Published OnlineFirst March 2, 2011; DOI: 10.1158/1078-0432.CCR-10-2156

Clinical Cancer Molecular Pathways Research

Aberrations of EZH2 in Cancer

Andrew Chase and Nicholas C.P. Cross

Abstract Control of expression is exerted at a number of different levels, one of which is the accessibility of and their controlling elements to the transcriptional machinery. Accessibility is dictated broadly by the degree of compaction, which is influenced in part by polycomb group . EZH2, together with SUZ12 and EED, forms the polycomb repressive complex 2 (PRC2), which catalyzes trimethylation of histone H3 lysine 27 (H3K27me3). PRC2 may recruit other polycomb complexes, DNA methyltransferases, and histone deacetylases, resulting in additional transcriptional repressive marks and chromatin compaction at key developmental loci. Overexpression of EZH2 is a marker of advanced and metastatic disease in many solid tumors, including prostate and breast cancer. Mutation of EZH2 Y641 is described in lymphoma and results in enhanced activity, whereas inactivating mutations are seen in poor prognosis myeloid neoplasms. No histone demethylating agents are currently available for treatment of patients, but 3-deazaneplanocin (DZNep) reduces EZH2 levels and H3K27 trimethylation, resulting in reduced cell proliferation in breast and prostate cancer cells in vitro. Furthermore, synergistic effects are seen for combined treatment with DNA demethylating agents and histone deacetylation inhibitors, opening up the possibility of refined epigenetic treatments in the future. Clin Cancer Res; 17(9); 2613–8. 2011 AACR.

Background trithorax homolog myeloid-lymphoid leukemia (MLL), is associated with transcriptional activation (Fig. 1A). Impor- DNA is wrapped around histone complexes termed tantly, many genes involved in development, stem cell nucleosomes, and gene accessibility is determined largely maintenance, and differentiation are targets of H3K27 by the local chromatin configuration. This configuration and H3K4 methylation. In embryonic (1, 2) and hemo- may impact on the ability of cofactors and enhancers to poietic (3) stem cells (HSC), promoters may carry both bind specific DNA sequences, either via direct interactions marks, termed a "bivalent" domain, and genes thus marked with nucleosome components or, more generally, by influ- are thought to be poised for transcriptional activation or encing the degree to which DNA and/or nucleosome com- repression with loss of H3K27 or H3K4 methylation, plexes are compacted into higher structures and, thus, the respectively. physical accessibility of specific recognition sequences. H3K27 methylation is catalyzed by the SET domain of Local chromatin structure is influenced, in part, by histone EZH2 and requires the presence of 2 additional proteins, usage but principally by covalent modifications to histone embryonic ectoderm development (EED) and suppressor tails and DNA methylation. Both PcG and Trx proteins play of zeste 12 (SUZ12). These proteins, together with the important roles in this process by modifying lysine residues histone binding proteins retinoblastoma binding within histone tails, resulting in repression or enhance- 4 (RBBP4) and RBBP7, comprise the core components of ment of transcription. the polycomb repressive complex 2 (PRC2; Fig. 1B). Other Two histone modifications, in particular, play crucial proteins such as PHD finger protein 1 (PHF1), which opposing roles in the epigenetic control of proliferation specifically stimulates H3K27 trimethylation rather than and differentiation. Trimethylation of histone H3 lysine 27 dimethylation (4), sirtuin 1 (SIRT1; ref. 5), and jumonji, AT (H3K27me3), catalyzed by the PcG enhancer of zeste rich interactive domain 2 (Jarid2; refs. 6, 7) have also been homolog 2 (EZH2), is associated with transcriptional described in PRC2 complexes and probably serve modulat- repression, whereas H3K4 methylation, catalyzed by the ing functions. A second polycomb complex, PRC1, cata- lyzes ubiquitination of histone H2A K119, which is also associated with a repressive chromatin structure. PRC1 Authors' Affiliation: Wessex Regional Genetics Laboratory, Salisbury, consists of several proteins including chromobox homolog and Human Genetics Division, University of Southampton Faculty of 2 (CBX2) or related homologs, which bind H3K27me3, Medicine, Southampton, United Kingdom ring finger protein 1A (RING1A), or RING1B, which cat- Corresponding Author: Andrew Chase, Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, United King- alyze ubiquitination and BMI1 polycomb ring finger onco- dom. Phone: 44-1722 336262; Fax: 44-1722 338095; E-mail: gene (BMI1) or polycomb group ring finger 6/Mel18 [email protected] (PCGF2), which modulate ubiquitination activity. doi: 10.1158/1078-0432.CCR-10-2156 According to the hierarchical model of PRC recruitment 2011 American Association for Cancer Research. first developed through genetic studies in Drosophila (8),

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A PRC2

H3K27 H3K27 H3K27 me me me Transcriptional repression X B

MLL SUZ12 EED RBBP4/7

Transcriptional activation EZH2

PolycombPolycomb represrepressivessive me me me complexcomplex (PRC2)(PRC H3K4 H3K4 H3K4 H3K27 H3K27 H3K27 me me me Bivalent domain with low level transcription Gene poised for later me me me activation or repression H3K4 H3K4 H3K4

C PRC2

H3K27 H3K27 H3K27 H3K27 me me me me

Chromatin compaction ub me H2KH2K119119 CytosineCyty osine aacc aac X Repression of targets e.g. HDAC PRC1 DNMT developmental and H2A DNA HHistoneistone differentiation genes uubiquitinationbiquitination metmethylationhylation ddeacetylationeacetylation

D DZNep

MethionineMethionine MethionineMethionine cyclecycle cyclecycle H3K27 H3K277 me3 me3 X PRC2 PRC2

TTranscriptionalransc repression TranscriptionalTranscri derepression © 2011 American Association for Cancer Research

Figure 1. A, PRC2 catalyzes H3K27me associated with transcriptional repression, whereas myeloid-lymphoid leukemia catalyzes methylation of H3K4 associated with transcriptional activation. In bivalent domains, both marks are present and associated with a low level of transcription; genes thus marked are thought to be poised for later transcriptional repression or activation. B, the PRC2 core components are EZH2, SUZ12, EED, and RBBP4 or RBBP7. C, PRC2 is recruited to DNA, resulting in H3K27me3. This mark facilitates recruitment of PRC1, which ubiquitinates H2AK119, DNMT, and HDACs, which contribute to chromatin compaction and transcriptional repression. D, Levels of EZH2 and H3K27me3 can be indirectly reduced by treatment with DZNep, resulting in transcriptional derepression.

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Aberrations of EZH2 in Cancer

PRC2 is first recruited to target genes and catalyzes methy- anchorage-independent colony growth and promotion of lation of H3K27. This step is followed by recruitment of invasion in vitro by overexpression of EZH2 in the breast PRC1 and ubiquitination of H2AK119 (Fig. 1C). This epithelial cell line H16N2 (25). In addition, ectopic EZH2 model would predict that targets of PRC1 and PRC2 largely increased the proliferation of mouse embryonic fibroblasts overlap, as has indeed been shown by RNA interference (33). (RNAi) depletion studies in human embryonic fibroblasts A remarkable connection has been described between (9). In HSCs, however, there is evidence for opposing roles PRC2 occupancy and the aberrant methylation of CpG for PRC1 and PRC2 (10–13). BMI1 is required for HSC islands at promoters seen in some cancers (34–36). Pro- repopulation (10, 12), whereas reduced levels of Suz12, moters found to have aberrant CpG island hypermethyla- Ezh2, or Eed result in increased HSC-progenitor prolifera- tion were also found to be enriched for PRC2 and H3K27 tion (13). In addition, genes known to be repressed by methylation. These sites were also found to be precisely CCAAT/enhancer binding protein alpha (CEBPA) or acti- those occupied by PRC2 in stem cells. Because PRC2 can vated by homeobox A9 (HoxA9) have been found to be recruit DNMTs (19), it seems that PRC2 may act as a differentially regulated by PRC1 and PRC2 (13). It is platform for aberrant de novo promoter methylation, currently not known whether the differential effects of although the precise contexts in which this occurs is still PRC1 and PRC2 seen in HSC also occur in other tissues. unclear. Although PRC2 in Drosophila is recruited to defined Polycomb Response Elements upstream of target genes, EZH2 mutations similar motifs have not been identified in vertebrates. It has Recent work has identified acquired EZH2 mutations in been suggested that recruitment may occur via intermedi- lymphoma and myeloid neoplasms. In lymphoma, a het- ary molecules, with evidence for involvement of the long erozygous missense mutation at amino acid Y641, within noncoding RNA hox transcript antisense RNA (HOTAIR; the SET domain, was initially identified by high throughput refs. 14, 15), nuclear inhibitor of protein Ser/Thr phospha- transcriptome sequencing. Various heterozygous muta- tase-1 (NIPP1; ref. 16), Pho repressive complex (PhoRC; tions at Y641 were subsequently found in 7% of follicular refs. 8, 17), and Jarid2 (18). lymphomas and 22% of diffuse large cell B-cell lymphomas It is clear that activating and repressive histone methyla- of germinal center origin (37). Mutations elsewhere in tion marks do not act in isolation but are intimately EZH2 were not seen. Although initially thought to result coordinated with the action of other epigenetic modifica- in a loss of catalytic activity, more detailed analysis showed tions (Fig. 1C). EZH2 can bind the DNA methyltransferases that Y641 mutants actually result in a gain of function. DNMT1, DNMT3A, and DNMT3B (19), which can result in Specifically, normal EZH2 displays greatest catalytic activity DNA methylation, at least in certain circumstances (20). for monomethylation of H3K27 and relatively weak effi- Knockdown of EZH2 can result in reexpression of genes ciency for the subsequent (mono- to di- and di- to tri- with H3K27 methylation and minimal DNA methylation methylation) reactions. Remarkably, Y641 mutants display but not genes that are hypermethylated (21). Recruitment very limited ability to do the first methylation reaction but of histone deacetylase (HDAC) proteins by PRC2 has been have enhanced catalytic efficiency for the subsequent reac- suggested as a further mechanism for transcriptional tions (38). Heterozygous Y641 mutants, thus, work in repression. PRC2 can bind HDAC via EED (22), and conjunction with wild-type EZH2 to increase levels of treatment of nonerythroid cells with the HDAC inhibitor H3K27me3 and may be functionally equivalent to EZH2 trichostatin A results in depletion of PRC2 and induction of overexpression. a-globin expression, a that is normally tightly In myeloid neoplasms, mutations have been described repressed and marked by hypoacetylation and the presence largely in poor prognosis myelodysplasia-myeloprolifera- of PRC2 and H3K27me3 (23). tive neoplasms (10 to 13%), myelofibrosis (13%), and various subtypes of myelodysplastic syndromes (6%; refs. EZH2 and cancer 39, 40). In contrast to the mutation of a single residue and Overexpression of EZH2 was first linked to cancer by gain of function seen in lymphoma, mutations were spread microarray studies of prostate cancer (24) and breast cancer throughout the gene and comprised missense, nonsense, (25). In prostate cancer, EZH2 overexpression is associated and premature stop codons, some of which were homo- with aggressive and metastatic disease. Similarly in breast zygous. Because the catalytic SET domain lies at the far C cancer, EZH2 expression is elevated in invasive carcinoma terminus, all nonsense and stop codon mutations would be and metastases, and increased expression is strongly asso- predicted to result in loss of histone methyltransferase ciated with a poor clinical outcome (25). Overexpression of activity and, thus, are clearly different functionally from EZH2 has also been described in other cancers including Y641 mutants. The fact that both activating and inactivat- bladder (26–28), gastric (29), lung (30), and hepatocel- ing mutations of EZH2 are associated with malignancy is lular carcinoma (31). Deletions of microRNA-101, a nega- remarkable and reflects the complex role that PcG genes tive regulator of EZH2 expression, have been described in play in cell fate decisions (41). prostate cancer, thus providing a mechanism for EZH2 Mutations of other PRC2 components have not overexpression (32). Experimental support for the onco- been reported, although SUZ12 (also known as JJAZ1) genic action of EZH2 has been provided by induction of fuses to juxtaposed with another zinc finger 1 (JAZF1)in

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endometrial stromal tumors (42). In addition, mutations ferential effects on gene reexpression patterns with different have been reported in a growing number of genes encoding combinatorial approaches with DZNep, DNA demethylat- functionally related epigenetic components. For example, ing agents, and HDAC inhibitors (54). In AML, combined inactivating mutations of ubiquitously transcribed tetratri- treatment with DZNep and the HDAC inhibitor panobino- copeptide repeat gene on X (UTX), an H3K27 stat induced a synergistic apoptotic effect upon primary demethylase, are seen in a wide range of malignancies and leukemia cells compared with normal cells (55). The com- may also be functionally equivalent to EZH2 overexpression plexity of the interactions between different epigenetic (43). Inactivating mutations of the PRC2 downstream sub- marks is highlighted by recent work showing downregula- strate DNMT3A are seen in acute myeloid leukemia (AML; tion of BMI1 and EZH2, by treatment with the HDAC ref. 44), and other PcG members such as ASXL1 (additional inhibitors valproic acid or sodium butyrate by mechanisms sex combs-like 1) are mutated in myeloid malignancies (45). that are currently unclear (56). The concept of "synthetic lethality" refers to the depen- Clinical-Translational Advances dency of a tumor on the presence of either 1 of 2 genes, but with resulting cell death if both are lost. Recently, a possible The therapeutic modulation of epigenetic marks has led "synthetic lethal" relationship between EZH2 and BRCA1 to improvements in treatment of some cancers, for exam- was described. BRCA1 plays a role in differentiation of ple, the use of DNA demethylating agents azacytidine and breast stem cells in addition to a well-documented role in decitabine for myelodysplastic syndrome (46, 47) and the DNA repair. In a mouse model of basal-type tumors (which HDAC inhibitor suberoylanilide hydroxamic acid (vorino- are generally poorly differentiated and do not express stat) for cutaneous T-cell lymphoma (48). In contrast to ERBB2, estrogen, or progesterone receptors and are, there- DNA demethylating agents and HDAC inhibitors, no thera- fore, without rational therapeutic targets), EZH2 expression pies that directly target histone methylation are clinically was found to be higher in BRCA1-deficient tumors com- available, despite the fact that there is experimental evi- pared with those that were wild-type. Remarkably, knock- dence for a potential therapeutic benefit for this approach. down of EZH2 by RNAi or by treatment with DZNep was Most experimental work on the inhibition of EZH2 activity 20 times more efficient at killing BRCA1-deficient cells has used the carbocyclic adenosine analog 3-deazanepla- (57). Further work has shown that EZH2 knockdown nocin (DZNep), a derivative of the naturally occurring can result in increased BRCA1 expression with a concomi- antibiotic neplanocin-A, in which ribose is replaced by a tant contribution to reduced proliferation (58). cyclopentyl ring (49). DZNep inhibits S-adenosylhomo- Although the development of histone demethylating cysteine hydrolase, a component of the methionine cycle, agents is an area of great interest, currently no compounds resulting in accumulation of the inhibitory S-adenosylho- are approved for treatment or in clinical trials. However, it mocysteine with a knock-on disruption of methylation of is clear that modulation of EZH2 levels and H3K27 methy- substrates by EZH2 (Fig. 1D). The effect of DZNep upon lation can be achieved by therapies primarily directed at histone methylation is, therefore, global rather than EZH2 DNA methylation or histone acetylation. Although there is specific (50). A comparison of DZNep action and specific an obvious rationale for inhibiting EZH2 function in knockdown of EZH2 by targeted RNAi has shown inter- malignancies in which this gene is overactive as a conse- esting differences; DZNep reduces levels of EZH2 protein quence of overexpression or Y641 mutation, the finding of but not the mRNA, whereas RNAi reduces both protein and inactivating mutations in myeloid neoplasms suggests that mRNA levels. Both strategies result in loss of H3K27 this approach will need to be employed with caution. methylation but differ somewhat in the pattern of genes Understanding how to effectively combine current treat- that are reexpressed (51). Inhibition of EZH2 by either ments with future histone demethylating agents will be a DZNep or RNAi leads to reduced proliferation in a subset major challenge in the coming years. of breast cancer cell lines (51) and reduced proliferation and invasiveness in prostate cancer cell lines (24, 51, 52). Disclosure of Potential Conflicts of Interest After initial work on DZNep as a single agent histone methylation inhibitor, in vitro experimental work pro- No potential conflicts of interest were disclosed. gressed to the use of combinatorial approaches to modify The costs of publication of this article were defrayed in part by the histone methylation, acetylation, and DNA methylation. In payment of page charges. This article must therefore be hereby marked breast cancer cell lines, DZNep treatment and HDAC advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. inhibition result in synergistic effects upon proliferation, apoptosis, differentiation, and cell cycle arrest (53). Chro- Received November 24, 2010; revised January 10, 2011; accepted January matin immunoprecipitation experiments have shown dif- 11, 2011; published OnlineFirst March 2, 2011.

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Aberrations of EZH2 in Cancer

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2618 Clin Cancer Res; 17(9) May 1, 2011 Clinical Cancer Research

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Aberrations of EZH2 in Cancer

Andrew Chase and Nicholas C.P. Cross

Clin Cancer Res 2011;17:2613-2618. Published OnlineFirst March 2, 2011.

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