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Molecular Pathways

Molecular Pathways: ProteinMethyltransferases inCancer

Robert A. Copeland

AbstractThe proteinmethyltransferases (PMT) constitute a large and important class of enzymes that catalyze site-

specific methylation of lysine or arginine residues on histones and other proteins. Site-specific histone

methylation is a critical component of chromatin regulation of gene transcription—a pathway that is often

genetically altered in human cancers. Oncogenic alterations (e.g., mutations, chromosomal translocations,

and others) of PMTs, or of associated proteins, have been found to confer unique dependencies of cancer

cells on the activity of specific PMTs. Examples of potent, selective small-molecule inhibitors of specific PMTs

are reviewed that have been shown to kill cancers cells bearing such oncogenic alterations, while having

minimal effect on proliferation of nonaltered cells. Selective inhibitors of the PMTs,DOT1L and EZH2, have

entered phase I clinical studies and additional examples of selective PMT inhibitors are likely to enter the

clinic soon. The current state of efforts toward clinical testing of selective PMT inhibitors as personalized

cancer therapeutics is reviewed here. Clin Cancer Res; 19(23); 6344–50. �2013 AACR.

BackgroundPosttranslational modifications of histone proteins

play a critical role in defining the local structure ofchromatin (the complex of DNA and histone proteinsthat make up chromosomes) and thereby control entireprograms of gene transcription within cells (1). Bothreversible small-molecule (e.g., acetylation, methylation,and phosphorylation) and protein (e.g., ubiquitinationand sumoylation) modifications of histone are known toaffect nucleosome compacting within chromatin andalso to serve as recognition loci for binding of transcrip-tion factors, polymerases, and auxillary proteins thateither facilitate or antagonize gene transcription (2).Among these various histone modifications (Fig. 1A),methylation of lysine and arginine residues seems toplay a particularly important role in control of genetranscription programs (3–5). These modifications arecatalyzed by a class of group-transfer enzymes known asthe protein methyltransferases (PMT; refs. 3, 6). ThePMT enzyme class is composed of two distinct familiesof enzymes, based on their active site structures and onthe amino acid to which they transfer methyl groups: theprotein lysine methyltransferases (PKMT) and the pro-tein arginine methyltransferases (PRMT; ref. 6). There isone exception to this general structural bifurcation of thePMT class. The enzyme DOT1L is biochemically a lysinemethyltransferase, but its active site structure is most

closely aligned with that of the protein arginine methyl-transferases (6). On the basis of active site structure, anumber of enzymes that had been previously annotatedas RNA methyltransferases can also be included withinthe family of PRMTs, and some of these enzymes havesubsequently been shown biochemically to catalyzeboth RNA and protein methylation (6, 7). Thus, thePMT class is composed of 96 enzymes within humans.Reaction fidelity is variable among the PMTs. In somecases, a single enzyme is responsible for site-specificmethylation of a unique histone location (e.g., DOT1Lmethylation of H3K79; see below). In other cases, sev-eral PMTs seem to methylate a common histone site butmay do so in a gene-specific manner (Fig. 1B). In yetother cases, a single enzyme may methylate multipleprotein substrates.

The PMTs constitute an interesting target class for cancertherapeutics both because of the critical role these enzymesplay in controlling cellular programs of gene transcriptionand because, increasingly, bioinformatic surveillance ofcancer genome databases are showing that a number ofthese enzymes are implicated in specific human cancers(5, 8); in a recent review, for example, Copeland listed over10 PMTs for which genetic alterations are found in specifichuman cancers (8).

PMTs may play critical roles in cancer cells in general,but their greatest value as therapeutic targets may be incases where the oncogenic alterations of PMTs (or ofother proteins that impact PMT activity; see below) asso-ciated with specific human cancers have been shown toconfer to cancer cells a unique dependency on the enzy-matic activity of the altered PMT for proliferation and/orsurvival (i.e., an addiction to PMT activity). Hence, areasonable working hypothesis is that selective inhibitionof the affected PMT would result in cell killing of cancer

Author's Affiliation: Epizyme, Inc., Cambridge, Massachusetts

Corresponding Author: Robert A. Copeland, Epizyme, Inc., 400 Techno-logy Square, Cambridge, MA 02139. Phone: 617-500-0707; Fax: 617-349-0707; E-mail: [email protected]

doi: 10.1158/1078-0432.CCR-13-0223

�2013 American Association for Cancer Research.

ClinicalCancer

Research

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cells bearing the genetic alteration with minimal affect onnonaltered cells. This would be expected to provide asignificant therapeutic index in vivo, with potent elimi-nation of affected tumor cells and limited attendantsafety concerns. Preclinical animal studies of potent,selective inhibitors of two PMTs, DOT1L (9) and EZH2(ref. 10; see below) have borne out these expectations and

have paved the way to clinical testing of PMT inhibitorsin patients with cancer.

Active site structure and enzymatic mechanism ofmethyl transfer

All PMTs use S-adenosyl methionine as a universalmethyl donor in much the same way that all kinases use

© 2013 American Association for Cancer Research

Euchromatin -

Transcriptionally permissive

Site-specific methylation of histones H3 & H4

PMTs

• Arginine (RMTs)• Lysine (KMTs)

CH3

CH3

CpG

PO4R

K KS

K

Ac

Ub

Heterochromatin -

Transcriptionally repressive

MLL1MLL2MLL3MLL4MLL5SET1ASET1BASH1

SET7/9

SUV39H1SUV39H2

G9aGLP

SETDB1CLL8RIZ1

PRDM3PRDM16

PRMT5 CARM1

NDS1NSD2NSD3SET2

SMYD2

EZH1EZH2

DOT1LCARM1PRMT6

SMYD3

Pr-SET7/8SUV4 20H1SUV4-20H2

SET9Pr-SET7SUV4-20

NSD1

PRMT1PRMT5

H3

A

B

N-A

N-S

S S -CK ... ... ... ... ... ... ... ...K K K K KKKT TR

RG G K K K K K

20531

R R V ...... -CHG G G G G G AL

2 4 8 9 17 26 27 36 79R R R

H4

Figure 1. Chromatinmodification affects genetranscription. A, chromatinconsists of histone proteins(red) around whichchromosomal DNA (blue) iswrapped. The histone proteinsundergo a variety ofposttranslational modifications,including methylation ofarginine (R) and lysine (K)residues catalyzed respectivelyby the PMT families of argininemethyltrasferases (RMT) andlysine methyltransferases(KMT). These posttranslationalmodifications affect the state ofcompacting of nucleosomes(histone-DNA units) along thechromosomes. Regions ofchromosomes can transitionfrom the open, transcriptionallypermissive state referred to aseuchromatin to the morecompact, transcriptionallyrespressive state known asheterochromatin. B, PMTscatalyze methylation of specificlysine and arginine residues onhistones H3 and H4. Theenzymes that catalyzemethylation of a specifichistone residue are listed inthe boxes.

PMTs in Cancer

www.aacrjournals.org Clin Cancer Res; 19(23) December 1, 2013 6345




ATP as a universal phosphate donor (Fig. 2). The crystalstructures of a number of PMTs have been solved toatomic resolution and reveal a well-organized S-adenosylmethionine–binding pocket, which is conformationallydistinct between the lysine and arginine methyltrans-ferases (3, 6, 11). In both cases, however, the S-adenosylmethionine–binding pocket is juxtaposed to a long chan-nel into which the methyl-accepting amino acid sidechain binds. This arrangement allows for close proximityand molecular orbital alignment between S-adenosylmethionine and the nitrogen of lysine or arginine forfacile methyl transfer. All of these enzymes transfer themethyl group directly from S-adenosyl methionine to theacceptor amino acid, so that the enzymatic reactionrequires the simultaneous binding of both substrates fortransfer to occur (3). These features of the enzymaticreaction of PMTs afford multiple opportunities for inhib-itor interactions with the enzymes. Indeed, small-mole-cule PMT inhibitors of various binding modalitieshave been reported: S-adenosyl methionine competitive,methyl acceptor competitive, noncompetitive, etc. (5, 8).This diversity of inhibitor-binding modalities distin-guishes the PMTs from other group-transfer enzymesthat have been targeted for cancer therapies (e.g., thekinases) and may allow greater flexibility in choosinginhibitors that offer the greatest chance for clinical trans-lation (12).

Role of PMTs in regulation of gene transcriptionHow site-specific methylation of histone lysines and

arginines controls gene transcription is incompletely under-

stood at present, but it is clear that methylation at specifichistone sites affects downstream transcription in differentways. For example, methylation of histone H3 on lysines 4(H3K4) and 79 (H3K79) has been implicated in the tran-scriptional activation of genes. In contrast, methylation atother locations, such as H3K9 and H3K27, are involved inrepression of gene transcription (13). These opposingeffects of methylation of different histone sites can play acritical role in cancer tumorigenesis when alterations in thelocation and amplitude of specific site methylation leadsto aberrant activation of oncogene transcription and/ortranscriptional repression of tumor suppressor genes. Itis also becoming clear that the effect of site-specific meth-ylation of histone sites on transcription cannot be under-stood in isolation, but depends on the context of othermodifications of proximal histone sites (14). Finally,emerging data suggest that methylation of one histone sitemay enhance or antagonize methylation of other histonesites. For example, data in multiple myeloma cells suggestthat elevated methylation of H3K36 antagonizes methyl-ation of H3K27, and likewise diminution of H3K36 meth-ylation may result in elevation of H3K27 methylationlevels (15).

Genetic alterations of PMT activity as drivers of cancerA variety of genetic alterations are seen in members of

the PMT enzyme class associated with specific humancancers. Ongoing surveillance of cancer genome data-bases is continuing to reveal additional examples ofamplifications and mutations within PMTs and withinPMT-associated proteins that seem to be specific to

© 2013 American Association for Cancer Research

S

CH3

CH3

SAM

PMT

+

+

–

S

SAHNH3

+NH3

+

NH2+

–

NH3+ H3C

CH3

Histone Histone

Lysine

O

ONH

NH2+

O

ONH

H3CNH+

O

ONH

CH3CH3

H3CN+

O

ONH

CH3

H3CNHN

HN

O

ONH

CH3 CH3

NHN

HN

O

ONH

CH3

NHHN

HN

O

ONH

H2N

HN

O

ONH

Arginine

Mono-methyl

lysine

Mono-methyl

arginine

Symmetrical

di-methyl

arginine

Asymmetrical

di-methyl

arginine

Di-methyl

lysine

Tri-methyl

lysine

HMT HMT

HMT HMT or

HMT

PKMTs

PRMTs

Figure 2. Chemical mechanism of PMT catalysis (left) and the products of lysine (top right), and arginine (bottom right) methylation. SAM, S-adenosylmethionine

Copeland

Clin Cancer Res; 19(23) December 1, 2013 Clinical Cancer Research6346




individual cancer types. Over the past decade, severalexamples have emerged of alterations of PMT activitythat seem to be critical drivers of genetically definedcancers (16). Some of these will be described here toexemplify the diversity of diver alterations observed toimpinge on this enzyme class.Indirect chromosomal translocation leading to ectopic

PMT activity. MML-rearranged leukemia is a devastatingform of acute leukemia that affects patients from infancythrough adulthood and is also prevalent among secondaryleukemia associated with the use of etoposide (and othertopoisomerase II inhibitors; ref. 17). This disease is univer-sally associated with a chromosomal translocation (11q23)affecting theMLL gene that encodes for thePMTMLL,whichnormally catalyzes the methylation of the H3K4 residue(18, 19). As a result of the translocation, the MLL proteinloses its enzymatic active site (hence, PMT activity) and isfused to any of a number of proteins within the AF or ENLprotein families (20, 21). Gene localization is conferred byrecognition elements within the N-terminal region of theMLL protein, and these are retained within the variousfusion proteins. Hence, the MLL fusion proteins localize tothe same gene locations aswild-typeMLL, but lack the abilityto catalyze histone methylation at H3K4. It has been recog-nized for some time that this chromosomal translocationplays a causal role in MML-rearranged leukemia, but themolecular mechanism of pathogenesis was not clear. Earlyattention focused on the loss of PMT activity associated withthe fusion proteins that results from the translocation, butthis was hard to reconcile with the residual H3K4 methyl-ation activity of the wild-typeMLL protein resulting from thesecond, unaffected allele. In 2005, Okada and colleagues(22) showed that another enzyme, DOT1L, binds to AF10,one of the various fusionpartner proteins associatedwith theMLL translocation, and thereby recruits DOT1L to ectopicgene locations at which the MLL fusion proteins reside.Subsequent studies revealed that other AF and ENL fusionpartners were also able to directly, or indirectly recruitDOT1L to MLL fusion–bound genes (23–25). The resultingectopic localization of DOT1L catalyzes H3K79methylationof genes otherwise under the control of MLL-catalyzedH3K4 methylation, including proleukemogenic genessuch as HOXA9 and MEIS1 (22, 26, 27). Methylation ofH3K79 is a transcriptional activationmark. Thus, the ectopiclocalization of DOT1L, due to the universal chromosomaltranslocation inMML-rearranged leukemia, results in elevat-ed transcription of a program of leukemogenic genes that inturn drive this proliferative disease. It has been hypothesizedthat MML-rearranged leukemia is uniquely dependent onDOT1L enzymatic activity and that selective inhibition ofDOT1Lwould lead to specific cell killing ofMML-rearrangedleukemia cells. This hypothesis was confirmed by genesilencing approaches (26) and by the use of potent andselective small-molecule inhibitors of DOT1L (see below;refs. 28–30).Direct chromosomal translocations involving PMTs.

WHSC1 (also referred to as MMSET or NSD2) is a PMTthat catalyzes the dimethylation of H3K36 (31, 32).

Methylation of this histone site is associated withregions that are transcriptionally active. The t(4;14)chromosomal translocation occurs in a subset of about15% of multiple myeloma (33, 34), and patients withthis translocation represent one of the worst prognosticsubgroups of multiple myeloma (35). The t(4;14) trans-location results in massive overexpression of WHSC1and of fibroblast growth factor receptor 3 (FGFR3) dueto the placement of the strong immunoglobulin H (IgH)intronic Em enhancer and 30 enhancer in the promoterregions of WHSC1 and FGFR3 genes, respectively. Whileapproximately 30% of t(4;14) patients have lost expres-sion of FGFR3, 100% retain overexpression of WHSC1,suggesting that WHSC1, rather than FGFR3, is theprimary driver of disease (35). The overexpression ofWHSC1 in t(4;14) translocated cells results in signifi-cantly elevated levels of dimethylated H3K36, as wouldbe expected from elevation of catalytic enzyme levels(15). Genetic knockdown of WHSC1 or disruption ofthe translocated allele in t(4;14) myeloma cells results ininhibition of cellular proliferation and of tumorigenic-ity. As expected, genetic knockdown of WHSC1 shows anaccompanying reduction in global levels of H3K36me2(15).

Point mutations affecting PMT activity. The most well-studied example of tumorigenic point mutations affectingPMTactivity is thatofmutationswithin the catalytic domainof EZH2 in germinal center diffuse large B-cell lymphomaand follicular lymphoma subsets of non-Hodgkin lympho-ma (NHL; 36–38). EZH2 (or the closely related EZH1) isthe catalytic subunit of a multiprotein complex knownas PRC2 (polycomb repressive complex 2) that is respon-sible for mono-, di-, and trimethylation of the H3K27 site.Trimethylated H3K27 is a translational repressive mark,and hypertrimethylation of H3K27 has always been foundto lead to tumorigenesis in various human cancers, pre-sumably due to the transcriptional repression of tumorsuppressor genes. Mutations at Tyr641 or Ala677 have beenfound to occur heterozygously in NHL patient groups(36, 37) and have been shown to be change-of-functionmutations with respect to the substrate specificity of theenzyme (38). The wild-type enzyme is most active inplacing the first methyl group on to H3K27 and its catalyticefficiency wanes with consecutive methylation cycles. Indirect contrast, themutations associatedwithNHL show theexact opposite substrate specificity; they are essentiallyunable to put the first methyl group on H3K27, but oncethat first methyl is on, the mutant enzymes are able toput the second methyl on and are extremely efficient atputting the third methyl group on. In the context of diseaseheterozygosity, the wild-type and mutant enzymes workin concert with one another to effect a tumorigenichypertrimethylated H3K27 phenotype (38). Two groupshave now shown that potent-, selective-, small-moleculeinhibitors of EZH2 selectively kill NHL cells bearing theseEZH2 mutations while having essentially no effect onthe proliferation of homozygous EZH2 wild-type cells(39, 40).

PMTs in Cancer





Synthetic lethal associations with PMT activity. In addi-tion to histone methylation, gene expression is alsoregulated by remodeling of nucleosomes in an ATP-dependent manner. Of the ATP-dependent chromatinremodelers, SWI/SNF complexes are emerging as bonafide tumor suppressors, as specific inactivating mutationsin several SWI/SNF subunits are found in human cancers(41). For instance, the INI1 (also known as SMARCB1 orhSNF5) subunit is inactivated in nearly all malignantrhabdoid tumors and atypical teratoid rhabdoid tumors,aggressive cancers of young children with no effectivetherapy (42). Tumorigenesis in INI1-deficient malignantrhabdoid tumors can be completely suppressed by tissuespecific codeletion of EZH2, suggesting an antagonisticrelationship between PRC2 and SWI/SNF activities (43).Recently, Knutson and colleagues (44) have shown thatpotent, selective inhibitors of EZH2 are effective in erad-icating INI1-deficient malignant rhabdoid tumors in cellculture and in a mouse xenograft model. Hence, althoughthe tumorigenetic driver of malignant rhabdoid tumorsoccurs in a pathway distinct from any PMT, it neverthelesscreates a synthetic lethal relationship that confers aunique sensitivity to selective EZH2 inhibition in thisdisease.

Clinical–Translational AdvancesPreclinical in vivo activity of selective PMT inhibitors

Selective inhibitors of several PMTs have beendescribed, and compounds targeting two particular PMTs,DOT1L and EZH2, have been reported to show dramaticantitumor activity in rodent models of disease (9,10, 40, 44). The DOT1L tool compound EPZ004777 wasthe first PMT inhibitor reported to show antitumor effectsin a disseminated mouse model of MLL-rearranged leu-kemia (28). Subsequent pharmacologic optimizationwithin this chemotype series resulted in the clinical can-didate DOT1L inhibitor EPZ-5676, which was also shownto eradicate MLL-rearranged tumors (�100% tumorgrowth inhibition) in a rat xenograft model (9, 45). Twodistinct EZH2 inhibitors have been shown to displaysignificant, dose-dependent antitumor activity in mousexenograft models of EZH2 mutant–bearing NHL tumors(60%–100% tumor growth inhibition in various tumormodels) and of INI1-deficient malignant rhabdoidtumors (�100%tumor growth inhibition; refs. 10, 40, 44).In all of these studies, the compounds were well toleratedby the rodents at doses that resulted in significant tumorgrowth inhibition, with no acute toxicity or weight lossobserved. These results provide a strong foundation forthe clinical testing of DOT1L and EZH2 inhibitors ingenetically defined patients with cancer and also portendthe general use of PMT inhibitors as personalized cancertherapeutics. Also, in all of these studies, the investigatorswere able to show a correlative relationship betweentumor growth inhibition and diminution of the relevanthistone methyl mark in tumor tissue as well as in surro-gate tissues such as skin and peripheral blood mononu-

clear cells. The ability to measure drug-induced loss ofsite-specific histone methylation in surrogate tissue bynoninvasive means provides a cogent basis for pharma-codynamics assessment of target engagement in clinicaltrials.

Clinical trialsAt the time of this writing, two PMT inhibitors have

entered phase I human clinical trials: the DOT1L inhib-itor EPZ-5676 and the EZH2 inhibitor EPZ-6438. Theprimary goal of both of these trials is to assess the safety ofthe drugs and to establish the maximum tolerated dosefor each.

The EPZ-5676 phase I trial is divided into two parts: adose-escalation portion to establish maximum tolerateddose and an expansion cohort of patients treated at themaximum tolerated dose. To accelerate dose escalation,eligibility is not restricted to genetically defined patients;patients with hematologic malignancies (mainly acutemyelogenous leukemia and acute lymphocytic leukemia)are eligible for this portion of the trial. Once the max-imum tolerated dose has been established, the expansioncohort study will begin exclusively in patients withleukemia involving the MLL rearrangement at 11q23. Inthis manner, the drug may be tested as early as possiblein the genetically defined patients for whom it wasdesigned.

The EZH2 inhibitor EPZ-6438 is being studied in aphase I trial of relapsed or refractory malignancies thathave failed all standard therapy. Again, the primary goalhere is to establish the safety and define the maximumtolerated dose of the drug. As with the EPZ-5676 trial, asecondary objective is to test EPZ-6438 as early aspossible in the genetically defined patients for whomthe drug was designed. Hence, once the maximumtolerated dose has been established, a phase IIa trial isplanned exclusively in NHL patients bearing mutationsin EZH2.

No data have yet been reported for either of thesetrials. Nevertheless, these trials represent a true water-shed in the development of PMT inhibitors as person-alized cancer therapeutics. The cancer community will belooking forward with great interest toward the outcomesof these trials. It is clear that these trials represent thevanguard of a much larger array of PMT inhibitors thatwill be entering clinical trials in the near future fortesting against genetically defined groups of patients withcancer.

Disclosure of Potential Conflicts of InterestR.A. Copeland has an ownership interest (including patents) in Epi-

zyme Inc. and is a consultant/advisory board member of Mersana.

AcknowledgmentsThe author thanks Dr. Roy M. Pollock for helpful suggestions.

Received June 24, 2013; revised July 21, 2013; accepted August 7, 2013;published OnlineFirst August 19, 2013.

Copeland





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Copeland





2013;19:6344-6350. Published OnlineFirst August 19, 2013.Clin Cancer Res Robert A. Copeland Molecular Pathways: Protein Methyltransferases in Cancer

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