Epigenetic dysregulation in hepatocellular carcinoma: focus on polycomb group proteins

Abstract

Hepatocellular carcinoma (HCC) development is characterized by the presence of epigenetic alterations, including promoter DNA hypermethylation and post-translational modifications of histone, which profoundly affect expression of a wide repertoire of genes critical for cancer development. Emerging data suggest that deregulation of polycomb group (PcG) proteins, which are key chromatin modifiers repressing gene transcription during developmental stage, plays a causative role in oncogenesis. PcG proteins assemble into polycomb repressive complex 1 (PRC1) and polycomb repressive complex 2 (PRC2) to impose the histone H3 lysine 27 trimethylation (H3K27me3) modification for repression. In this review, we will first recapitulate the mechanisms of two key epigenetic pathways: DNA methylation and histone modifications. Specifically, we will focus our discussion on the molecular roles of PcG proteins. Next, we will highlight recent findings on PcG proteins, their clinicopathological implication and their downstream molecular consequence in hepatocarcinogenesis. Last but not least, we will consider the therapeutic potential of targeting enhancer of zeste homolog 2 (EZH2) as a possible treatment for HCC. Improving our understanding on the roles of PcG proteins in hepatocarcinogenesis can benefit the development of epigenetic-based therapy.

Keywords

liver cancer / epigenetics / histone modifications / polycomb group proteins / enhancer of zeste homolog 2 (EZH2)

References

[1] Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin2011; 61(2): 69–90

[2] Ferlay Ja. GLOBOCAN 2008, Cancer Incidence and Mortality Worldwide: IARC CancerBase. 2008; Available from: http://globocan.iarc.fr/(Accessed on October 1, 2012)

[3] Tang ZY. Hepatocellular carcinoma—cause, treatment and metastasis. World J Gastroenterol2001; 7(4): 445–454

[4] Jones PA, Baylin SB. The epigenomics of cancer. Cell2007; 128(4): 683–692

[5] Jones PA, Laird PW. Cancer epigenetics comes of age. Nat Genet1999; 21(2): 163–167

[6] Riggs AD. X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet1975; 14(1): 9–25

[7] Holliday R, Pugh JE. DNA modification mechanisms and gene activity during development. Science1975; 187(4173): 226–232

[8] Kondoh N, Wakatsuki T, Hada A, Shuda M, Tanaka K, Arai M, Yamamoto M. Genetic and epigenetic events in human hepatocarcinogenesis. Int J Oncol2001; 18(6): 1271–1278

[9] Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet2002; 3(6): 415–428

[10] Turker MS. The establishment and maintenance of DNA methylation patterns in mouse somatic cells. Semin Cancer Biol1999; 9(5): 329–337

[11] Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet1998; 19(2): 187–191

[12] Wong CM, Ng YL, Lee JM, Wong CC, Cheung OF, Chan CY, Tung EK, Ching YP, Ng IO. Tissue factor pathway inhibitor-2 as a frequently silenced tumor suppressor gene in hepatocellular carcinoma. Hepatology2007; 45(5): 1129–1138

[13] Tung EK, Wong CM, Yau TO, Lee JM, Ching YP, Ng IO. HAI-2 is epigenetically downregulated in human hepatocellular carcinoma, and its Kunitz domain type 1 is critical for anti-invasive functions. Int J Cancer2009; 124(8): 1811–1819

[14] Gama-Sosa MA, Slagel VA, Trewyn RW, Oxenhandler R, Kuo KC, Gehrke CW, Ehrlich M. The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res1983; 11(19): 6883–6894

[15] Lister R, Ecker JR. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res2009; 19(6): 959–966

[16] Kanai Y. Genome-wide DNA methylation profiles in precancerous conditions and cancers. Cancer Sci2010; 101(1): 36–45

[17] Ehrlich M. DNA methylation in cancer: too much, but also too little. Oncogene2002; 21(35): 5400–5413

[18] Saito Y, Kanai Y, Sakamoto M, Saito H, Ishii H, Hirohashi S. Expression of mRNA for DNA methyltransferases and methyl-CpG-binding proteins and DNA methylation status on CpG islands and pericentromeric satellite regions during human hepatocarcinogenesis. Hepatology2001; 33(3): 561–568

[19] Kornberg RD, Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell1999; 98(3): 285–294

[20] Böhm L, Crane-Robinson C. Proteases as structural probes for chromatin: the domain structure of histones. Biosci Rep1984; 4(5): 365–386

[21] Strahl BD, Allis CD. The language of covalent histone modifications. Nature2000; 403(6765): 41–45

[22] Jenuwein T, Allis CD. Translating the histone code. Science2001; 293(5532): 1074–1080

[23] Lewis EB. A gene complex controlling segmentation in Drosophila. Nature1978; 276(5688): 565–570

[24] Levine SS, King IF, Kingston RE. Division of labor in polycomb group repression. Trends Biochem Sci2004; 29(9): 478–485

[25] Otte AP, Kwaks TH. Gene repression by Polycomb group protein complexes: a distinct complex for every occasion? Curr Opin Genet Dev2003; 13(5): 448–454

[26] Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 2002; 298(5595): 1039–1043

[27] Sing A, Pannell D, Karaiskakis A, Sturgeon K, Djabali M, Ellis J, Lipshitz HD, Cordes SP. A vertebrate Polycomb response element governs segmentation of the posterior hindbrain. Cell2009; 138(5): 885–897

[28] Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y. Role of histone H3 lysine 27 methylation in X inactivation. Science2003; 300(5616): 131–135

[29] Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell2008; 32(2): 232–246

[30] Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell2007; 129(7): 1311–1323

[31] Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K, Koseki H, Fuchikami T, Abe K, Murray HL, Zucker JP, Yuan B, Bell GW, Herbolsheimer E, Hannett NM, Sun K, Odom DT, Otte AP, Volkert TL, Bartel DP, Melton DA, Gifford DK, Jaenisch R, Young RA. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell2006; 125(2): 301–313

[32] Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev2006; 20(9): 1123–1136

[33] Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young RA, Jaenisch R. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature2006; 441(7091): 349–353

[34] Juan AH, Kumar RM, Marx JG, Young RA, Sartorelli V. Mir-214-dependent regulation of the polycomb protein Ezh2 in skeletal muscle and embryonic stem cells. Mol Cell2009; 36(1): 61–74

[35] Montgomery ND, Yee D, Chen A, Kalantry S, Chamberlain SJ, Otte AP, Magnuson T. The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation. Curr Biol2005 24;15(10): 942–947

[36] Pasini D, Bracken AP, Jensen MR, Lazzerini Denchi E, Helin K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J2004; 23(20): 4061–4071

[37] Cao R, Zhang Y. SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol Cell2004; 15(1): 57–67

[38] Cai MY, Tong ZT, Zheng F, Liao YJ, Wang Y, Rao HL, Chen YC, Wu QL, Liu YH, Guan XY, Lin MC, Zeng YX, Kung HF, Xie D. EZH2 protein: a promising immunomarker for the detection of hepatocellular carcinomas in liver needle biopsies. Gut2011; 60(7): 967–976

[39] Sasaki M, Ikeda H, Itatsu K, Yamaguchi J, Sawada S, Minato H, Ohta T, Nakanuma Y. The overexpression of polycomb group proteins Bmi1 and EZH2 is associated with the progression and aggressive biological behavior of hepatocellular carcinoma. Lab Invest2008; 88(8): 873–882

[40] Sudo T, Utsunomiya T, Mimori K, Nagahara H, Ogawa K, Inoue H, Wakiyama S, Fujita H, Shirouzu K, Mori M. Clinicopathological significance of EZH2 mRNA expression in patients with hepatocellular carcinoma. Br J Cancer2005; 92(9): 1754–1758

[41] Au SL, Wong CC, Lee JM, Fan DN, Tsang FH, Ng IO, Wong CM. Enhancer of zeste homolog 2 epigenetically silences multiple tumor suppressor microRNAs to promote liver cancer metastasis. Hepatology2012; 56(2): 622–631

[42] Cai MY, Hou JH, Rao HL, Luo RZ, Li M, Pei XQ, Lin MC, Guan XY, Kung HF, Zeng YX, Xie D. High expression of H3K27me3 in human hepatocellular carcinomas correlates closely with vascular invasion and predicts worse prognosis in patients. Mol Med2011; 17(1–2): 12–20

[43] Takigawa Y, Brown AM. Wnt signaling in liver cancer. Curr Drug Targets2008; 9(11): 1013–1024

[44] Cheng AS, Lau SS, Chen Y, Kondo Y, Li MS, Feng H, Ching AK, Cheung KF, Wong HK, Tong JH, Jin H, Choy KW, Yu J, To KF, Wong N, Huang TH, Sung JJ. EZH2-mediated concordant repression of Wnt antagonists promotes β-catenin-dependent hepatocarcinogenesis. Cancer Res2011; 71(11): 4028–4039

[45] Gramantieri L, Fornari F, Callegari E, Sabbioni S, Lanza G, Croce CM, Bolondi L, Negrini M. MicroRNA involvement in hepatocellular carcinoma. J Cell Mol Med2008; 12(6A): 2189–2204

[46] Ji J, Wang XW. New kids on the block: diagnostic and prognostic microRNAs in hepatocellular carcinoma. Cancer Biol Ther2009; 8(18): 1686–1693

[47] Huntzinger E, Izaurralde E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet2011; 12(2): 99–110

[48] Zheng F, Liao YJ, Cai MY, Liu YH, Liu TH, Chen SP, Bian XW, Guan XY, Lin MC, Zeng YX, Kung HF, Xie D. The putative tumour suppressor microRNA-124 modulates hepatocellular carcinoma cell aggressiveness by repressing ROCK2 and EZH2. Gut2012; 61(2): 278–289

[49] Varambally S, Cao Q, Mani RS, Shankar S, Wang X, Ateeq B, Laxman B, Cao X, Jing X, Ramnarayanan K, Brenner JC, Yu J, Kim JH, Han B, Tan P, Kumar-Sinha C, Lonigro RJ, Palanisamy N, Maher CA, Chinnaiyan AM. Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science2008; 322(5908): 1695–1699

[50] Sander S, Bullinger L, Klapproth K, Fiedler K, Kestler HA, Barth TF, Möller P, Stilgenbauer S, Pollack JR, Wirth T. MYC stimulates EZH2 expression by repression of its negative regulator miR-26a. Blood2008; 112(10): 4202–4212

[51] Cao Q, Mani RS, Ateeq B, Dhanasekaran SM, Asangani IA, Prensner JR, Kim JH, Brenner JC, Jing X, Cao X, Wang R, Li Y, Dahiya A, Wang L, Pandhi M, Lonigro RJ, Wu YM, Tomlins SA, Palanisamy N, Qin Z, Yu J, Maher CA, Varambally S, Chinnaiyan AM. Coordinated regulation of polycomb group complexes through microRNAs in cancer. Cancer Cell2011; 20(2): 187–199

[52] Squazzo SL, O’Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res2006; 16(7): 890–900

[53] Kirmizis A, Bartley SM, Farnham PJ. Identification of the polycomb group protein SU(Z)12 as a potential molecular target for human cancer therapy. Mol Cancer Ther2003; 2(1): 113–121

[54] Wang WH, Studach LL, Andrisani OM. Proteins ZNF198 and SUZ12 are down-regulated in hepatitis B virus (HBV) X protein-mediated hepatocyte transformation and in HBV replication. Hepatology2011; 53(4): 1137–1147

[55] Studach LL, Menne S, Cairo S, Buendia MA, Hullinger RL, Lefrançois L, Merle P, Andrisani OM. A subset of Suz12/PRC2 target genes is activated during HBV replication and liver carcinogenesis associated with hepatitis B virus X protein.Hepatology2012; 56(4): 1240–1251

[56] Gao Z, Zhang J, Bonasio R, Strino F, Sawai A, Parisi F, Kluger Y, Reinberg D. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol Cell2012; 45(3): 344–356

[57] Morey L, Pascual G, Cozzuto L, Roma G, Wutz A, Benitah SA, Di Croce L. Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells. Cell Stem Cell2012; 10(1): 47–62

[58] van der Lugt NM, Alkema M, Berns A, Deschamps J. The Polycomb-group homolog Bmi-1 is a regulator of murine Hox gene expression. Mech Dev1996; 58(1–2): 153–164

[59] Akasaka T, Kanno M, Balling R, Mieza MA, Taniguchi M, Koseki H. A role for mel-18, a polycomb group-related vertebrate gene, during theanteroposterior specification of the axial skeleton. Development1996; 122(5): 1513–1522

[60] Effendi K, Mori T, Komuta M, Masugi Y, Du W, Sakamoto M. Bmi-1 gene is upregulated in early-stage hepatocellular carcinoma and correlates with ATP-binding cassette transporter B1 expression. Cancer Sci2010; 101(3): 666–672

[61] Wang H, Pan K, Zhang HK, Weng DS, Zhou J, Li JJ, Huang W, Song HF, Chen MS, Xia JC. Increased polycomb-group oncogene Bmi-1 expression correlates with poor prognosis in hepatocellular carcinoma. J Cancer Res Clin Oncol2008; 134(5): 535–541

[62] Schuringa JJ, Vellenga E. Role of the polycomb group gene BMI1 in normal and leukemic hematopoietic stem and progenitor cells. Curr Opin Hematol2010; 17(4): 294–299

[63] Xu CR, Lee S, Ho C, Bommi P, Huang SA, Cheung ST, Dimri GP, Chen X. Bmi1 functions as an oncogene independent of Ink4A/Arf repression in hepatic carcinogenesis. Mol Cancer Res2009; 7(12): 1937–1945

[64] Chiba T, Zheng YW, Kita K, Yokosuka O, Saisho H, Onodera M, Miyoshi H, Nakano M, Zen Y, Nakanuma Y, Nakauchi H, Iwama A, Taniguchi H. Enhanced self-renewal capability in hepatic stem/progenitor cells drives cancer initiation. Gastroenterology2007; 133(3): 937–950

[65] Chiba T, Miyagi S, Saraya A, Aoki R, Seki A, Morita Y, Yonemitsu Y, Yokosuka O, Taniguchi H, Nakauchi H, Iwama A. The polycomb gene product BMI1 contributes to the maintenance of tumor-initiating side population cells in hepatocellular carcinoma. Cancer Res2008; 68(19): 7742–7749

[66] O’Loghlen A, Muñoz-Cabello AM, Gaspar-Maia A, Wu HA, Banito A, Kunowska N, Racek T, Pemberton HN, Beolchi P, Lavial F, Masui O, Vermeulen M, Carroll T, Graumann J, Heard E, Dillon N, Azuara V, Snijders AP, Peters G, Bernstein E, Gil J. MicroRNA regulation of Cbx7 mediates a switch of Polycomb orthologs during ESC differentiation. Cell Stem Cell2012; 10(1): 33–46

[67] Karamitopoulou E, Pallante P, Zlobec I, Tornillo L, Carafa V, Schaffner T, Borner M, Diamantis I, Esposito F, Brunner T, Zimmermann A, Federico A, Terracciano L, Fusco A. Loss of the CBX7 protein expression correlates with a more aggressive phenotype in pancreatic cancer. Eur J Cancer2010; 46(8): 1438–1444

[68] Pallante P, Terracciano L, Carafa V, Schneider S, Zlobec I, Lugli A, Bianco M, Ferraro A, Sacchetti S, Troncone G, Fusco A, Tornillo L. The loss of the CBX7 gene expression represents an adverse prognostic marker for survival of colon carcinoma patients. Eur J Cancer2010; 46(12): 2304–2313

[69] Forzati F, Federico A, Pallante P, Abbate A, Esposito F, Malapelle U, Sepe R, Palma G, Troncone G, Scarfò M, Arra C, Fedele M, Fusco A. CBX7 is a tumor suppressor in mice and humans. J Clin Invest2012; 122(2): 612–623

[70] Brown JL, Mucci D, Whiteley M, Dirksen ML, Kassis JA. The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol Cell1998; 1(7): 1057–1064

[71] Wilkinson FH, Park K, Atchison ML. Polycomb recruitment to DNA in vivo by the YY1 REPO domain. Proc Natl Acad Sci USA2006; 103(51): 19296–19301

[72] Notarbartolo M, Giannitrapani L, Vivona N, Poma P, Labbozzetta M, Florena A M, Porcasi R, Rosario Muggeo V M, Sandonato L, Cervello M, Montalto G, D’Alessandro N. Frequent alteration of the Yin Yang 1/Raf-1 kinase inhibitory protein ratio in hepatocellular carcinoma. OMICS: A Journal of Integrative Biology2011; 15(5): 267–272

[73] Zhang S, Jiang T, Feng L, Sun J, Lu H, Wang Q, Pan M, Huang D, Wang X, Wang L, Jin H. Yin Yang-1 suppresses differentiation of hepatocellular carcinoma cells through the downregulation of CCAAT/enhancer-binding protein alpha. J Mol Med (Berl)2012; 90(9): 1069–1077

[74] Zhang L, Cai X, Chen K, Wang Z, Wang L, Ren M, Huang A, Tang H. Hepatitis B virus protein up-regulated HLJ1 expression via the transcription factor YY1 in human hepatocarcinoma cells. Virus Res2011; 157(1): 76–81

[75] García E, Marcos-Gutiérrez C, del Mar Lorente M, Moreno JC, Vidal M. RYBP, a new repressor protein that interacts with components of the mammalian polycomb complex, and with the transcription factor YY1. EMBO J1999; 18(12): 3404–3418

[76] Tavares L, Dimitrova E, Oxley D, Webster J, Poot R, Demmers J, Bezstarosti K, Taylor S, Ura H, Koide H, Wutz A, Vidal M, Elderkin S, Brockdorff N. RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. Cell2012; 148(4): 664–678

[77] Chen D, Zhang J, Li M, Rayburn ER, Wang H, Zhang R. RYBP stabilizes p53 by modulating MDM2. EMBO Rep2009; 10(2): 166–172

[78] Baylin SB, Jones PA. A decade of exploring the cancer epigenome- biological and translational implications. Nat Rev Cancer2011; 11(10): 726–734

[79] Chiang PK, Cantoni GL. Perturbation of biochemical transmethylations by 3-deazaadenosine in vivo. Biochem Pharmacol1979; 28(12): 1897–1902

[80] Tan J, Yang X, Zhuang L, Jiang X, Chen W, Lee PL, Karuturi RK, Tan PB, Liu ET, Yu Q. Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev2007; 21(9): 1050–1063

[81] Miranda TB, Cortez CC, Yoo CB, Liang G, Abe M, Kelly TK, Marquez VE, Jones PA. DZNep is a global histone methylation inhibitor that reactivates developmental genes not silenced by DNA methylation. Mol Cancer Ther2009; 8(6): 1579–1588

[82] Fiskus W, Wang Y, Sreekumar A, Buckley KM, Shi H, Jillella A, Ustun C, Rao R, Fernandez P, Chen J, Balusu R, Koul S, Atadja P, Marquez VE, Bhalla KN. Combined epigenetic therapy with the histone methyltransferase EZH2 inhibitor 3-deazaneplanocin A and the histone deacetylase inhibitor panobinostat against human AML cells. Blood2009; 114(13): 2733–2743

[83] Cheng LL, Itahana Y, Lei ZD, Chia NY, Wu Y, Yu Y, Zhang SL, Thike AA, Pandey A, Rozen S, Voorhoeve PM, Yu Q, Tan PH, Bay BH, Itahana K, Tan P. TP53 genomic status regulates sensitivity of gastric cancer cells to the histone methylation inhibitor 3-deazaneplanocin A (DZNep). Clin Cancer Res2012 1;18(15): 4201–4212

[84] Chiba T, Suzuki E, Negishi M, Saraya A, Miyagi S, Konuma T, Tanaka S, Tada M, Kanai F, Imazeki F, Iwama A, Yokosuka O. 3-Deazaneplanocin A is a promising therapeutic agent for the eradication of tumor-initiating hepatocellular carcinoma cells. Int J Cancer2012; 130(11): 2557–2567

[85] Chen Y, Lin MC, Yao H, Wang H, Zhang AQ, Yu J, Hui CK, Lau GK, He ML, Sung J, Kung HF. Lentivirus-mediated RNA interference targeting enhancer of zeste homolog 2 inhibits hepatocellular carcinoma growth through down-regulation of stathmin. Hepatology2007; 46(1): 200–208

Acknowledgements

The study was supported by Hong Kong Research Grants Council General Research Fund (HKU 782411M to C. M. Wong), the University of Hong Kong Seed Funding Programme for Basic Research (200811159061 to C. M. Wong) and Hong Kong Research Grants Council Collaborative Research Fund (HKU 7/CRG/09 to I.O.L. Ng). I.O.L. Ng is Loke Yew Professor in Pathology.

Conflict of interest All authors declare no conflict of interest.

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