review article cancer epigenetics: new therapies and new...

Hindawi Publishing CorporationJournal of Drug DeliveryVolume 2013 Article ID 529312 9 pageshttpdxdoiorg1011552013529312

Review ArticleCancer Epigenetics New Therapies and New Challenges

Eleftheria Hatzimichael12 and Tim Crook3

1 Department of Haematology University Hospital of Ioannina St Niarchou Avenue 45110 Ioannina Greece2 Computational Medicine Center Jefferson Medical College Thomas Jefferson University Philadelphia PA 19107 USA3Division of Cancer Research Medical Research Institute University of Dundee Hospital and Medical School Dundee DD1 9SY UK

Correspondence should be addressed to Eleftheria Hatzimichael ehatzimccuoigr

Received 3 December 2012 Accepted 20 January 2013

Academic Editor Evangelos Briasoulis

Copyright copy 2013 E Hatzimichael and T CrookThis is an open access article distributed under theCreativeCommonsAttributionLicense which permits unrestricted use distribution and reproduction in anymedium provided the originalwork is properly cited

Cancer is nowadays considered to be both a genetic and an epigenetic disease The most well studied epigenetic modification inhumans isDNAmethylation however it becomes increasingly acknowledged thatDNAmethylation does notwork alone but ratheris linked to othermodifications such as histonemodifications Epigenetic abnormalities are reversible and as a result novel therapiesthat work by reversing epigenetic effects are being increasingly exploredThe biggest clinical impact of epigenetic modifying agentsin neoplastic disorders thus far has been in haematologicalmalignancies and the efficacy ofDNMT inhibitors andHDAC inhibitorsin blood cancers clearly attests to the principle that therapeutic modification of the cancer cell epigenome can produce clinicalbenefit This paper will discuss the most well studied epigenetic modifications and how these are linked to cancer will give a briefoverview of the clinical use of epigenetics as biomarkers and will focus in more detail on epigenetic drugs and their use in solidand blood cancers

1 Introduction

It has been thirty years since the ldquowar on cancerrdquo was dec-lared yet in 2008 the most recent year for which incidenceand mortality rates are available almost 127 million peoplewere diagnosed with cancer and more than 75 million diedof the disease [1] Enormous progress has been made in theunderstanding of the molecular basis of carcinogenesis andthe complete sequencing of the human genome represents amilestone in this quest [2] The situation though is far morecomplex than a simple catalogue of genes and despite thisprogress the discovery of anticancer drugs remains a highlychallenging endeavor and cancer a hard-to-cure disease

Traditionally the development of cancer is thought tobe largely due to the accumulation of genetic defects suchas mutations amplifications deletions and translocationsaffecting the cancer cell machinery and providing the cancercell with the advantage to survive and metastasize In addi-tion interactions between cancer cells and their microen-vironment further support these processes [3] Of equalimportance is a second system that cells use to determinewhen and where a particular gene will be expressed duringdevelopment This system is overlaid on DNA in the form of

epigenetic marks that are heritable during cell division but donot alter theDNA sequence [4]The pattern of these chemicaltags is called the epigenome of the cell whereas epigenetics isthe study of these marks that lead to changes in gene expres-sion in the absence of corresponding structural changes inthe genome It is now well recognized that tumorigenesis is amultistep process involving multiple genetic and epigeneticalterations with the latter often termed epimutations thatcontribute to the progressive transformation of normal cellstowards a malignant phenotype so that cancer is nowadaysconsider to be both a genetic and an epigenetic disease[5 6] Epigenetic abnormalities are reversible and as a resultnovel therapies that work by reversing epigenetic effectsare being increasingly explored More recently increasingevidence suggests that genetic and epigenetic mechanismsintertwine and take advantage of each other duringmalignanttransformation

There are many chemical modifications that affect notonly DNA but also RNA and proteins and create differentepigenetic layers The most well studied epigenetic modifi-cation in humans is DNA methylation however it becomesincreasingly acknowledged that DNA methylation does notwork alone but rather is linked to other modifications such

2 Journal of Drug Delivery

as histonemodificationsThis paperwill discuss themost wellstudied epigenetic modifications and how these are linked tocancer give a brief overview of the clinical use of epigeneticsas biomarkers and focus in more detail on epigenetic drugsand their use in solid and blood cancers

2 DNA Methylation

DNA methylation consists of the addition of a methyl groupto carbon 5 of the cytosine within the dinucleotide CpGRegions of DNA in the human genome ranging from 05to 5 kb that are CG rich are called CpG islands and areusually found in the promoters of genes Approximately halfof all gene promoters have CpG islands that whenmethylatedlead to transcriptional silencingDe novoDNAmethylation isbrought about by DNA methyltransferases (DNMT) 3A and3B that convert cytosine residues of CpG dinucleotides into5-methylcytosine whereas DNA methylation is maintainedby DNMT1 5-methylcytosine can be further convertedinto 5-hydroxymethyl-21015840-deoxycytidine by the Ten-Eleven-Translocation (TET) family enzymes [7] The function andsignificance of 5-hydroxymethylation are still unclear andunder investigation Although methylation of DNA in 51015840promoters has been well studied and has been shown tosuppress gene expression recently DNA methylation wasdescribed downstream of the promoters in intra- and inter-genic regions [8] as well in CpG shores that is regions withlower CpG density neighboring CpG islands [9]

3 Histone Modifications

Histones are proteins around which DNA winds to formnucleosomes A nucleosome is the basic unit of DNA pack-aging within the nucleus and consists of 147 base pairs ofgenomic DNAwrapped twice around a highly conserved his-tone octamer consisting of 2 copies each of the core histonesH2AH2BH3 andH4Histones however are not only pack-aging elements but also critical regulators of gene expressionHistone tails may undergo many posttranslational chemicalmodifications such as acetylation methylation phosphory-lation ubiquitylation and sumoylation that constitute a codenamed the ldquohistone coderdquo These modifications can alter thechromatin structure from an open to a closed condensedform and vice versa Histone modifications act except forchromatin packaging on various other biological processesincluding transcriptional repression gene activation andDNA repair [10]Three classes of histone interacting proteinshave been described thus far based on their function thewriters that place histone modifications the erasers that canremove these modifications and finally the readers that rec-ognize the histonemodifications and can deliver nucleosomehistone or DNA-modifying enzymes

31 Histone Acetylation Histone acetylation occurs at eitherarginine-(R) or lysine-(K) residues and is a dynamic andreversible process that is regulated by two enzyme familieshistone acetyltransferases (HAT) and histone deacetylases(HDAC) HATs catalyse the transfer of an acetyl group to the

120576-amino group of the lysine residue on the histone proteinanduse acetyl-CoAas a cofactor As a result chromatin adoptsa more relaxed form (euchromatin) allowing the recruitmentof transcription factors HDACs reverse the acetylation oflysine residues and the local chromatin architecture becomescondensed (heterochromatin) Acetylation of lysine 16 of his-tone 4 (H4K16) appears to be crucial in chromatin folding andin the switch from the euchromatin state to heterochromatin[11] Histone acetylation can also promote transcription byproviding binding sites to proteins that are involved in geneactivation such as the bromodomain-containing family ofproteins [12]

32 Histone Methylation Histones can also be methylatedat their lysine-(K) and arginine-(R) residues Lysine residuescan be monomethylated dimethylated or trimethylatedwhereas arginine residues can be mono- or dimethylatedMethyl marks are written by S-adenosylmethionine (SAM)-dependent methyltransferases and erased by either theJumonji family of demethylases [13] or the lysine-specifichistone demethylases 1 (LSD1) and 2 (LSD2) [14] Histonemethylation at lysine and arginine residues does not alterthe chromatic structure but rather acts as binding sites forother proteins that may condense chromatin [15] or haveother effects The different levels of lysine methylation arerecognized by different methyl-lysine-binding domains andmay be associated with either transcription activation orrepression H3K4me3 for example promotes transcriptionwhereas H3K27me3 is associated with gene silencing [10]Arginine methylation of histone proteins has recently beenshown to antagonize other histone marks further increasingthe histone code complexity [16]

4 Cancer and Epigenetic Modifications

In cancer a global process of genomic hypomethylationoccurs mostly at DNA-repetitive regions which results inactivation of genes with growth and tumour promotingfunctions and loss of genome stability and imprinting [17] Incontrast there are site-specific increases in CpG methylationin areas of the genome with a high density of CpG termedCpG islands causing transcriptional silencing of tumoursuppressor genes (TSG) such as BRCA1 [18] hMLH1 [19]VHL [20] BIK [21] andMGMT [22 23]

Cancer contains not only DNA methylation aberrationsbut also major disruption of the histone modification land-scape [24] Histone modifiers have been shown to be targetsof aberrations andor mutations in cancer such as mutateddeacetylases [25] and amplified histone methyltransferasesand demethylases [26]

41WhenGeneticsMeets Epigenetics in Cancer Deregulationof the epigenetic machinery can also occur due to activationor inactivation of the epigenetic regulatory proteins In otherwords the enzymes that maintain andmodify the epigenomeare themselves frequent targets for mutation andor epimu-tation in neoplasia [27] for example DNA methyltrans-ferases themselves have been found to be genetically altered

Journal of Drug Delivery 3

in malignancies such as DNMT3A [28] and DNMT3B inpancreatic and breast cancer cells [29] Somatic DNMT3Amutations have been described in approximately 20of acutemyeloid leukemia (AML) patients especially in those withan intermediate risk cytogenetic profile and although theydid not affect the 5-methylcytosine content [30] they wereassociated with poor clinical outcome [30 31] How thelack of effect of DNMT3A mutations on 5-methylcytosinecontent is linked to an otherwise poor clinical outcome isnot yet fully understood It has been suggested that the R882DNMT3A mutations alter functions of DNMT3A such asits ability to bind other proteins involved in transcriptionalregulation and localization to chromatin regions containingmethylated DNA [30] Loss-of-function TET2 mutationswere also identified in myeloid neoplasms in 20ndash30 [3233] and have been associated with both good [34] and badprognoses [35]

Genome sequencing has also revealed the presence ofmetabolic mutations in patients with myelodysplastic syn-dromes (MDS) and AML related to the isocitrate dehy-drogenase (IDH) 1 and IDH2 genes [36] These mutationshave been reported in approximately 30 of patients withnormal karyotype AML [37 38] and have been linkedto the disruption of various processes such as bone mar-rowmicroenvironment changes and impaired differentiationsuggesting a proleukemogenic effect In an AML cohortIDH1 and IDH2 mutations were mutually exclusive withTET2 mutations while they shared the similar epigeneticdefects with the TET2mutants Epigenetic profiling revealedthat AML patients with IDH12 mutations displayed globalhypermethylation and a specific hypermethylation signature[39] MLL is another epigenetic modifier that is commonlymutated in acute leukemias andmainly due to translocationsIn normal karyotype AML cases the incidence ofMLL partialtandem duplications (MLL-PTD) is up to 8 whereas incases of trisomy 11 the incidence reaches 25 [40] FavorableAMLs such as those with t(8 21) are MLL-PTD negative[41] As MLL is a H3K4 methyltransferase translocationsthat replace the methyltransferase domain affect its func-tion and have been linked with leukaemic transformation[42] Mutations affecting the Polycomb repressive complex(PRC) components such as EZH2 can also affect histonemodifications and have recently been reported EZH2 isthe enzymatic component of the PRC2 complex and is aH3K27methyltransferase Overexpression of EZH2 has beenreported in various epithelial neoplasms and several typesof leukemia [43ndash45] and has been shown to be due toat least in part the loss of transcriptional repression ofspecificmicroRNAs [44] Activatingmutations of EZH2 havebeen reported in B-cell lymphomas [46] whereas missensenonsense and frameshift mutations have been reported invarious myeloid malignancies [47 48] In AML 3 cases sofar have been described to carry EZH2mutations [27]

5 Clinical Use of Epigenetics

At present there are twomajor areas of interest in the clinicaluse of epigenetics namely biomarkers and therapeutics Wenow consider these areas

51 Cancer Biomarkers Methylated genomic DNA has anumber of properties which make it an attractive moleculefor biomarker utility First it is stable in biofluids such asblood urine and saliva Second in the majority of casesmethylation in CpG is acquired during malignant trans-formation and is therefore specific to neoplasia Third thetechniques used for detection of methylated DNA are readilyamenable to automation

Several studies have explored the methylation status ofgene promoters and its associationwith clinical parameters inprimary patient samples from patients with haematologicalmalignancies and solid tumours Various methodologieshave been used such as methylation-specific PCR (MSP)methylation-specific restriction enzyme digestion HpaII tinyfragment enrichment by ligation-mediated PCR (HELP)bisulphite sequencing and pyrosequencing Either singlegenes or panels of genes in microarrays were studied InMDS and AML methylation of several genes has beenreported such as MEG3 SNRPN [49] Plk2 [50] cyclin-dependent kinase inhibitors e-cadherin [51] and variousothers reviewed in [52] In multiple myeloma methylation oftheVHLpromoter has been shown to correlatewith bone dis-ease [20] andmethylation of the bcl-2 interacting killer (BIK)promoter has been shown to predict relapsedrefractorydisease [21] while methylated FHIT has been shown to bean independent adverse prognostic factor [53]

In a study by Shen et al [54] a panel of 10 hypermethylatedgenes was identified in patients with MDS Quantitativepyrosequencing in a large cohort showed that patients withhigher levels of methylation for these genes had shortermedian overall and progressive-free survival (PFS) inde-pendent of age sex and the International Prognostic Scor-ing System (IPSS) Similarly in solid tumours numerousmethylated genes have been described A substantial bodyof experimental evidence exists mechanistically associatingacquired chemotherapy resistance with changes in the cancercell epigenome and a number of genes have been identified inwhich increased CpG island methylation and transcriptionaldownregulation are associated with resistance to specificagents such hMLH1 [55] and Plk2 [56] in ovarian cancer Ofnote methylation-dependent silencing of the methyl trans-feraseMGMT in glioblastoma multiforme confers sensitivityto the alkylating agent temozolomide [23] but as with manysuch candidate biomarkers clinical application to informpatient management is not yet routine

The list of genes reported to bemethylated in haematolog-ical neoplasms is extensive and although several have beenlinked to clinical parameters and have been associated withsurvival or response to treatment none of these markers hasbeen used so far in the clinic to guide diagnosis or treatmentas opposed to gene mutations such as NPM1 and FLT3 thatare now widely used to risk classify AML patients

One of the major goals of investigators in oncology isthat of individualized cancer therapy Investigators continueto identify genes whose transcriptional silencing affectssensitivity to chemotherapeutic agents The challenge nowis to translate these findings into clinically usable tests toinform optimal deployment of anticancer drugs It remainsunlikely that a single genemethylation test will be sufficiently


informative to guide individual patient management and it ismore likely that panels of genes will be required

52 Cancer Therapeutics Both epigenetic proteins and pro-tein markers are good targets for the development of newanticancer treatments The proof-of-concept for epigenetictherapies is the FDA and EMEA approval of demethylatingagents and histone acetylase (HDAC) inhibitors for thetreatment of MDS AML and certain types of lymphomasrespectively However we should not forget that these agentsare nonselective and their side effects are not clearly known

521 DNAMethyltransferase Inhibitors (DNMTis) or Demeth-ylating Agents The two most well studied and in clinicaluse DNA methyltransferase inhibitors (DNMTi) are theazanucleosides azacytidine (5-azacytidine) and decitabine(5-aza1015840-2-deoxycytidine) Both are approved for use in themyelodysplastic syndromes and low-blast count AML andhave improved the survival of patients with these diseases[57]

Unfortunately clinical trials with DNMTi in solid tum-ours did not have the same results A phase 1 study ofdecitabine with interleukin-2 inmelanoma and renal cell car-cinoma showed that decitabine caused grade 4 neutropeniain most patients [58] Myelosuppression was also the pre-dominant toxicity observed in a study combining decitabinewith carboplatin [59] However in a phase II trial low-dosedecitabine was found to restore sensitivity to carboplatin inpatients with heavily pretreated ovarian cancer resulting ina high response rate (RR) and prolonged PFS [60] In bothstudies there was evidence that decitabine induced dose-dependent demethylation in marker genes such as MLH1RASSF1A HOXA10 and HOXA11 [60] It is possible thatsuch an approach could efficiently be coupled with the useof epigenetic biomarkers predictive of chemosensitivity [56]

A major likely reason for the disappointing activity ofdemethylating agents in solid tumours is limited incorpora-tion into cells which are proliferating relatively slowly Theselimitations may be less relevant for newer DNMTis whichare independent of replication for incorporation into DNAA second explanation for these results is that agents suchas azacytidine which cause global hypomethylation likelyreactivate expression of multiple silenced genes includingoncogenes and tumour suppressors in different cell typesand in different cancers Demethylation could therefore causeboth therapeutic and deleterious effects For example theoncogene NT5E is overexpressed in aggressive metastaticmelanomas yet transcriptionally silenced by methylation inbreast cancer with more favorable prognosis [61]

A third and key possible explanation why DNMTi haveadvanced less rapidly in the clinic in solid tumours thanin haematological malignancies is that of toxicity Bothdecitabine and azacytidine are active in haematologicalmalignancy at lower (less toxic) doses than are required fordemethylation in epithelial malignancies It is clearly of inter-est therefore that transient exposure of cells to low (relativelynon-toxic) doses of these agents could induce a ldquomemoryrdquoresponse with sustained reduction in CpG islandmethylationand reactivation of expression of previously silenced genes

[62] These observations imply that low-dose decitabine andazacytidinemayhavewider uses inmanagement of neoplasticdisease than previously believed In a recently reported phaseII trial Matei et al [60] showed that pretreatment withlow-dose azacytidine restored sensitivity to carboplatin inpatients with drug resistant epithelial ovarian cancer andresulted in a high response rate and significantly improvedclinical outcomes This study clearly attests to the utility oflow-dose azacytidine in solid tumours and sets the scene forfurther studies

Newer azanucleosides are zebularine S-110 and SGI-1027that have shown antiproliferative activity in cell lines [63 64]but have not entered the clinical trial setting yet

522 Histone Deacetylase Inhibitors (HDACi) The HDACscatalyse removal of acetyl groups from lysine residues inthe histones and functionally are transcriptional repressorsHDACs are divided into five classes class I comprisesHDAC1 HDAC2 HDAC3 and HDAC8 class IIa comprisesHDAC4 HDAC5 HDAC7 and HDAC9 class IIb containsHDAC6 and HDAC10 class III comprises the sirtuins SIRT1-SIRT7 while class IV contains only HDAC11 [65] Thediscovery of HDACi actually preceded the discovery ofHDACs Sodium butyrate was the first HDACi describedto induce acetylation [66] and later on trichostatin (TSA)a fungal antibiotic currently used in in vitro experimentsand valproic acid a widely used antiepileptic were identifiedValproic acid in particular has been used in combinationwith DNMTi andor chemotherapy in patients with haema-tological malignancies [67 68]

Currently HDACi that have been developed focus onclass I and class II HDACs and can be further distinguishedinto chemically distinct subgroups based on their structurealiphatic acids (phenylbutyrate valproic acid) benzamides(entinostat) cyclic peptides (romidepsin) and hydroxamates(TSA vorinostatSAHA) Several HDACi are currently beingtested in phase II-III trials while two of them vorinostat andromidepsin are the first FDA and EMEA approved agents forthe treatment of progressive or recurrent cutaneous T celllymphoma (CTCL) as second lines of treatment in 2006 and2009 respectively [69] but convincing clinical evidence ofactivity of these agents in other cancer types is still lacking[70] In non-small-cell lung cancer a number of HDACi suchas entinostat vorinostat Pivanex and CI-994 are in earlyphases of clinical development and first results have beenreported [70 71] However it appears that HDACi may needrational combinations to counterbalance the inherent poten-tial of these compounds to reactivate tumor-progressiongenes [72] Newer compounds such as givinostat (ITF2357)have also been developed Givinostat has been shown toselectively target cells harboring the JAK2 V617F mutation[73] and has been tested in combination with hydroxyureain patients with polycythemia vera in a phase II study(NCT00928707) Panobinostat (LBH589) has shown activityas monotherapy in patients with Hodgkinrsquos lymphoma whorelapsed or were refractory to autologous transplantation [74]but limited activity in MDS [75] However in solid tumorsthe results of panobinostat monotherapy or in combinationwith other agents were rather disappointing [76 77] Second


generation HDACi such as ACY-1215 are more selective andhave recently entered the clinical trial setting [78] It would bereally interesting to see the efficacy and safety profile of suchcompounds

HDACi however do not deacetylate histones only Itbecomes increasingly recognized that HDACi deacetylaseother nonhistone proteins that are transcription factorssignal transducers or even the products of oncogenes orTSG that are involved in oncogenesis [79] This could partlyexplain the unacceptable toxicity [80] as well as the lack ofefficacy of some compounds [81]

523 Combination of DNMTi and HDACi The recognitionthat a subset of TSGs are silenced by a combination of CpGhypermethylation and histone hypoacetylation has promptedtesting of combinations of the two classes of agents andtrials of these are in progress There is initial evidenceto suggest that such combinations may greatly increaseclinical efficacy without unacceptable toxicity For examplein multiply pretreated metastatic non-small-cell lung cancerpatients the combination of azacytidine and the histonedeacetylase inhibitor entinostat produced objective clinicalresponses and importantly four of 19 treated patients hadtherapeutic responses to further agents given immediatelyafter epigenetic therapy [82] Evidence that demethylation iskey to the responses was shown by analysis from peripheralblood samples of a set of four marker genes The therapy waswell tolerated These encouraging results are currently beingextended in further studies The combination of decitabineand pegylated interferon alfa-2b was tested in patients withunresectable or metastatic solid tumours (NCT00701298) Inongoing trials the combination of azacytidine and entinostatis undergoing testing in resected stage I non-small-cell lungcancer (NCT01207726) and oral azacytidine in combinationwith carboplatin or Abraxane (nanoparticle paclitaxel) isbeing evaluated in patients with refractory solid tumours(NCT01478685)

In elderly previously untreated AML patients and high-risk MDS patients the combination of azacytidine andlenalidomide an immunomodulator drug is currently underinvestigation (NCT01442714) Both drugs as monotherapieshave already shown efficacy in this group of patients so theircombination seems very promising Sequential treatment ofazacytidine and lenalidomide in elderly patients with AMLalso showed encouraging clinical and biologic activity [83]

In a recent Phase I study decitabine was combined withbortezomib for the treatment of elderly poor risk AMLpatients and the combination showed good preliminaryactivity since response rates were very encouraging [84]

6 Future Promise Therapeutics

The use of epidrugs on the intent to restore sensitivity tocytotoxic or hormonal drugs is a major goal in the settingof solid tumors [85ndash87] Restoring hormonal sensitivityin breast cancer is of uppermost clinical importance andhas been intensively studied over the last decades In total25 of breast cancers have the estrogen receptor-alpha (ERalpha) repressed mainly due to hypermethylation of the ER

promoter and do not respond to endocrine therapy andalmost all hormone-sensitive tumors turn to be refractoryat some point It appears now that epigenetic therapy seemsto offer a promising tool to restorereverse hormonal sen-sitivity Recent studies found that decitabine and histoneHDACi such as trichostatin A entinostat and scriptaid canrestore expression of ER mRNA and functional protein andaromatase along with the enzymatic activity of aromataseindicating a potential to restore long term responsiveness of asubset of ER-negative tumors to endocrine therapy [87ndash89]

Given the complexity and heterogeneity of the cancercell epigenome it is highly likely that some form of epige-nomic profiling of individual cancers will be required toinform optimal use of the available agents which inducemodification of the cancer cell epigenome For exampleit would clearly be important to determine the epigenomeof chemotherapy resistant cancer cells to identify poten-tially deleterious silenced genes before deploying epige-netic therapeutic strategies in an attempt to pharmacolog-ically reverse resistance Malignant melanoma is an inter-esting example of such an approach In this tumor typeloss of 5-hydroxymethylcytosine (5-hmC) has diagnosticand prognostic implications which relates to downregu-lation of IDH2 and TET family enzymes Reintroducingactive TET2 or IDH2 was found to suppress melanomagrowth and increase tumor-free survival in animal models[90]

Identifying the epigenetically modified genes which areprincipally involved in tumor resistance can be achievedby comparative analysis of diagnostic (pretreatment) biopsywith a second biopsy at disease relapse Such rebiopsyingis rapidly becoming the standard of care in oncology forexample in breast cancer [91]

The ability of the physician to exploit therapeutic oppor-tunities created by epigenetic changes in the cancer cellepigenomemay also offer new approaches to cancer manage-ment For example ASS1 which encodes arginine succinatesynthetase the rate-limiting enzyme in arginine biosynthesisis silenced by methylation in some cancer types includingrenal cell carcinoma hepatocellular carcinoma malignantmelanoma glioblastoma multiforme (GBM) and platinum-resistant epithelial ovarian cancer ASL encoding argininesuccinate lyase (a second key enzyme in arginine biosyn-thesis) is also silenced by CpG island methylation in GBM[92] Loss of either gene confers arginine auxotrophy andsensitivity to arginine deiminase These observations implya further form of epigenetic therapy in which biochemicalabnormalities resulting from epigenetic changes can be tar-geted for clinical benefit

As we previously discussed several epigenetic modifierssuch as EZH2 IDH12 and DNMT3A are genetically alteredin cancer These epigenetic modifiers provide now newtherapeutic targets for clinical development What seems tobe needed though is a better selection of patients who willbenefit from such treatments as well as identification of newdruggable targets and compounds such as histone kinases[93] or inhibitors of histone methyltransferases [94] andsirtuins [95]


7 Conclusions

The biggest clinical impact of epigenetic modifying agentsin neoplastic disorders thus far has been in haematologicalmalignancies and the efficacy of DNMTis and HDACi inblood cancers clearly attests to the principle that therapeuticmodification of the cancer cell epigenome can produceclinical benefit Although the efficacy of epigenetic therapy insolid tumours remains as yet unproven there is every reasonto believe that more rational use of existing agents perhapsinformed by individual patient epigenetic profiling willimprove the therapeutic index of this approach Furthermorean increasing number of viable new therapeutic targets areemerging from increased understanding of the epigeneticregulatory circuitry and its derangement in neoplasia

Conflict of Interests

The authors have no conflict of interests to declare

Acknowledgments

T Crook is a Scottish senior clinical fellow in MedicalOncology E Hatzimichael is a scholar of the Hellenic Societyof Hematology Foundation and a visiting scientist at theComputational Medicine Centre Jefferson Medical CollegeThomas Jefferson University Work in the laboratory of TCrook is supported by the Chief ScientificOfficer of ScotlandThe Leng Foundation andThe Anonymous Trust

References

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[2] E S Lander L M Linton B Birren et al ldquoInitial sequencingand analysis of the human genomerdquo Nature vol 409 pp 860ndash921 2001

[3] D Hanahan and R AWeinberg ldquoHallmarks of cancer the nextgenerationrdquo Cell vol 144 no 5 pp 646ndash674 2011

[4] P A Jones and P W Laird ldquoCancer epigenetics comes of agerdquoNature Genetics vol 21 no 2 pp 163ndash167 1999

[5] E J Geutjes P K Bajpe and R Bernards ldquoTargeting theepigenome for treatment of cancerrdquoOncogene vol 31 pp 3827ndash3844 2012

[6] P A Jones and S B Baylin ldquoThe fundamental role of epigeneticevents in cancerrdquoNature Reviews Genetics vol 3 no 6 pp 415ndash428 2002

[7] M Tahiliani K P Koh Y Shen et al ldquoConversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalianDNAbyMLLpartner TET1rdquo Science vol 324 no 5929 pp 930ndash935 2009

[8] A K Maunakea R P Nagarajan M Bilenky et al ldquoConservedrole of intragenic DNA methylation in regulating alternativepromotersrdquo Nature vol 466 no 7303 pp 253ndash257 2010

[9] K D Hansen W Timp H C Bravo et al ldquoIncreased methy-lation variation in epigenetic domains across cancer typesrdquoNature Genetics vol 43 no 8 pp 768ndash775 2011

[10] T Kouzarides ldquoChromatin modifications and their functionrdquoCell vol 128 no 4 pp 693ndash705 2007

[11] M D Shahbazian and M Grunstein ldquoFunctions of site-specific histone acetylation and deacetylationrdquo Annual Reviewof Biochemistry vol 76 pp 75ndash100 2007

[12] P Filippakopoulos S Picaud M Mangos et al ldquoHistonerecognition and large-scale structural analysis of the humanbromodomain familyrdquo Cell vol 149 pp 214ndash231 2012

[13] Y I Tsukada J Fang H Erdjument-Bromage et al ldquoHistonedemethylation by a family of JmjC domain-containing pro-teinsrdquo Nature vol 439 no 7078 pp 811ndash816 2006

[14] Y Shi F Lan CMatson et al ldquoHistone demethylationmediatedby the nuclear amine oxidase homolog LSD1rdquo Cell vol 119 no7 pp 941ndash953 2004

[15] A L Nielsen M Oulad-Abdelghani J A Ortiz E Rembout-sika P Chambon and R Losson ldquoHeterochromatin formationin mammalian cells interaction between histones and HP1ProteinsrdquoMolecular Cell vol 7 no 4 pp 729ndash739 2001

[16] E Guccione C Bassi F Casadio et al ldquoMethylation of histoneH3R2 by PRMT6 and H3K4 by an MLL complex are mutuallyexclusiverdquo Nature vol 449 no 7164 pp 933ndash937 2007

[17] M Esteller ldquoMolecular origins of cancer epigenetics in cancerrdquoNew England Journal of Medicine vol 358 no 11 pp 1148ndash10962008

[18] A Dobrovic and D Simpfendorfer ldquoMethylation of the BRCA1gene in sporadic breast cancerrdquo Cancer Research vol 57 no 16pp 3347ndash3350 1997

[19] G Deng A Chen J Hong H S Chae and Y S Kim ldquoMethy-lation of CpG in a small region of the hMLH1 promoterinvariably correlates with the absence of gene expressionrdquoCancer Research vol 59 no 9 pp 2029ndash2033 1999

[20] E Hatzimichael G Dranitsaris A Dasoula et al ldquoVon Hippel-Lindau methylation status in patients with multiple myeloma apotential predictive factor for the development of boneDiseaserdquoClinical Lymphoma and Myeloma vol 9 no 3 pp 239ndash2422009

[21] E Hatzimichael A Dasoula V Kounnis et al ldquoBcl2-interactingkiller CpG methylation in multiple myeloma a potential pre-dictor of relapsedrefractory disease with therapeutic implica-tionsrdquo Leukemia amp Lymphoma vol 53 pp 1709ndash1713 2012

[22] M Esteller ldquoEpigenetics provides a new generation of onco-genes and tumour-suppressor genesrdquo British Journal of Cancervol 94 no 2 pp 179ndash183 2006

[23] M Esteller J Garcia-Foncillas E Andion et al ldquoInactivationof the DNA-repair gene MGMT and the clinical response ofgliomas to alkylating agentsrdquo New England Journal of Medicinevol 343 no 19 pp 1350ndash1354 2000

[24] M F Fraga E Ballestar A Villar-Garea et al ldquoLoss of acety-lation at Lys16 and trimethylation at Lys20 of histone H4 is acommon hallmark of human cancerrdquo Nature Genetics vol 37no 4 pp 391ndash400 2005

[25] S RoperoM F Fraga E Ballestar et al ldquoA truncatingmutationof HDAC2 in human cancers confers resistance to histonedeacetylase inhibitionrdquo Nature Genetics vol 38 no 5 pp 566ndash569 2006

[26] P A C Cloos J Christensen K Agger et al ldquoThe putativeoncogene GASC1 demethylates tri- and dimethylated lysine 9on histone H3rdquo Nature vol 442 no 7100 pp 307ndash311 2006

[27] E Hatzimichael G Georgiou L Benetatos and E BriasoulisldquoGene mutations and molecularly targeted therapies in acutemyeloid leukemiardquo American Journal of Blood Research vol 3pp 29ndash51 2013


[28] X J Yan J Xu Z H Gu et al ldquoExome sequencing identifiessomatic mutations of DNA methyltransferase gene DNMT3Ain acute monocytic leukemiardquo Nature Genetics vol 43 no 4pp 309ndash317 2011

[29] L Simo-Riudalbas S A Melo andM Esteller ldquoDNMT3B geneamplification predicts resistance to DNA demethylating drugsrdquoGenes Chromosomes andCancer vol 50 no 7 pp 527ndash534 2011

[30] T J Ley L Ding M J Walter et al ldquoDNMT3A mutations inacutemyeloid leukemiardquoTheNew England Journal of Medicinevol 363 pp 2424ndash2433 2010

[31] FThol F Damm A Ludeking et al ldquoIncidence and prognosticinfluence of DNMT3A mutations in acute myeloid leukemiardquoJournal of Clinical Oncology vol 29 no 21 pp 2889ndash2896 2011

[32] F Delhommeau S Dupont V Della Valle et al ldquoMutation inTET2 inmyeloid cancersrdquoNewEngland Journal ofMedicine vol360 no 22 pp 2289ndash2301 2009

[33] S Weissmann T Alpermann V Grossmann et al ldquoLandscapeof TET2 mutations in acute myeloid leukemiardquo Leukemia vol26 pp 934ndash942 2012

[34] O Kosmider V Gelsi-BoyerM Cheok et al ldquoTET2mutation isan independent favorable prognostic factor in myelodysplasticsyndromes (MDSs)rdquo Blood vol 114 no 15 pp 3285ndash3291 2009

[35] W C Chou S C Chou C Y Liu et al ldquoTET2 mutation isan unfavorable prognostic factor in acute myeloid leukemiapatients with intermediate-risk cytogeneticsrdquoBlood vol 118 pp3803ndash3810 2011

[36] P S Ward J Patel D R Wise et al ldquoThe common fea-ture of leukemia-associated IDH1 and IDH2 mutations is aneomorphic enzyme activity converting 120572-ketoglutarate to 2-hydroxyglutaraterdquo Cancer Cell vol 17 no 3 pp 225ndash234 2010

[37] E R Mardis L Ding D J Dooling et al ldquoRecurring mutationsfound by sequencing an acute myeloid leukemia genomerdquo NewEngland Journal of Medicine vol 361 no 11 pp 1058ndash10662009

[38] D Rakheja S Konoplev L J Medeiros and W Chen ldquoIDHmutations in acute myeloid leukemiardquo Human Pathology vol43 pp 1541ndash1551 2012

[39] M E Figueroa O Abdel-Wahab C Lu et al ldquoLeukemic IDH1and IDH2 mutations result in a hypermethylation phenotypedisrupt TET2 function and impair hematopoietic differentia-tionrdquo Cancer Cell vol 18 pp 553ndash567 2010

[40] G Rege-Cambrin E Giugliano L Michaux et al ldquoTrisomy11 in myeloid malignancies is associated with internal tandemduplication of both MLL and FLT3 genesrdquo Haematologica vol90 no 2 pp 262ndash264 2005

[41] C SteudelMWermkeM Schaich et al ldquoComparative analysisof MLL partial tandem duplication and FLT3 internal tandemduplication mutations in 956 adult patients with acute myeloidleukemiardquo Genes Chromosomes and Cancer vol 37 no 3 pp237ndash251 2003

[42] A V Krivtsov and S A Armstrong ldquoMLL translocations his-tone modifications and leukaemia stem-cell developmentrdquoNature Reviews Cancer vol 7 no 11 pp 823ndash833 2007

[43] S Varambally S M Dhanasekaran M Zhou et al ldquoThe poly-comb group protein EZH2 is involved in progression of prostatecancerrdquo Nature vol 419 no 6907 pp 624ndash629 2002

[44] L Benetatos E Voulgaris G Vartholomatos and E Hatz-imichael ldquoNon-coding RNAs and EZH2 interactions in cancerlong and short tales from the transcriptomerdquo InternationalJournal of Cancer 2012

[45] J A Simon andCA Lange ldquoRoles of the EZH2histonemethyl-transferase in cancer epigeneticsrdquo Mutation Research vol 647no 1-2 pp 21ndash29 2008

[46] C J Sneeringer M P Scott K W Kuntz et al ldquoCoordinat-ed activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3(H3K27) in human B-cell lymphomasrdquo Proceedings of theNational Academy of Sciences of the United States of Americavol 107 no 49 pp 20980ndash20985 2010

[47] T Ernst A J Chase J Score et al ldquoInactivating mutations ofthe histonemethyltransferase gene EZH2 inmyeloid disordersrdquoNature Genetics vol 42 no 8 pp 722ndash726 2010

[48] G Nikoloski S M C Langemeijer R P Kuiper et al ldquoSomaticmutations of the histone methyltransferase gene EZH2 inmyelodysplastic syndromesrdquo Nature Genetics vol 42 no 8 pp665ndash667 2010

[49] L Benetatos E Hatzimichael A Dasoula et al ldquoCpGmethyla-tion analysis of theMEG3 and SNRPN imprinted genes in acutemyeloid leukemia and myelodysplastic syndromesrdquo LeukemiaResearch vol 34 no 2 pp 148ndash153 2010

[50] L Benetatos A Dasoula E Hatzimichael et al ldquoPolo-likekinase 2 (SNKPLK2) is a novel epigenetically regulated genein acute myeloid leukemia and myelodysplastic syndromesgenetic and epigenetic interactionsrdquo Annals of Hematology vol90 pp 1037ndash1045 2011

[51] J R Melki P C Vincent and S J Clark ldquoConcurrent DNAhypermethylation ofmultiple genes in acutemyeloid leukemiardquoCancer Research vol 59 no 15 pp 3730ndash3740 1999

[52] M A McDevitt ldquoClinical applications of epigenetic markersand epigenetic profiling in myeloid malignanciesrdquo Seminars inOncology vol 39 pp 109ndash122 2012

[53] S Takada K Morita K Hayashi et al ldquoMethylation status offragile histidine triad (FHIT) gene and its clinical impact onprognosis of patients withmultiplemyelomardquo European Journalof Haematology vol 75 no 6 pp 505ndash510 2005

[54] L ShenH Kantarjian Y Guo et al ldquoDNAmethylation predictssurvival and response to therapy in patients withmyelodysplas-tic syndromesrdquo Journal of Clinical Oncology vol 28 no 4 pp605ndash613 2010

[55] Y Watanabe H Ueda T Etoh et al ldquoA change in promotermethylation of hMLH1 is a cause of acquired resistance toplatinum-based chemotherapy in epithelial ovarian cancerrdquoAnticancer Research vol 27 no 3 B pp 1449ndash1452 2007

[56] N Syed H M Coley J Sehouli et al ldquoPolo-like kinase Plk2is an epigenetic determinant of chemosensitivity and clinicaloutcomes in ovarian cancerrdquo Cancer Research vol 71 no 9 pp3317ndash3327 2011

[57] P Fenaux G J Mufti E Hellstrom-Lindberg et al ldquoEfficacy ofazacitidine compared with that of conventional care regimensin the treatment of higher-risk myelodysplastic syndromes arandomised open-label phase III studyrdquoThe Lancet Oncologyvol 10 no 3 pp 223ndash232 2009

[58] J A Gollob and C J Sciambi ldquoDecitabine up-regulates S100A2expression and synergizes with IFN-120574 to kill uveal melanomacellsrdquo Clinical Cancer Research vol 13 no 17 pp 5219ndash52252007

[59] K Appleton H J Mackay I Judson et al ldquoPhase I and phar-macodynamic trial of the DNA methyltransferase inhibitordecitabine and carboplatin in solid tumorsrdquo Journal of ClinicalOncology vol 25 no 29 pp 4603ndash4609 2007


[60] D Matei F Fang C Shen et al ldquoEpigenetic resensitization toplatinum in ovarian cancerrdquo Cancer Research vol 72 pp 2197ndash2205 2012

[61] H Wang S Lee C L Nigro et al ldquoNT5E (CD73) is epige-netically regulated in malignant melanoma and associated withmetastatic site specificityrdquo British Journal of Cancer vol 106 pp1446ndash1452 2012

[62] H C Tsai H Li L Van Neste et al ldquoTransient low doses ofDNA-demethylating agents exert durable antitumor effects onhematological and epithelial tumor cellsrdquo Cancer Cell vol 21pp 430ndash446 2012

[63] J C Cheng C B Matsen F A Gonzales et al ldquoInhibition ofDNA methylation and reactivation of silenced genes by zebu-larinerdquo Journal of the National Cancer Institute vol 95 no 5pp 399ndash409 2003

[64] J Datta K Ghoshal W A Denny et al ldquoA new class ofquinoline-based DNA hypomethylating agents reactivatestumor suppressor genes by blocking DNA methyltransferase 1activity and inducing its degradationrdquo Cancer Research vol 69no 10 pp 4277ndash4285 2009

[65] A J M de Ruijter A H van Gennip H N Caron S Kempand A B P van Kuilenburg ldquoHistone deacetylases (HDACs)characterization of the classical HDAC familyrdquo BiochemicalJournal vol 370 no 3 pp 737ndash749 2003

[66] M G Riggs R GWhittaker J R Neumann and VM Ingramldquon-butyrate causes histone modification in HeLa and Frienderythroleukaemia cellsrdquoNature vol 268 no 5619 pp 462ndash4641977

[67] E Raffoux A Cras C Recher et al ldquoPhase 2 clinical trial of 5-azacitidine valproic acid and all-trans retinoic acid in patientswith high-risk acute myeloid leukemia or myelodysplasticsyndromerdquo Oncotarget vol 1 pp 34ndash42 2010

[68] A O Soriano H Yang S Faderl et al ldquoSafety and clinicalactivity of the combination of 5-azacytidine valproic acidand all-trans retinoic acid in acute myeloid leukemia andmyelodysplastic syndromerdquoBlood vol 110 no 7 pp 2302ndash23082007

[69] H M Prince M J Bishton and S J Harrison ldquoClinical studiesof histone deacetylase inhibitorsrdquo Clinical Cancer Research vol15 no 12 pp 3958ndash3969 2009

[70] S E Witta R M Jotte K Konduri et al ldquoRandomized phaseII trial of erlotinib with and without entinostat in patients withadvanced non-small-cell lung cancer who progressed on priorchemotherapyrdquo Journal of Clinical Oncology vol 30 pp 2248ndash2255 2012

[71] C Gridelli A Rossi and P Maione ldquoThe potential role ofhistone deacetylase inhibitors in the treatment of non-small-celllung cancerrdquo Critical Reviews in OncologyHematology vol 68no 1 pp 29ndash36 2008

[72] K T Lin Y W Wang C T Chen C M Ho W H Su andY S Jou ldquoHDAC inhibitors augmented cell migration andmetastasis through induction of PKCs leading to identificationof low toxicity modalities for combination cancer therapyrdquoClinical Cancer Research vol 18 pp 4691ndash4701 2012

[73] V Guerini V Barbui O Spinelli et al ldquoThe histone deacetylaseinhibitor ITF2357 selectively targets cells bearing mutatedJAK2V617Frdquo Leukemia vol 22 no 4 pp 740ndash747 2008

[74] A Younes A Sureda D Ben-Yehuda et al ldquoPanobinostat inpatients with relapsedrefractory Hodgkinrsquos lymphoma afterautologous stem-cell transplantation results of a phase II studyrdquoJournal of Clinical Oncology vol 30 pp 2197ndash2203 2012

[75] S Dimicoli E Jabbour G Borthakur et al ldquoPhase II studyof the histone deacetylase inhibitor panobinostat (LBH589)in patients with low or intermediate-1 risk myelodysplasticsyndromerdquo American Journal of Hematology vol 87 no 1 pp127ndash129 2012

[76] J H Strickler A N Starodub J Jia et al ldquoPhase I study of beva-cizumab everolimus and panobinostat (LBH-589) in advancedsolid tumorsrdquoCancer Chemotherapy and Pharmacology vol 70no 2 pp 251ndash258 2012

[77] HWangQ Cao andA ZDudek ldquoPhase II study of panobino-stat and bortezomib in patientswith pancreatic cancer progress-ing on gemcitabine-based therapyrdquoAnticancer Research vol 32pp 1027ndash1031 2012

[78] L Santo T Hideshima A L Kung et al ldquoPreclinical activ-ity pharmacodynamic and pharmacokinetic properties of aselective HDAC6 inhibitor ACY-1215 in combination withbortezomib in multiple myelomardquo Blood vol 119 no 11 pp2579ndash2589 2012

[79] B N Singh G Zhang Y L Hwa J Li S C Dowdy and SW Jiang ldquoNonhistone protein acetylation as cancer therapytargetsrdquo Expert Review of Anticancer Therapy vol 10 no 6 pp935ndash954 2010

[80] A Cashen M Juckett A Jumonville et al ldquoPhase II studyof the histone deacetylase inhibitor belinostat (PXD101) forthe treatment of myelodysplastic syndrome (MDS)rdquo Annals ofHematology vol 91 pp 33ndash38 2012

[81] J D Hainsworth J R Infante D R Spigel E R ArrowsmithR V Boccia and H A Burris ldquoA phase II trial of panobinostata histone deacetylase inhibitor in the treatment of patients withrefractory metastatic renal cell carcinomardquo Cancer Investiga-tion vol 29 no 7 pp 451ndash455 2011

[82] R A Juergens J Wrangle F P Vendetti et al ldquoCombinationepigenetic therapy has efficacy in patients with refractoryadvanced non-small cell lung cancerrdquo Cancer Discovery vol 1pp 598ndash607 2011

[83] D A Pollyea H E Kohrt L Gallegos et al ldquoSafety efficacy andbiological predictors of response to sequential azacitidine andlenalidomide for elderly patients with acute myeloid leukemiardquoLeukemia vol 26 pp 893ndash901 2012

[84] W Blum S Schwind S S Tarighat et al ldquoClinical andpharmacodynamic activity of bortezomib and decitabine inacute myeloid leukemiardquo Blood vol 119 pp 6025ndash6031 2012

[85] L Shen Y Kondo S Ahmed et al ldquoDrug sensitivity predictionby CpG islandmethylation profile in theNCI-60 cancer cell linepanelrdquo Cancer Research vol 67 no 23 pp 11335ndash11343 2007

[86] M E Hegi D Sciuscio A Murat M Levivier and R StuppldquoEpigenetic deregulation of DNA repair and its potential fortherapyrdquo Clinical Cancer Research vol 15 no 16 pp 5026ndash50312009

[87] P Raha SThomas and P N Munster ldquoEpigenetic modulationa novel therapeutic target for overcoming hormonal therapyresistancerdquo Epigenomics vol 3 pp 451ndash470 2011

[88] G J Sabnis O Goloubeva S Chumsri N Nguyen S Sukumarand A M H Brodie ldquoFunctional activation of the estrogenreceptor-120572 and aromatase by the HDAC inhibitor entinostatsensitizes ER-negative tumors to letrozolerdquo Cancer Researchvol 71 no 5 pp 1893ndash1903 2011

[89] D Sharma N K Saxena N E Davidson and P M VertinoldquoRestoration of tamoxifen sensitivity in estrogen receptor-negative breast cancer cells tamoxifen-bound reactivated ERrecruits distinctve corepressor complexesrdquoCancer Research vol66 no 12 pp 6370ndash6378 2006


[90] C G Lian Y Xu C Ceol et al ldquoLoss of 5-hydroxymethylcyto-sine is an epigenetic hallmark of melanomardquo Cell vol 150 pp1135ndash1146 2012

[91] A Sharma T Crook A Thompson and C Palmieri ldquoSurgicaloncology why biopsying metastatic breast cancer should beroutinerdquo Nature Reviews Clinical Oncology vol 7 no 2 pp 72ndash74 2010

[92] N Syed J Langer K Janczar et al ldquoEpigenetic status of argini-nosuccinate synthetase and argininosuccinate lyase modulatesautophagy and cell death in glioblastomardquo Cell Death andDisease vol 4 article e458 2013

[93] D Huertas M Soler J Moreto et al ldquoAntitumor activityof a small-molecule inhibitor of the histone kinase HaspinrdquoOncogene vol 31 pp 1408ndash1418 2012

[94] J Tan X Yang L Zhuang et al ldquoPharmacologic disruptionof polycomb-repressive complex 2-mediated gene repressionselectively induces apoptosis in cancer cellsrdquo Genes and Devel-opment vol 21 no 9 pp 1050ndash1063 2007

[95] E Lara A Mai V Calvanese et al ldquoSalermide a Sirtuin inhibi-tor with a strong cancer-specific proapoptotic effectrdquoOncogenevol 28 pp 781ndash791 2009

Submit your manuscripts athttpwwwhindawicom

PainResearch and TreatmentHindawi Publishing Corporationhttpwwwhindawicom Volume 2014

The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014

Hindawi Publishing Corporationhttpwwwhindawicom

Volume 2014

ToxinsJournal of

VaccinesJournal of

Hindawi Publishing Corporation httpwwwhindawicom Volume 2014

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014

AntibioticsInternational Journal of

ToxicologyJournal of


StrokeResearch and TreatmentHindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Drug DeliveryJournal of



Advances in Pharmacological Sciences

Tropical MedicineJournal of


Medicinal ChemistryInternational Journal of


AddictionJournal of



BioMed Research International

Emergency Medicine InternationalHindawi Publishing Corporationhttpwwwhindawicom Volume 2014


Autoimmune Diseases


Anesthesiology Research and Practice

ScientificaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Journal of


Pharmaceutics


MEDIATORSINFLAMMATION

of


as histonemodificationsThis paperwill discuss themost wellstudied epigenetic modifications and how these are linked tocancer give a brief overview of the clinical use of epigeneticsas biomarkers and focus in more detail on epigenetic drugsand their use in solid and blood cancers

2 DNA Methylation

DNA methylation consists of the addition of a methyl groupto carbon 5 of the cytosine within the dinucleotide CpGRegions of DNA in the human genome ranging from 05to 5 kb that are CG rich are called CpG islands and areusually found in the promoters of genes Approximately halfof all gene promoters have CpG islands that whenmethylatedlead to transcriptional silencingDe novoDNAmethylation isbrought about by DNA methyltransferases (DNMT) 3A and3B that convert cytosine residues of CpG dinucleotides into5-methylcytosine whereas DNA methylation is maintainedby DNMT1 5-methylcytosine can be further convertedinto 5-hydroxymethyl-21015840-deoxycytidine by the Ten-Eleven-Translocation (TET) family enzymes [7] The function andsignificance of 5-hydroxymethylation are still unclear andunder investigation Although methylation of DNA in 51015840promoters has been well studied and has been shown tosuppress gene expression recently DNA methylation wasdescribed downstream of the promoters in intra- and inter-genic regions [8] as well in CpG shores that is regions withlower CpG density neighboring CpG islands [9]

3 Histone Modifications

Histones are proteins around which DNA winds to formnucleosomes A nucleosome is the basic unit of DNA pack-aging within the nucleus and consists of 147 base pairs ofgenomic DNAwrapped twice around a highly conserved his-tone octamer consisting of 2 copies each of the core histonesH2AH2BH3 andH4Histones however are not only pack-aging elements but also critical regulators of gene expressionHistone tails may undergo many posttranslational chemicalmodifications such as acetylation methylation phosphory-lation ubiquitylation and sumoylation that constitute a codenamed the ldquohistone coderdquo These modifications can alter thechromatin structure from an open to a closed condensedform and vice versa Histone modifications act except forchromatin packaging on various other biological processesincluding transcriptional repression gene activation andDNA repair [10]Three classes of histone interacting proteinshave been described thus far based on their function thewriters that place histone modifications the erasers that canremove these modifications and finally the readers that rec-ognize the histonemodifications and can deliver nucleosomehistone or DNA-modifying enzymes

31 Histone Acetylation Histone acetylation occurs at eitherarginine-(R) or lysine-(K) residues and is a dynamic andreversible process that is regulated by two enzyme familieshistone acetyltransferases (HAT) and histone deacetylases(HDAC) HATs catalyse the transfer of an acetyl group to the

120576-amino group of the lysine residue on the histone proteinanduse acetyl-CoAas a cofactor As a result chromatin adoptsa more relaxed form (euchromatin) allowing the recruitmentof transcription factors HDACs reverse the acetylation oflysine residues and the local chromatin architecture becomescondensed (heterochromatin) Acetylation of lysine 16 of his-tone 4 (H4K16) appears to be crucial in chromatin folding andin the switch from the euchromatin state to heterochromatin[11] Histone acetylation can also promote transcription byproviding binding sites to proteins that are involved in geneactivation such as the bromodomain-containing family ofproteins [12]

32 Histone Methylation Histones can also be methylatedat their lysine-(K) and arginine-(R) residues Lysine residuescan be monomethylated dimethylated or trimethylatedwhereas arginine residues can be mono- or dimethylatedMethyl marks are written by S-adenosylmethionine (SAM)-dependent methyltransferases and erased by either theJumonji family of demethylases [13] or the lysine-specifichistone demethylases 1 (LSD1) and 2 (LSD2) [14] Histonemethylation at lysine and arginine residues does not alterthe chromatic structure but rather acts as binding sites forother proteins that may condense chromatin [15] or haveother effects The different levels of lysine methylation arerecognized by different methyl-lysine-binding domains andmay be associated with either transcription activation orrepression H3K4me3 for example promotes transcriptionwhereas H3K27me3 is associated with gene silencing [10]Arginine methylation of histone proteins has recently beenshown to antagonize other histone marks further increasingthe histone code complexity [16]

4 Cancer and Epigenetic Modifications

In cancer a global process of genomic hypomethylationoccurs mostly at DNA-repetitive regions which results inactivation of genes with growth and tumour promotingfunctions and loss of genome stability and imprinting [17] Incontrast there are site-specific increases in CpG methylationin areas of the genome with a high density of CpG termedCpG islands causing transcriptional silencing of tumoursuppressor genes (TSG) such as BRCA1 [18] hMLH1 [19]VHL [20] BIK [21] andMGMT [22 23]

Cancer contains not only DNA methylation aberrationsbut also major disruption of the histone modification land-scape [24] Histone modifiers have been shown to be targetsof aberrations andor mutations in cancer such as mutateddeacetylases [25] and amplified histone methyltransferasesand demethylases [26]

41WhenGeneticsMeets Epigenetics in Cancer Deregulationof the epigenetic machinery can also occur due to activationor inactivation of the epigenetic regulatory proteins In otherwords the enzymes that maintain andmodify the epigenomeare themselves frequent targets for mutation andor epimu-tation in neoplasia [27] for example DNA methyltrans-ferases themselves have been found to be genetically altered




































7 Conclusions




Acknowledgments


References







































































































Volume 2014

ToxinsJournal of

VaccinesJournal of















AddictionJournal of






Autoimmune Diseases




Journal of


Pharmaceutics



of




































7 Conclusions




Acknowledgments


References







































































































Volume 2014

ToxinsJournal of

VaccinesJournal of















AddictionJournal of






Autoimmune Diseases




Journal of


Pharmaceutics



of












































































Volume 2014

ToxinsJournal of

VaccinesJournal of















AddictionJournal of






Autoimmune Diseases




Journal of


Pharmaceutics



of

review article cancer epigenetics: new therapies and new...

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