshorylates histone h3 to differentially regulate the bin-ding of hP1 isoforms and antagonize hP1-mediated transcriptional re-pression. Jang SM, azebi S, Soubigou G, Muchardt C. EMBO Rep. 2014 Jun;15(6):686-94• Citrullination of histone h3 interferes with hP1-mediated transcriptional repression. Sharma P, azebi S, England P, Christensen T, Møller-Larsen a, Petersen T, Batsché E, Muchardt C. PLoS Genet. 2012 Sep;8(9):e1002934

Christian MUCHARDT

Keywords:

• Transcription

• Chromatin

• Silencing

• Inflammation


SynopsisManage inflammation in breast cancer with small molecules favouring chromatin-dependent gene silencing.

AbstractIn breast cancer, the invasion front forms an inflammatory microenvironment affecting cell identity within the stroma and favouring epithelial to mesenchymal transition at the edge of the tumour. a range of pro-inflammatory cytokines involved in this process are regulated by hP1 proteins, a family of chromatin-dependent transcriptional silencers. The lab is exploring pathways allowing to reinforce the silencing activity of these proteins with small molecules.

SELECTED REFERENCES

> Research Center; Town: Institut Pasteur, Paris

> Administrative affiliations: Institut Pasteur - uRa 2578

> Tech Transfer Office: Institut Pasteur www.pasteur.fr

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Christian MUCHARDT


Objectives:• Control inflammation in the context of cancer by enhancing the efficiency of chromatin-

dependent transcriptional silencing

Tools:• Small molecules enhancing transcriptional silencing at pro-inflammatory cytokine

promoters

Unique selling points:• a novel avenue to the management of inflammation• a druggable regulator of inducible genes


71

project / expertise

Results• A series of proinflammatory cytokines use HP1 proteins to remain « off » in the absence of pro-in-flammatory stimulation.• This mechanism of repression is highly regulated by enzymes writing epigenetic marks on histone H3 (including PADI4).

Perspectives• Small molecules able to dampen the activity of these enzymes have the potential to reduce inflam-mation.

A druggable regulator of cytokine genes


Christian MUCHARDT

72

Epigenetics and Cancer

Grants • La Fondation pour la Recherche Médicale (FRM) amorçage de jeunes équipes 2013, 283000EuR (awarded november 25th 2013) ; Inserm CR1 new recruit funding (50K per year, 2015 and 2016).

Major publications over the past four years• Sedic M, Skibinski a, Brown n, Gallardo M, Mulligan P, Martinez P, Keller PJ, Glover E, Richardson aL, Cowan J, Toland aE, Ravichandran K, Rieth-man h, naber SP, naar aM, Blasco Ma, hinds PW, Kuperwasser C. (2015). haploinsufficiency for BRCa1 leads to cell-type-specific genomic instabi-lity and premature senescence. nature Communications, 6, article number: 7505.• Toiber D, Erdel F, Silberman DM, Zhong L, Mulligan P, Sebastian C, Cosen-tino C, Martinez-Pastor B, Giacosa1, agustina D’urso S, naar aM, Rippe K, and Mostoslavsky R. (2013). SIRT6 recruits SnF2h to sites of Dna breaks, modulating genomic stability through chromatin remodeling. Molecular Cell. aug 22;51(4):454-68; Epub 2013 Jul 31.

• Mulligan P, Yang F, Di Stefano L, Ji JY, Ouyang J, nishikawa JL, Wang Q, Kulkarni M, najafi-Shoushtari Sn, Mostoslavsky R, Gygi SP, Gill G, Dyson nJ and näär aM. (2011). a SIRT1-LSD1 co-repressor complex regu-lates notch target gene expression and development. Molecular Cell. Jun 10;42(5):689-99. Epub 2011 May 19. • Di Stefano L, Walker Ja, Burgio G, Corona D, Mulligan P, näär aM and Dyson nJ. (2011). Functional antagonism between histone h3K4 demethy-lases in vivo. Genes and Development. Jan 1;25(1):17-28.

Peter MULLIGAN

Keywords:

• Epigenetics

• Chromatin Regulation

• Molecular Biology

• Cancer Cell Biology


SynopsisWe purify and characterize chromatin-regulatory complexes containing candidate oncoproteins or tumor suppressors to understand epigenetic mechanisms in cancer.

AbstractThe naD+ dependent histone deacetylase SIRT1 promotes chromatin compaction via mechanisms that include deacetylation of histone h4 lysine 16 (h4K16), acetylation of which is sufficient to prevent higher order chromatin compaction. SIRT1 also regulates a broad spectrum of cellular and cancer processes, including genome stability, energy metabolism, apoptosis, cell growth, angiogenesis and metastasis. In order to understand how this single factor regulates such diverse processes in normal and cancer cells we use biochemical and molecular/cell biology approaches to identify and validate novel SIRT1-interactors that might link it to specific gene loci or cellular pathways. The potential of SIRT1 to act as a sensor of abnormal cancer cell metabolism, an emerging cancer hallmark, is another research interest. Collectively, these studies will guide preclinical evaluation of SIRT1 as a drug target and development of new epigenetic therapies for cancer.

SELECTED REFERENCES

> Research Center; Town: Centre de Recherche en Cancérologie de Lyon (CRCL), Lyon

> Administrative affiliations: Inserm uMR 1052 - CnRS 5286 - Centre Léon Bérard - université Claude-Bernard Lyon 1

> Tech Transfer Office: Pulsalys www.pulsalys.fr

73

Peter MULLIGAN


Objectives:• Identify epigenetic regulators with potential use as cancer drug targets and/or

biomarkers • Gain mechanistic insights into gene/genome regulation and cancer hallmark/pathway

regulation by such factors• Develop therapeutic approaches for cancer based on basic research findings

Tools:• Biochemical purification and analysis of proteins and complexes• Molecular/Cell biology assays for functional and mechanistic analysis of candidate

epigenetic regulators of cancer• Shared institutional core facilities for murine cancer models and high throughput drug

testing/development

Unique selling points:• Strong track record in both epigenetics and cancer fields from postdoctoral fellowship

(author on first papers describing LSD1 as histone demethylase, and CDYL as candidate tumor suppressor, for instance)

• Expertise in analysis of histone deacetylase SIRT1• Team is ideally positioned for cancer research: based in the Cancer Research Center of

Lyon; clinical partnerships with Centre Leon Berard cancer hospital and hospices Civils de Lyon.


74

Peter MULLIGAN

project / expertise

Results• Immunopurification of epitope-tagged SIRT1 and mass spectrometry identified po-lypeptides. Shown is A silver-stained SDS-PAGE gel of the purification. (partially pu-blished in Mulligan P. et al., Mol. Cell. 2011)

Perspectives• Identification of novel SIRT1-interacting proteins was used to show for the first time that SIRT1 regulates the Notch cellular and cancer signaling Pathway, and interacts with histone demethylase LSD1 (Mulligan P. et al., 2011). Ongoing work is aimed at Characterizing other, unpublished, complexes identified.

Results• SIRT1 expression is lower in mammary tissues of women carrying somatic BRCA1 mutations. (a) Images of IHC staining and quantification of SIRT1 levels in epithelial cells from WT (n=10) and BRCA1mut/+ (n=10) breast tissues. Allred score methodology was used to measure SIRT1 antibody staining. Student’s two-tailed t-test was used to calculate P value. (*) indicates P value within the 0.05 level of significance. (Published in Sedic M, Skibinski A, Brown N, Gallardo M, Mulli-gan P, et al., Nature Comm., 2015)

Perspectives• Deregulation of SIRT1 expression in specific cancer contexts suggests it might be a clinically useful biomarker in cancer. Current work in our la-boratory is aimed at establishing if SIRT1 downre-gulation in BRCA1 mutant allele carriers might be a mechanistic event in tumor initiation or malignant progression. These studies will establish if SIRT1 downregulation is a mechanistic biomarker for breast cancer risk.

Purification and Characterization of Novel SIRT1–interacting proteins

SIRT1 expression is deregulated in several cancer contexts including familialBRCA1 mutant breast cancer


75

Molecular Assemblies and genome Integrity

Grants • anR Chapinhib• La ligue contre le cancer• Le Canceropole

Major publications over the past four years• Jiao, Y., et al. (2012). Surprising complexity of the asf1 histone chaperone-Rad53 kinase interaction. Proc natl acad Sci u S a, Feb 21;109(8):2866-71.• abascal F, et al. (2013) Subfunctionalization via adaptive evolution in-fluenced by genomic context: the case of histone chaperones aSF1a and aSF1b, Mol Biol Evol. aug;30(8):1853-66 • Pietrobon V, et al. (2014) The Chromatin assembly Factor 1 Promotes Rad51-Dependent Template Switches at Replication Forks by Counterac-ting D-Loop Disassembly by the RecQ-Type helicase Rqh1, PLoS Biol.

2014 Oct 14;12(10):e1001968• andreani J, et al. (2014) Evolution of protein interactions: from interac-tomes to interfaces. arch Biochem Biophys. 554:65-75. • Richet n, et al. (2015) Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with aSF1 at the replication fork, nucleic acids Research 18;43(3):1905-17

Patents • 1 patent (WO 2013/072636 al)

Keywords:

• histone chaperone

• Replication

• Dna damage signaling

• Evolution

• Epigenetic

SynopsisFocused on the complexes involved in maintaining genome integrity, we characterize the structure of the complexes, develop new methods for the prediction of their conformations and design inhibitory compounds capable of disrupting these interactions.

AbstractIn all leaving systems, genotoxic stresses activate specific interactions networks to protect the genome and the epigenome. Our team is particularly interested in analyzing the conservation/plasticity of these networks and to explore how far this information can be used to predict protein-protein interactions mode or to design molecules that specifically block one of these interactions. We tackle these issues combining both, experimental and computational approaches. We focus our experimental research on a special class of protein-protein interaction regulators called assembly chaperones. We are interested in unraveling how these assembly chaperones promote correct interactions between partners, in the proper cell context, and at the right moment. We concentrate on histones chaperones that play a central role in regulating Dna accessibility to replication, transcription, epigenetic modification and repair machineries, and more recently on proteasome chaperones.

SELECTED REFERENCES

> Research Center; Town: Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette

> Administrative affiliations: CEa, CnRS uMR 9198 université Paris-Sud

> Tech Transfer Office: CEa www.cea.fr

Françoise OCHSENBEIN


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Objectives:• Our objectives is to characterize the structure of the complexes, develop new methods for the prediction of their conformations and design inhibitory compounds capable of disrupting these interactions. We focused our researches on complexes involved in maintaining genome and epigenome integrity.

Tools:• Protein expression and purification for structural biology• nuclear Magnetic resonance• X ray crystallography• Microcalorimetry• Protein-protein interaction• Sequence analysis, coevolution analysis• Protein evolution• in silico docking• Protein/peptide/peptidomimetics in silico design• Cellular biology

Unique selling points:• Our team has 20 years expertize in structural biology, protein design and sequence-structure relation prediction• Since the past decade, we have focused our researches in unravelling the role of molecular chaperones dedicated to complex assemblies, and more particularly to histone chaperones. • In molecular docking we developed new in silico tools incorporating protein coevolution for the prediction of protein-protein and protein-peptide interaction mode.



77

project / expertise

Results• Design of specific inhibitor of a histone cha-perone and its applications in breast cancer therapy

Perspectives• Extend the approach for other applications to new challenging new target in the epigenetic area

CHAPTAR



78

Genetic and Epigenetic aspects of primary bone tumors development and bone mineralization

Grants • Susan Komen• Regional grant for Epigenetic network

Major publications over the past four years• Lamoureux F, Baud’huin M, Rodriguez Calleja L, Jacques C, Berreur M, Rédini F, Lecanda F, Bradner JE, heymann D, Ory B. Selective inhibition of BET bromodomain epigenetic signalling interferes with the bone-associa-ted tumour vicious cycle. nat Commun. 2014 Mar 19.• Lamoureux F, Baud’huin M, Ory B, Guiho R, Zoubeidi a, Gleave M, hey-mann D, Rédini F. Clusterin inhibition using OGX-011 synergistically en-hances zoledronic acid activity in osteosarcoma.. Oncotarget. 2014 aug 4.

• Ramsey MR, Wilson C, Ory B, Rothenberg M, Faquin W, Mills aa and Elli-sen LW. FGFR2 signaling underlies p63 oncogenic function in squamous cell carcinoma. J Clin Invest. 2013 July 8.• Ory B, Ramsey MR, Wilson C, Vadysirisack DD, Rothenberg MS, Rocco JW, Ellisen LW.• a microRna-dependent program controls p53-independent survival and chemosensitivity in human and murine squamous cell carcinoma. J Clin Invest (IF:16.59). 2011; 121(2):809–820.• Ory B and Ellisen LW. a microRna-dependent circuit controls p63/p73 homeostasis, cell survival and chemosensitivity: p53 family cross-talk meets therapeutic opportunity. Oncotarget. 2011; 2(3):259-64.

Benjamin ORY

> Research Center; Town: nantes university Medical School, nantes

> Administrative affiliations: InSERM u957, nantes university Medical School

> Tech Transfer Office: SaTT Ouest Valorisation www.ouest-valorisation.fr

Keywords:

• microRnas

• Bromodomain

• hSP

• Primary bone tumors

• Bone mineralization


SynopsisOur team‘s goal is to uncover the genetic and epigenetic mechanisms underlying the primary bone tumour development and its associated microenvironment process, the bone mineralisation regulation.

AbstractOur team focus in particular on cellular stress endured by bone tumour cells as well as the cells belonging to their direct microenvironment. To reach these goals, we set up a multidisciplinary team composed by researchers, clinicians, engineers and technicians specialized in the specific aspects of this project. we propose innovative approaches looking at those physiological and pathological aspects through the prism of genetic and epigenetic. With a focus on cellular stress, our team plans to understand both critical primary bone tumour development steps and pathological calcified tissue remodeling.We make the bet that using different biological contexts and models as diverse as vascular calcifications, genetic associated bone disorders and primary bone tumours will lead to identify new fundamental pathways governing bone-remodeling process both in physiological and pathological context.

SELECTED REFERENCES

79


Objectives:• how does the genome integrate intrinsic and environmental signals?• Epigenetic regulation of gene expression in primary bone tumors and bone mineralization process• Identify new genes implicated in bone mineralization regulation

Tools:• molecular biology• in vivo models of primary bone tumors, osteoporosis, normal bone physiology• human samples

Unique selling points:• expertise in genetic and epigenetic associated to in vivo model• access to clinical samples of primary bone tumors, ectopic calcification and genetic associated bone disorders

Benjamin ORY


80

project / expertise

BET inhibition represses Osteosarcoma development

Perspectives

Role of the BET bromodomain proteins in primary bone tumors

Benjamin ORY


81

project / expertise

ΔNp63α promotes TGFβ-induced metastasis by silencing a microRNA network restraining wound healing

Perspectives

Role of the microRNAs in Primary Bone Tumor Metastatic Dissemination

Benjamin ORY


82

B cell diseases and epigenetics

Grants • Cancéropôle Grand Ouest, Reseau épigénétique• association Laurette Fugain• Ligue contre le cancer

Major publications over the past four years• Konsta OD in JaI (2016), Font Immunol (2015), Front Genet (2014), eLS (2015)• Le Dantec C in Viruses (2015)• Thabet Y in JaI (2013, 2012)• Garaud S in J Immunol (2012, 2010, 2009)• Mankai a in Cancer Res (2008)

Patents • Processes for the diagnosis, prognosis and monitoring of the progression of Chronic Lymphoid Leukaemia (CLL) and/or of Systemic Lupus Erythe-matosus (SLE) using membrane STIM 1, EP15156694,0

Yves RENAUDINEAU

> Research Center; Town: Laboratory of Immunology and Immunotherapy, ChRu Brest

> Administrative affiliations: Inserm ESPRI, ERI29/Ea2216

> Tech Transfer Office: SaTT Ouest Valorisation, www.ouest-valorisation.fr

Keywords:

• B cell diseases (cancer, autoimmunity, transplantation)

• Dna methylation/hydroxymethylation

• human endogenous retroviruses

Pu-Ph, PharmD, PhD.Contact: [email protected]

Synopsisunderstanding the role of Dna methylation/hydroxymethylation in B cells diseases

AbstractStarting from the observation that Dna demethylation affects human endogenous retrovirus (hERV) expression in B cells from patients with leukaemia (CLL) and autoimmune diseases (lupus, Sjögren’s syndrome) we further demonstrated (1) the major consequences of hERV over-expression in B cells, (2) the pathways regulating Dna methylation in B cells, (3) the reversibility of the process, and (4) the epigenetic cross-talk between B cells and epithelial cells.Our research projects combine fundamental tasks (mechanisms controlling Dna methylation/hydroxymethylation in B cells and its reversibility), clinical tasks (based on the development of nGS using (hydroxyl)MethylChIPSeq to characterize new biomarkers), and therapeutical tasks (drug candidate discovery).

SELECTED REFERENCES

83

Yves RENAUDINEAU


Objectives:• Study the impact of Dna methylation/hydroxymethylation in B cell diseases• Propose new biomarkers and therapeutic approaches• Improve existing immunotherapy protocols

Tools:• Epigenetic plateform (nGS, ChIP…)• Flow cytometry plateform• Epigenetic bioinformatic tools (CpG array, MethylChIPSeq…)• RTqPCR, Western blot, transfection• Biobank collection with clinical annotation (CLL, autoimmunity…)

Unique selling points:• Biobank (CLL, autoimmunity…)• Expertise in B cell diseases• Expertise in immunotherapy• Expertise in human endogenous retroviruses• Large panel of tools including bioinformatic tools to study Dna methylation/hydroxymethylation


84

Yves RENAUDINEAU


project / expertise

Results• DNA demethylation/hydroxymethyla-tion characterize CLL B cells• Modifications associated with di-sease activity• Modifications associated with thera-peutic response• Reversible process

Perspectives• Characterize new biomarkers for disease activity and therapeutic res-ponse• Develop new epigenetic drugs used alone or in combination with existing drugs

Results• Minor salivary gland DNA de-methylation is associated with B cell infiltration• Reversible process under anti-B cell therapy

Perspectives• Characterize new biomarkers for disease activity and therapeu-tic response• Develop new epigenetic drugs used alone or in combination with existing drugs

DNA demethylation/hydroxymethylation in B cells from chronic lymphocytic leukemia

Infiltrating B cells and tumoral B cells control epithelial DNA demethylation/hydroxymethylation in MALT lymphoma and Sjögren’s syndrome

Figure 1: B cell lymphoproliferation characterize chronic lymphocytic leukemia (a) as well as global Dna demethylation (5mC) as determi-ned by FaCS (B) and after bisulfite sequencing at gene locus (C).

Figure 2: The majority of salivary gland MaLT lymphoma are though to develop from longstan-ding Sjögren’s syndrome (SS) and such evolution is associated with important modifications of Dna methylation in epithelial cells affecting salivary gland functions. Interstingly, such mecha-nism is reversible (after treatment with rituximab) and related to lymphocyte infiltration.

85

Non-coding RNAs in development and disease

Grants • Programme avenir 2008-2011• ERC Starting Grant 2009-2014 • Epigenesys network of Excellence in Epigenetics and Systems Biology (FP7-RISE1) 2012-2015• anR Générique 2014-2018

Major publications over the past four years• Vallot* C., Ouimette* JF., Makhlouf M., Féraud O., Pontis J. Côme J., Martinat C., Bennaceur-Griscelli a., Lalande M. and Rougeulle C. (2015) Erosion of X chromosome inactivation in human pluripotent cells initiates with XaCT coating and depends on a specific heterochromatin landscape. Cell Stem Cell. 16: 533-46.• Chen h., aksoy I., Gonnot F., Osteil P., aubry M., hamela C., Rognard C., ho-chard a., Voisin S., Fontaine E., Mure M., afanassieff M., Cleroux E., Guibert S., Chen J., Vallot C., acloque h., Genthon C., Donnadieu C., De Vos J., Sanla-ville D., Guérin JF., Weber M., Stanton LW., Rougeulle C., Pain B., Bourillot PY., and Savatier P. (2015) Reinforcement of STaT3 activity reprograms human embryonic stem cells to naïve-like pluripotency. nature Com. 6: 7095.

• Makhlouf* M., Ouimette* JF., Oldfield* a., navarro P., neuillet D. and Rou-geulle C. (2014) a prominent and conserved role for YY1 in Xist transcrip-tional activation. nature Com. 5, 4878.• Vallot C., huret C., Lesecque Y., Resch a., Oudrhiri n., Bennaceur-Griscelli a., Duret L. and Rougeulle C. (2013) XaCT, a long non-coding transcript coating the active X chromosome in human pluripotent cells. nature Genet. 45:239-41. Epub Jan 20. • Chureau C., Chantalat S., Romito a., Galvani a., Duret L., avner P. and Rougeulle C. (2011) Ftx is a non-coding Rna which affects Xist expression and chromatin structure within the X-inactivation center region. hum. Mol. Genet., 20: 705-718.

Patents • Rogner u., Spyropoulos D., Rougeulle C. and avner, P. (2000) Identification of neural defects associated with the nucleosomal assembly Protein 1l2 Gene. uS Patent n°202 111.

Claire ROUGEULLE

> Research Center; Town: Epigénétique et Destin Cellulaire (EDC), Paris

> Administrative affiliations: university Paris Diderot- CnRS; uMR7216

> Tech Transfer Office: Idfinnov www.idfinnov.com

Keywords:

• non-coding Rnas

• Epigenetics

• X-chromosome inactivation

• Stem cells

PhD.Contact: [email protected]

SynopsisWe investigate the function of non-coding Rnas in controlling gene expression programs in stem cells, differentiation and development and their involvement in pathological contexts (cancer).

AbstractLong non-coding Rnas (lncRnas) play central roles in the epigenetic control of gene expression and they contribute to cellular identity and cell fate. LncRnas are also frequently found associated with diseases, in particular cancers. Our main question is to understand how lncRnas regulate gene expression and contribute to cellular identities, in physiological and pathological contexts. Our projects are also devoted to multi-species analyses to investigate the contribution of lncRnas to the plasticity of epigenetic regulation in evolution. We study in particular X-chromosome inactivation (XCI) as one of the most striking example of developmentally regulated epigenetic processes involving lncRnas. XCI is tightly linked to cellular state and instability of XCI is observed in various poorly differentiated contexts including human pluripotent stem cells and in cancers.

SELECTED REFERENCES

86


Claire ROUGEULLE


Objectives:• To characterize the molecular network controlling X-chromosome inactivation in mouse and human and to determine the contribution of long non-coding Rnas (lncRnas) to species-specific variations • To address the link between lncRna, pluripotency, differentiation and development• To investigate on a larger scale the contribution of lncRnas and epigenetic alteration to pathological states (cancer)

Tools:• Mouse and human pluripotent stem cells coupled to animal models• State of the art genome engineering• Transcriptomic and epigenomic approaches (Rna-seq and ChIP-seq)• Single cell imaging

Unique selling points:• Multispecies analysis of long non-coding Rnas and epigenetic regulations• Development of a unique approach to visualize chromosome transcription territories• Combined expertise in mouse and human pluripotent stem cells • Genome engineering in human pluripotent stem cells • animal models for long non-coding Rnas • Investigation of epigenomic and transcriptomic alterations in pathologies (autism, cancer) through collaborations

87


Claire ROUGEULLE

project / expertise

Results• Identification of Ftx, a conserved X-linked lncRNA, which produces several nuclear isoforms and contains intronic miRNAs deregulated in cancer• Ftx expression peaks at the onset of X-inactivation (A)• Impaired X-inactivation in Ftx mutant cells, as moni-tored by counting the number of cells with Xist RNA cloud (B)• Impaired differentiation of Ftx mutant cells (C)

Perspectives• We are exploring the function of Ftx ex vivo (ES cells) and in vivo (KO mice)• We are studying the function of the FTX human or-tholog• We are investigation the putative contribution of Ftx and of the embedded miRNAs to cancer

Results• Characterization of a pluripotent-specific epigeno-mic landscape of the inactive X chromosome (ChIP-seq, A)• Identification of XACT, a human-specific long non-coding RNA (RNA-seq, B)• XACT coats the active X chromosome in human pluripotent stem cells (PSC) (RNA-FISH, C)• XACT expression is restricted to pluripotent cells and correlates with unstable X-inactivation (RNA-FISH, D)

Perspectives• We are addressing the function of XACT and the mechanisms by which it coats active X chromo-somes • We are aslo exploring the contribution of XACT to unstable X-inactivation in cancer

Contribution of the long non-coding RNA Ftx to X-inactivation and cell differentiation

Regulation of X chromosome inactivation in humans

88

Laboratory for Epigenetics & Environment

Grants • InCa: Translational Cancer Research Mechanisms of tissue invasion in neuroendocrine tumors: towards a concept of epithelio-neural transition ? (2015-2018).• aviesan/InSERM: Molecular dissection of epigenetic mechanisms of MEn1/MLL and MEn1//PcG/YY1 complexes involved in the tumorige-nesis of islet cells (DEMEnIS)(2014-2017).• aviesan/InSERM: EpiChem-Seq: Chemical scanning of Dna methylation in leukemia progression and maintenance, (2014-2017).• Eu FP7 REaDna: Revolutionary approaches for Dna analysis (2009-2012).• Eu FP7 CaGEKID: Cancer genomics of the kidney (2010-2014).

Major publications over the past four years• Myrtue nielsen, h., how-Kit, a., Guerin, C., Castinetti, F., Moen Vollan, h. K., De Micco, C., Daunay, a., Taieb, D., Van Loo, P., Besse, C., Kristensen, V.n. hansen, L.L., Barlier, a., Sebag, F., and J. Tost (2015) Copy number varia-tions alter methylation and parallel IGF2 overexpression in adrenal tumors, Endocrine Rel. Cancer, 22, 953-967.• how Kit, a., Dejeux, E., Dousset, B., Renault, V., Baudry, M., Terris, B. and J. Tost (2015) Dna methylation profiles distinguish different subtypes of gastroenteropancreatic neuroendocrine tumors. Epigenomics, in press.

• Klajic, J., Busato, F., Edvardsen, h., Touleimat, n., Fleischer, T., Bukholm, I. R., Borresen-Dale a.-L., Lonning, P. E., Tost, J., V. n. Kristensen (2014) Dna Methylation status of key cell cycle regulators such as CDKna2/p16 and CCna1 correlates with treatment response to doxorubicin and 5-fluorou-racil in locally advanced breast tumors. Clin Cancer Res., 20, 6357-6366.• Scelo, G., Riazalhosseini, Y., Greger, L., Letourneau, L., …Tost, J., Banks, R.E., Brazma, a.and G. M. Lathrop GM. (2014) Variation in genomic landscape of clear cell renal cell carcinoma across Europe. nat. Commun., 5, 5135.• Fleischer, T., Frigessi, a., Johnson, K.C., Edvardsen, h., Touleimat, n., Klajic, J., Riis, M., haakensen, V.D., Wärnberg, F., naume, B., helland, a., Børre-sen-Dale, a.-L., Tost, J., Christensen, B.C. and V.n. Kristensen (2014) Ge-nome-wide Dna methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis. Genome Biology, 15, 435.• Fleischer, T., Edvardsen, h., Solvang, h.K., Daviaud, C., naume, B., Børre-sen-Dale, a.-L., Kristensen, V., and J. Tost (2014) Integrated analysis of high-resolution Dna methylation profiles, gene expression, germline geno-types and clinical end points in breast cancer patients. Int. J. Cancer, 134, 2615-2625.• Touleimat, n., and J. Tost (2012) a complete pipeline for Infinium Methy-lation 450K BeadChip data processing using subset quantile normalization for accurate Dna methylation estimation, Epigenomics, 4, 325-341.

Jörg TOST

> Research Center; Town: CEa - Institut de Génomique, Centre national de Génotypage, Evry

> Administrative affiliations: CEa

> Tech Transfer Office: DSV/CEa, Partenariats industriels et valorisation

Keywords:

• EPIGEnOMICS

• Dna METhYLaTIOn

• BIOInFORMaTICS

• DaTa InTEGRaTIOn

PhD, head Laboratory for Epigenetics & Environment Contact: [email protected] - [email protected]

SynopsisThe Laboratory for Epigenetics & Environment has set-up a high-throughput environment for the accurate and comprehensive analysis of the multilayered epigenome using state-of-the-art technologies and the associated bioinformatic and data integration tools, that is unique in France.

AbstractThe laboratory works on the development and application of technologies to analyze Dna methylation and other epigenetic modifications including histone modifications, chromatin accessibility as well as small and long non-coding Rnas. Technologies have been implemented for both investigating target loci at high-resolution and comprehensive genome-wide analyses. The second research area is the development of bioinformatic and biostatistic tools for the processing of such data. The main focus of the Epigenetics group has been the analysis of Dna methylation patterns implicated in tumorigenesis more recently the alteration of the epigenetic profiles in function of environmental exposure. The laboratory has authored or co-authored more than 100 publications in the last ten years. In the field of cancer epigenetics the research programs address particularly the integrated analysis of epigenetic modifications in breast and renal cancer (Eu funded ICGC project), melanoma and neuroendocrine tumors.

SELECTED REFERENCES

89

Jörg TOST


Objectives:• analyze comprehensively the different layers of the epigenome using state-of-the-art high-throughput technologies • Develop and implement the bioinformatic and biostatistical tools to analyze the generated data • Develop molecular signatures for the prediction and monitoring of the response to treatment, assessment of the metastatic potential and other parameters of clinical interest

Tools:• high-throughput technologies for Dna methylation analysis (nGS, Beadarrays, Pyrosequencing)• Chromatin analysis (ChIP-seq/aTaC-seq)• Small Rna and long (non-coding) Rna analysis (Rna-seq, smallRna-seq) • Bioinfomatics/Biostatistics/Data integration

Unique selling points:• Large variety of of state-of-the art technologies and protocols (nGS, microarray) implemented to comprehensively analyze the different layers of the epigenome• Standardized data processing with comprehensive quality control tools and visual exploratory analyses• Quantitative high-resolution technologies for validation and replication availableTechnological and bioinformatic expertise • Biostatistical algorithms for e.g. determining epigenetic small signatures for the prediction of response based on epigenetic markers• Data integration of the analyzed epigenetic, genetic and transcriptomic alterations with public databases


90

project / expertise

Results• Functionally relevant mutations were identified in active regu-latory elements of ccRCC. The use of whole-genome sequen-cing data of 100 patients affected by ccRCC and epigenetic data (ChIP-seq and ATAC-seq) from renal cancer cell lines and normal renal tissue lines enabled the identification of mutation islands located in those regulatory elements. Among those, nu-merous mutated promoters have previously been shown to be involved in urogenital cancers. Moreover, the use of RNA-seq data highlighted the association between some mutation islands and gene expression changes.. This pioneer work in the inte-gration of genetic and epigenetic data consists describes for the first time non-coding mutations located on active regulatory elements identified on a cell type relevant to the study.

Perspectives• The decrease of sequencing costs will enable to obtain whole genome coverage of cancer-related mutations in larger cohorts of ccRCC patients facilitating the identification of recurrent mutations in gene regulatory elements identified in disease relevant cell types.

Results• There is currently great interest in mutation detection for the genotype-driven personalized treatment of cancer patients. However, the response of each patient is variable and molecu-lar signatures to predict the response prior to start of the treat-ment would allow to select the most efficient and best-tolerated treatment of each patient. We used the DNA methylation profile of 450K CpGs throughout the genome to develop a predictive signature for the response to vemurafenib in BRAF mutated metastatic melanoma patients. A suite of prediction algorithms based on mutational information criteria and normalized graph cut algorithms was used to reduce the dimensions of the data set while maximizing the recognition ratio of desired signals and at the same time minimize the classification error for recognition tasks. A signature of 9 CpGs was predictive for the non-res-ponse to the investigated treatment

Perspectives• The developed methylation signature is currently under investigation in a replication cohort. With the adaption of the treatment scheme in the clinics the signatures will be continuously revised in function of the commonly used treatment regimens.

Functional annotation of non-coding mutations using high-throughput epigenomic data in ccRCC

DNA methylation based signatures to predict treatment outcome for personalized cancer therapy

Jörg TOST


91

Control of Gene Expression

Grants • ITMO Cancer • FRM Equipe

Major publications over the past four years• P. Briata, W.J. Lin, M. Giovarelli, M. Pasero, C.F. Chou, M. Trabucchi, M.G. Rosenfeld, C.Y. Chen, R. Gherzi (2012). PI3K/aKT signaling determines a dynamic switch between distinct KSRP functions favoring skeletal myoge-nesis. Cell Death & Differ Mar;19(3):478-87.• E. Repetto, P. Briata, n. Kuziner, B.D. harfe, M.T. McManus, R. Gherzi, M.G. Rosenfeld, M. Trabucchi (2012) Let-7b/c enhance the stability of a tissue-specific mRna during mammalian organogenesis as part of a feedback loop involving KSRP. Plos Genetics Jul;8(7): e1002823.• Q. hu, B. Tanasa*, M. Trabucchi*, W. Li, J. Zhang, K.a. Ohgi, D.W. Rose, C.K. Glass, M.G. Rosenfeld (2012) DICER- and aGO3-dependent generation of retinoic acid-induced DR2 alu Rnas regulates human stem cell prolifera-tion. nature structural & molecular biology 19:1168-1175.• S. Bottini, a. Bernini, M. De Chiara, D. Garlaschelli, O. Spiga, M. Dioguardi, E. Vannuccini, a. Tramontano, n. niccolai (2013) ProCoCoa: a quantitative approach for analyzing protein core composition. Computational biology and chemistry 43:29-34.

• S. Saccani and M. Trabucchi (2015) Regulation of stimulus-inducible gene expression in myeloid cells. Seminars in Immunology. (Review)• E. Repetto, L. Lichtenstein, Z. hizir, n. Tekaya, M. Benahmed, J.B. Ruida-vets, L.E. Zaragosi, R. Ruimy, J. Ferrières, P. Barbry, L.O. Martinez, M. Tra-bucchi. (2015) RnY-derived small Rnas as a signature of Coronary artery Disease. BMC Medicine (accepted).

Patents • n° EP 13 306 439.4 –Dosage of RnY-derived small Rnas as a novel biomarkers for atherosclerosis related disorder, the coronary artery disease (2013).

Michele TRABUCCHI

> Research Center; Town: Centre Méditerranéen de Médecine Moléculaire (C3M), nice

> Administrative affiliations: Inserm u1065, université nice-Sophia-antipolis


Keywords:

• Gene expression control

• noncoding Rnas

• Ribonucleoprotein complex

• Protein/Rna interaction


SynopsisIntegrated point of view of gene expression from molecular, biochemical, bioinformatics approaches and validation in vivo or in patient cohorts.

AbstractSmall Rnas are crucial components of gene expression regulation and play a role in many biological processes including development and tissue homeostasis, and pathogenesis. Over the past years, we have used high-throughput transcriptomic and proteomic analyses, coupled with in vivo studies in animal models and patient cohorts, documenting the importance of the generation of novel classes of small Rnas that operate through a very complex network of interactions to finely control gene expression programs in physiopathological events. a proteomic approach has been used to identify complexes involved in biogenesis and targeting mechanisms of regulatory small Rnas, and a deep sequencing one to determine the regulation of direct target Rnas. In collaboration with clinical-oriented teams, we are investigating the implication of the discovered mechanisms in pathological events.

SELECTED REFERENCES

92

Michele TRABUCCHI


Objectives:• how do noncoding Rnas regulate gene expression (biochemical mechanisms in both immune and tumoral cell models)?• What is the function of noncoding Rnas in the pathogenesis of inflammatory diseases sensu lato?• how would environmental cues dysregulate expression and function of noncoding Rnas?

Tools:• mass-spectrometry analyses to investigate the function and the dynamism of ribonucleoprotein complexes associated to noncoding Rnas• high-throughput sequencing approaches to study expression regulation of noncoding Rnas and target-Rnas of Rna binding proteins (such as Gro-seq and CLIP-seq)• Transgenic animal models to investigate the function of noncoding Rnas in the pathogenesis of human disorders.

Unique selling points:• Strong background and expertise in Rna biology and gene expression control fields, recognized by successfully developing a series of important, complex stories to the point that they survived scrutiny at the most rigorous journals, including nature, nature Struct & Mol Biol, Plos Genetics, and BMC Medicine• From molecular to clinical study: integrated point of view of gene expression from molecular, biochemical, bioinformatics, in cells, ex vivo, in vivo, to patient cohorts


93

Michele TRABUCCHI

project / expertise

Results• Our data published in Nature (2009) elevated the terminal loop of miRNA precursors as important element to harbor RNA-binding proteins to finely modulate miRNA processing in a cell type specific fashion,

Perspectives• Basic research on novel Mecha-nisms of gene Expression control mediated by miRNAs

Results• KSRP-dependent expre-ssion of miR-155 regulate the inflam-matory respo-nse in activated macro-phages

Perspectives• Studying the pathological role of miR-155 and its mode of ac-tion in a mouse model forbreast cancer (MMTV-PyVT mouse line)

Subject 1

Subject 2


94

Epigenetics and epithelial stemness, differentiation and carcinogenesis

Grants • Equipe labellisée LIGuE 2007-2013 : MuC4-ErbB2 and pancreatic can-cer chemoresistance • anR 2016-2018: DRuG_MuC4, SIRIC OnCOLille, LnCC, Région nPdC.

Major publications over the past four years• Skrypek n, Vasseur R, Vincent a, Duchêne B, Van Seuningen I, Jonckheere n. The oncogenic receptor ErbB2 modulates gemcitabine and irinotecan/Sn-38 chemoresistance of human pancreatic cancer cells via hCnT1 trans-porter and multidrug-resistance associated protein MRP-2. Oncotarget. 2015 May 10;6(13):10853-67. • Vincent a, Kazmierczak C, Duchêne B, Jonckheere n, Leteurtre E, Van Seuningen I. Cryosectioning the intestinal crypt-villus axis: an ex vivo method to study the dynamic of epigenetic modifications from stem cells to differentiated cells. Stem Cell Res. 2015 Jan;14(1):105-13• Renaud F, Vincent a, Mariette C, Crépin M, Stechly L, Truant S, Copin MC, Porchet n, Leteurtre E, Van Seuningen I*, Buisine MP*. MuC5aC

hypomethylation is a predictor of microsatellite instability independently of clinical factors associated with colorectal cancer. Int J Cancer. 2015 Jun 15;136(12):2811-21• Skrypek n, Duchene B, hebbar M, Leteurtre E, Van Seuningen I, Jonc-kheere n. The MuC4 mucin mediates gemcitabine resistance of human pancreatic cancer cells via the concentrative nucleoside transporter family. Oncogene, 2013 Mar 28;32(13):1714-1723• Jonckheere n, Skrypek n, and Van Seuningen I. Mucins and tumor resis-tance to chemotherapeutic drugs. Biochim Biophys acta (BBa) - Reviews on Cancer 2014 apr 29;1846(1):142-151• Vincent a, Van Seuningen I. On the epigenetic origin of cancer stem cells. Biochim Biophys acta -Rev Cancer. 2012 apr 1;1826(1):83-88 • Jonckheere n, Skrypek n, Frénois F, Van Seuningen I. Membrane-bound mucin modular domains: from structure to function. Biochimie, 2013 Jun;95(6):1077-86

Isabelle VAN SEUNINGEN

> Research Center; Town: Jean-Pierre aubert Research Center, Lille, France

> Administrative affiliations: Inserm uMR-S 1172, université de Lille, ChRu de Lille

> Tech Transfer Office: SaTT nord sattnord.fr

Keywords:

• Mucin

• Cancer

• Epigenetics

• Epithelium

• Gastrointestinal


SynopsisOur laboratory studies mechanisms of tumor resistance to chemotherapeutic drug treatments and the role of epigenetics in stem cell plasticity. a focus is made on the role of oncogenic mucins in these processes.

Abstract1- Role of MuC1 and MuC4 mucins in pancreatic, oeso-gastric, colonic and renal carcinogenesis and tumor resistance. In vitro (2D and 3D cell lines), in vivo (animal models) and ex vivo (patient material) studies. Regulation, intracellular signalling, structure-function relationship, intracellular trafficking.2- Epigenetic regulation (Dna methylation, histone modifications) and regulation by miRna of the 11p15 mucin genes and of MuC1 and MuC4 mucin genes in epithelial cancers. application to the prognosis/classification of epithelial tumors, 3- Cancer stem cell, chemoresistance, and tumor dormancy (model of the intestinal crypt-villus axis),4- Translational research with hospital partners. Mucins and other markers as diagnostic/prognostic, predictive factors (therapy orientation), patient management.

SELECTED REFERENCES

95



Objectives:• Develop specific epidrugs targeting proteins involved in stem cell differentiation • Develop specific drugs (PPI inhibitors) of the MuC4-ErbB2 oncogenic complex

Tools:• Collection of human and murine 3D cellular models (colon, pancreas, stomach, kidney)• Transgenic mouse of pancreatic carcinogenesis (Pdx-1-Cre;LStopL-KrasG12D)• Muc1, Muc4, Muc2, Muc5ac KO mice models

Unique selling points:• International visibility and expertise on mucin biology• Discovery of 3 mucin genes: MuC4, MuC5aC and MuC5B. • unique and specific (antibodies, promoter constructs) tools to study genes encoding mucins and translated products (= high molecular weight O-glycoproteins)• 3D organoids expertise and collection of 3D cellular models (pancreas, colon, stomach, kidney)• CRISPR-Cas9 technology to develop new and unique 3D cellular models


96

project / expertise

Results• We have deciphered the mechanisms of tumor resistance linked to MUC1 and MUC4 mucin altered expression in epithelial cancer cells. We have also shown that their mem-brane partners (ErbB receptor family) are also involved in these resistance mechanisms (Jonckheere et al., BBA-Rev Cancer 2014). We have identified the mechanism of interac-tion between MUC4 and ErbB2 in human can-cer cells (Jonckheere et al., Biochimie 2013).

Perspectives• We want to develop specific drugs (protein-protein interaction inhibitors) targeting MUC4 domains (ANR 2016-2018) to inhibit oncoge-nic activity of MUC4-ErbB2 complex. We also want to target proteins conveying tumor resis-tance linked with overexpression of MUC4-ErbB2 and MUC1-EGFR complexes.

Results• We have started characterizing epigenetic land-scapes to discriminate aberrant marks (good can-didates for tumour detection) from cancer stem cell specific profiles (Vincent and Van Seuningen, BBA-Rev Cancer 2012). We also have set up an original method of crypt-villus axis cryosectioning to precisely study epigenetic modifications during the differentiation process (Vincent et al., Stem Cell Res 2015). We have also set-up 3D organoids mo-dels to develop a 3D biobank to screen efficiency of future epidrugs that we will design.

Perspectives• We want to identify what epigenetics can teach us about the origin of cancer stem cells. We also want to identify epigenetic reprogramming processes to design new epidrugs that will specifically target cancer stem cells.

Mucins, ErbBs and tumor chemoresistance

Epigenetics and cancer stem cell plasticity



97

Major publications over the past four years• hiriart E, Verdel a. Chromosome Res. 2013 Dec;21(6-7):653-63. doi: 10.1007/s10577-013-9393-5 Long noncoding Rna-based chromatin control of germ cell differenciation: a yeast perspective• Yamashita a, Shichino Y, Tanaka h, hiriart E, Touat-Todeschini L, Vavasseur a, Ding DQ, hiraoka Y, Verdel a, Yamamoto M. Open Biol. 2012 hexanu-cleotide motifs mediate recruitment of the Rna elimination machinery to silent meiotic genes. Mar;2(3):120014. doi:10.1098/rsob. 120014.

• hiriart E, Vavasseur a, Touat-Todeschini L, Yamashita a, Gilquin B, Lambert E, Perot J, Shichino Y, nazaret n, Boyaukt C, Lachuer J, Perazza D, Yama-moto M, Verdel a. EMBO J. 2012 May 16;31(10)/2296-308. doi:10.1038/emboj.2012.105. Epub 2012 apr 20 Mmi1 Rna surveillance machinery directs Rnai complex RITS to specific meiotic genes in fission yeast.

André VERDEL

> Research Center; Town: Institut albert Bonniot (IaB), Grenoble

> Administrative affiliations: Inserm u823/université Grenoble alpes

> Tech Transfer Office: Floralis www.floralis.fr

Keywords:

• aRn

• Epigenetics

• Chromatin

• Transcription

• Transcriptomics

• Proteomics

Ph.D. Contact: [email protected]

Attractive synopsisWe used the yeast model system to uncover new epigenetic mechanisms part of which are likely to be conserved in human and involved in cancer.

AbstractRecently, the process of Rna interference (Rnai) was found to act on, or near, chromatin in many eukaryotes including fungi, plants, drosophila and vertebrates. In the fission yeast Schizosaccharomyces pombe, where the molecular mechanisms are among the most detailed, Rnai silences transcription by triggering formation of heterochromatin. heterochromatin is conserved among eukaryotes and plays essential roles in chromosome segregation and in maintenance of genomic stability. heterochromatin or heterochromatin-like structures are involved in long-term silencing of key genes during cellular differentiation and development. as a consequence, malfunctions in heterochromatin assembly greatly contribute to the appearance or progression of various diseases, such as cancer.Our team focuses on understanding how Rna can modulate gene expression in an epigenetic manner by acting directly on the chromosome.By coupling innovative and interdisciplinary approaches to classical yeast molecular genetics, protein affinity purifications and microscopy techniques we are exploring fundamental aspects of Rna-driven heterochromatin formation in fission yeast. as Rna-based chromatin modification is evolutionary conserved, our studies have the potential to bring general insights into how Rna modulates chromatin structure and function in humans.

SELECTED REFERENCES

RNA and Epigenetics

98

André VERDEL


Tools:• We use yeast as a reference model to study epigenetic mechanisms, as well as high throughput sequencing, transcriptomics and state of the art quantitative preteomics, in addition to classical yeast genetics, molecular and cellular biology.

RNA and Epigenetics

99

Molecular basis of glioma cancer stem cells properties and functional intra tumor heterogeneity

Grants • CanCEROPOLE PaCa (2015)• anR• InCa PLBIO

Major publications over the past four years• Vo DD …..Duca M. aCS Chem Biol. 2014• Fareh M …… Virolle T. Cell Death Differ. 2012• Turchi L …… Virolle T. Stem Cells. 2013• Burel-Vandenbos F…… Virolle T. neuro Oncol. 2013• nayernia Z ….. Virolle T*, Preynat Seauve O*. (equal contribution). Bioma-terials. 2013

Patents • Brevet publié : FR2963020 - WO2012010768 a1 – Procédé d’obtention d’un extrait et extrait pour le traitement d’un cancer. 27/01/2012- unSa n/REF FR1059250.• Demande de dépôt de brevet Europeen 21 June 2013: submission num-ber 1000197860, applicant number EP13305855.2.• Déclaration d’invention et demande de dépôt de brevet 2015 pour le com-posé DVXXX. Etude de brevetabilité positive, cabinet Becker & associés. V/REF : 696 GB épigénétique n/REF : DB1773, cabinet BECKER & asso-ciés.

Keywords:

• Cancer stem cells

• Glioblastoma

• Chemical compounds

• Differentiation

SynopsisInnovative therapeutic strategy against cancer stem cells using chemical compounds: turning glioma stem cells into indolent cells.

AbstractGlioblastomas (GBM) are the most common form of primary brain tumors afflicting adult patients of all ages. These vascularized and infiltrating tumors remain incurable and lead to a fatal outcome in less than 18 months. One of the most striking features of GBM functional heterogeneity resides in the coexistence of GBM stem-like or progenitor cells (GSC) and non mitotic, indolent differentiated cells, in variable proportions. Such a functional heterogeneity confuses the prognosis and constitutes a major difficulty for conventional anti-tumor therapies because of the persistence of GSC. By combining molecular/cellular biology and chemical studies in collaboration with Dr M Duca (ICn, nice), two complementary disciplines, we have designed and characterized chemical compounds capable of turning GSC into indolent cells, constituting putative innovative therapeutic agents.

SELECTED REFERENCES


Thierry VIROLLE

> Research Center; Town: Institut de Biologie Valrose (iBV) nice

> Administrative affiliations: Inserm u 1091 - CnRS uMR 7277 - université nice Sophia antipolis


100

Thierry VIROLLE


Objectives:• Targeting glioblastoma stem cells through their commitment into indolent tumor cells

Tools:• Primary culture of glioblastoma stem cells/ tumor tissues • Small molecule compounds• miRna

Unique selling points :• Innovative therapeutic approach based on physiological commitment of cancer stem

cells into a more differentiated indolent tumor cell • use of small molecule compounds capable of targetting key miRna involved in cancer

stem cell plasticity • Combination of these small molecule compounds with the treatement of reference

against glioblastoma


101

project / expertise

Results• DVXXX and derivative molecules are capable to inhibit stemness and clonal prolifération of glioma stem cells.• DVXXX and derivative molecules sensitize glio-ma stem cells to Temodal treatment (treatment of reference for glioblastoma)• No toxicity

Perspectives• Proof of principle in vivo• Clinical trials

Targeting glioblastoma stem cells


Thierry VIROLLE

102

Molecular and Cellular Biology of HNSCC and Prostate Cancer

Grants • CIT funded multi-omic analysis and bioinformatics support (>1000K€) • national and Eu funds (various)

Major publications over the past four years• a Poor Prognosis Subtype of hnSCC Is Consistently Observed across Methylome, Transcriptome, and miRnome analysis CLInICaL CanCER RESEaRCh 2013• Biological and clinical relevance of transcriptionally active human papillo-mavirus (hPV) infection in oropharynx squamous cell carcinoma InTERna-TIOnaL JOuRnaL OF CanCER 2010

• anO1 amplification and expression in hnSCC with a high propensity for future distant metastasis and its functions in hnSCC cell lines BRITISh JOuRnaL OF CanCER 2010 • The Oncogenic MicroRna hsa-miR-155-5p Targets the Transcription Factor ELK3 and Links It to the hypoxia Response PLOS OnE 2014

Bohdan WASYLYK

Keywords:

• Biomarkers

• Therapeutic targets

• Multi-omics

BSc, Ph.D.Contact: [email protected]

SynopsisWe generate foundational discoveries with clinical perspectives using an approach that flows from the patient to the laboratory and back to the patient, and combines unique state-of-the-art methodology, pre-clinical models, clinical expertise, patient samples and bioinformatics.

AbstracthnSCC (head and neck Squamous Cell Carcinoma) is a prevalent cancer with poor prognosis and an urgent need for new therapeutic options and biomarkers. In a collaboration between the IGBMC (a world renowned research institute), clinicians at the Strasbourg Cancer hospital (Centre Paul Strauss) and the bioinformatics team of the national Cancer Ligue (CIT program), we have used high-quality patient material and different whole genome approaches (Dna methylation, miRnas, mRnas, Dna copy number) to identify pathways associated with poor prognosis and propensity for future metastasis. We are currently validating a unique miRna signature for poor prognosis and exploiting the miRnas for therapeutic purposes. Bioinformatic analysis of available datasets (including TCGa,The Cancer Genome atlas) has led to the identification of a potential signature (biomarker) for sensitivity to EGFR inhibitors. Experiments are in progress to validate these results in high throughput studies in pre-clinical models, with perspectives to move to Phase I/II studies.

SELECTED REFERENCES

> Research Center; Town: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Strasbourg

> Administrative affiliations: CnRS uMR 7104 - Inserm u 964 - université de Strasbourg


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Bohdan WASYLYK


Objectives:• Resolve the lack of new and effective therapeutic options for hnSCC, a prevalent

cancer with poor prognosis.• Repurpose and improve the use of targeted therapies

Tools:• State of the art methodology in a world leading institute (IGBMC)• Large clinically annotated tumour collection at the Strasbourg Cancer hospital (CPS)

sustained by local prevalence of hnSCC.• advanced data mining and bioinformatics capacity, nourished by cross-analysis of large

data sets from many cancers (CIT, Ligue Contre le Cancer).

Unique selling points:• unique signature of poor prognosis subgroup of hnSCC, based on a combined 4-omic

analysis of our patient cohort. • unique signature to select patients for targeted therapy with EGFR inhibitors. • unique capacity to validate and exploit these signatures using our clinical expertise

(patients, tumour samples; CPS, PI: alain Jung), functional analysis (high throughput screening, pre-clinical models, PI: B Wasylyk) and data-mining / bioinformatics (CIT, PI: a De Reynies).

104


Bohdan WASYLYK

project / expertise

Results

Perspectives• Validate epigenetic si-gnature of poor prognosis based on miRNAs and use them as therapeutic agents

Results• The lack of validated predictive biomarkers precludes effective patient selection for targeted therapies.• We found a potential biomarker by multi-omic large-dataset analysis. • One subtype of patients overexpresses EGFR ligands.• This subtype of HNSCC cell lines responds better to EGFR-inhibitors.

Perspectives• Develop a clinically useful biomarker to select HNSCC patients for EGFR-inhibitor therapy and repurposed drug combinations.• Validate our findings in large patient cohorts and pre-clinical models (patient samples, xenografts, cancer cell lines, etc).

PrognostaMirs to identify and treat poor prognosis HNSCC

Effective targeted therapy for HNSCC

105

Laboratory « Epigenetic Regulation of Cell Identity » headed by Michael Weber

Grants • aTIP/avenir Grant (2011)• InCa (2014), Plan Cancer (2014)• ERC Consolidator Grant (2014)

Major publications over the past four years• auclair G, Borgel J, Sanz La, Vallet J, Guibert S, Dumas M, Cavelier P, Girardot M, Forné T, Feil R, Weber M. EhMT2 directs Dna methylation for efficient gene silencing in mouse embryos. Genome Res 2015 • auclair G, Guibert S, Bender a, Weber M. Ontogeny of CpG island methy-lation and specificity of DnMT3 methyltransferases during embryonic deve-lopment in the mouse. Genome Biol 2014

• Bender a, Weber M. Dna methylation: an identity card for brain cells. Genome Biol 2013• Guibert S, Forné T, Weber M. Global profiling of Dna methylation erasure in mouse primordial germ cells. Genome Res 2012• Guibert S, Weber M. Epigenetics: erase for a new start. nature 2012• Borgel J, Guibert S, Li Y, Chiba h, Schübeler D, Sasaki h, Forné T, Weber M. Targets and dynamics of promoter Dna methylation during early mouse development. nature Genetics 2010

Michael WEBER

Keywords:

• Dna methylation

• Methylome

• Dna methyltransferase

• Bisulfite sequencing

• Embryonic development


SynopsisWe employ state-of-the-art genome-wide epigenome technologies and functional tools to study the role of Dna methylation in the control of normal and malignant cell identities in mammals.

AbstractEpigenetic marks such as Dna methylation undergo dynamic changes during cell differentiation and their deregulation is causally involved in many human diseases and the appearance of cancerous phenotypes. Our objectives are to understand how Dna methylation marks influence gene expression states and contribute to maintain stable heritable cellular identities. We also aim at identifying factors that maintain or remodel Dna methylation marks during normal development and cellular transformation. Our scientific questions imply the use of technologies to map epigenetic marks on a genome-wide scale, combined with bioinformatics analysis and molecular biology. These techniques are applied on various experimental models such as primary cells, mouse ES cells, and in vivo mouse models.

SELECTED REFERENCES

> Research Center; Town: CnRS uMR7242, Strasbourg

> Administrative affiliations: CnRS - université de Strasbourg

> Tech Transfer Office: CnRS Délégation alsace www.alsace.cnrs.fr

106

Michael WEBER


Objectives:• Map the dynamics of Dna methylation in mammalian cells • understand the role of Dna methylation in the maintenance of cell identities • Identify molecular pathways that remodel Dna methylation patterns

Tools:• Genome-wide methylomes by nGS (RRBS, WGBS) • Bioinformatic integration of nGS data (epigenome, transcriptome, cistrome)• Mouse embryology and genetics • Genetic and epigenetic engineering in mammalian cells

Unique selling points:• Our team is a pioneer for the genome-wide analysis of Dna methylation in mammalian

genomes• We offer a unique expertise for the generation and analysis of methylomes at single

base resolution by next Generation Sequencing (RRBS, WGBS, ox-BS). • We master tools for the isolation of embryonic cell populations and genetic manipulation

of Dna methylation in the mouse


107

Michael WEBER


project / expertise

Results• We generated genome-wide maps of DNA methy-lation acquisition in the mouse embryo and showed that the enzymes DNMT3A/DNMT3B play both redundant and specific functions in embryonic DNA methylation.

Results• We showed that the histone methyltransferase EHMT2 (G9a) is critical to recruit repressive DNA methylation at genes during embryonic develop-ment, suggesting a functional interconnection between histone methylation and DNA methylation pathways in mammalian development

Subject 1

Subject 2

108

Epigenetics and Cell Fate

Grants • Jonathan Weitzman is the co-ordinator of the Laboratoire d’excellence LaBEX Who am I? an interdisciplinary consortium dedicated to defining the molecular and cellular basis od identity in health and disease • Weitzman group received a proof of concept grant from SaTT idfinnov for his work on theileriosis.

Major publications over the past four years• Cock-Rada aM*, Medjkane S*, Janski n, Yousfi n, Perichon M, Chausse-pied M, Chluba J, Langsley G, Weitzman JB. SMYD3 promotes cancer inva-sion by epigenetic upregulation of the metalloproteinase MMP-9. (2012) Cancer Research 72:810-20• Cock-Rada aM, Weitzman JB. The methylation landscape of tumor metas-tasis. (2013) Biology of the Cell doi: 10.1111/boc.201200029.• Marsolier J*, Pineau S*, Medjkane S, Perichon M, Yin Q, Flemington E, Weitzman MD, Weitzman JB. OncomiR addiction is generated by a miR-155 feedback loop in Theileria-transformed leukocytes. (2013) PLoS Pathogens 9(4):e1003222. doi: 10.1371/journal.ppat.1003222• Medjkane S, Perichon M, Marsolier J, Dairou J, Weitzman JB. Theileria induces oxidative stress and hIF1α activation that are essential for host leukocyte transformation (2013) Oncogene doi: 10.1038/onc.2013.134

• Weitzman MD*, Weitzman JB*. What’s the damage? The impact of pa-thogens on pathways that maintain host genome integrity. (2014) Cell host & Microbe 15:283-294. doi:10.1016/j.chom.2014.02.010• Cheeseman K, Weitzman JB, Medjkane S. L’épigénome au coeur de la cancérogénèse. (2014) BioFutur 359:44-47• Marsolier J, Perichon M, DeBarry JD, Villoutreix BO, Chluba J, Lopez T, Garrido C, Zhou XZ, Lu KP, Fritsch L, ait-Si-ali S, Mhadhbi M, Medjkane S, Weitzman JB. Theileria parasites secrete a prolyl isomerase to maintain host leukocyte transformation. (2015) nature 520:378-82

Patents • WO2015032998, « Pin1 inhibitors for use in the prevention and/or treat-ment of theileriosis, and related applications », Marsolier J, Weitzman J, Medjkane S & Perichon M

Jonathan WEITZMAN

Keywords:

• Lysine Methylation

• Parasite-induced transformation

• microRna circuitry


SynopsisWe investigate the molecular mechanisms underlying transformation inspired by an innovative parasite-induced model system.

AbstractOur team studies the role of Lysine methylation in defining cancer phenotypes and cellular identities. We are interested in deciphering the epigenetic changes that characterize tumor progression and how infectious agents hijack the genetic and epigenetic machinery of their host cells to drive tumorigenesis. We use integrated genomic and proteomic approaches to investigate the enzymes involved in the lysine methylome in cancer and infected cells and their contribution to the plasticity of cellular phenotypes. Recent projects have focused on the role of the SMYD3 histone Methyltransferase in metastasis (Cancer Research 2012), a regulatory feedback loop driven by the miR-155 oncomiR (PLoS Pathogens 2013), parasite-induced effects on host metabolism and the Warburg effect (Oncogene 2013) and the role of prolyl isomerization in oncogenic signalling (nature 2015).

SELECTED REFERENCES

> Research Center; Town: Epigénétique et Destin Cellulaire (EDC), Paris

> Administrative affiliations: université Paris Diderot - CnRS uMR 7216

> Tech Transfer Office: Idfinnov www.idfinnov.com

109

Jonathan WEITZMAN


Objectives:• To link signaling pathways to nuclear effects on the epigenome• To learn lessons from how parasites hijack host cells to drive transformation• To identify key mechanistic events for potential drug targeting

Tools:• a battery of in vitro and in vivo assays for tumor growth and invasion• a platform for functional epigenomic analysis• Methylome proteomics investigations and genome-wide Chromatin Immunoprecipitation (ChIP) analysis

Unique selling points :• a unique parasite-induced transformation model• Linking infection and tumorigenesis• Mechanistic insights into oncogenic signaling pathways• Linking signaling to epigenetic changes in host nucleus• Testing for small molecule inhibitors• Developing epigenome-wide analysis of target loci


110

Jonathan WEITZMAN

project / expertise

Results• The intracellular parasite Thei-leria transforms host leukocytes: infected TBL3 cells formed co-lonies when grown in soft agar and the transformed phenotype was reversed by incubating with Buparvaquone (+Bup).• Infection-induced transfor-mation involves the SMYD3 Histone methyltransferase and miR155 oncomiR pathways.• Cock-Rada et al. Cancer Re-search (2012)Marsolier et al. PLoS Pathogens (2013)

Perspectives• We study the SMYD3 Lysine methyltransferase in a range of human cancer models to identify targets for intervention.

Results• Theileria-infected cells form tumors in vivo and tumor growth is inhibited by anti-parasite drugs.• Inhibitors of the Pin1 prolyl isomerase block Xenograft tumor growth in a zebra-fish assay for tumor growth and invasive-ness• Marsolier et al. Nature (2015). Perspectives• We are exploring the role of epigenetic enzymes in parasite-induced transforma-tion

Infection-induced oncogenic signaling pathways

Infection-induced oncogenic signaling pathways


french academic strengths in epigenetics …...- innovative therapies (epigenetics; hadrontherapy)...

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