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DNA and Histone Methylation in Liver Cancer

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Part of the book series: Cancer Drug Discovery and Development ((CDD&D))

Abstract

Epigenetic alterations, such as alterations of histone modification and DNA methylation, occur in a genome-wide manner under precancerous conditions resulting from hepatitis B virus (HBV) or hepatitis C virus (HCV) infection followed by chronic hepatitis and cirrhosis, or aberrant lipogenesis and abnormal metabolism of reactive oxygen species that characterize the pathophysiology of non-alcoholic steatohepatitis (NASH). Once DNA methylation alterations occur at the precancerous stage, they are stably preserved on DNA double strands through methylation maintenance by DNA methyltransferase 1 (DNMT1). DNA methylation alterations associated with abnormalities of DNA methyltransferase, such as overexpression of DNMT1 and splicing alterations of DNMT3B, participate in multistage hepatocarcinogenesis from the precancerous stage to the malignant progression stage and are correlated with aggressiveness of hepatocellular carcinomas (HCCs) and poorer outcome of affected patients. A number of tumor-related genes, such as ATK3, APC, BMP4, CCL20, CDH1, CDKN2A, CDKN2B, CSPG2, DAB2IP, DCC, DLC1, DPT, DPYSL3, EMILIN2, FZD7, GRASP, GSTP1, HIST1H4F, IGFALS, MGMT, MZB1, NAT2, NEFH, NFATC1, PAX4, PDSS2, PER3, PROZ, PYCARD, RASSF1A, SPDY1, RUNX3, SCGB1D1, SFN, SMPD3, SOCS1, TIMP3, TLX3, TM6SF1, TRIM33, TRIM58, WFDC6, WNK2 and ZFP41, are known to be silenced by DNA hypermethylation in human HCCs. It is believed that DNA methylation alterations could be excellent biomarkers for carcinogenetic risk estimation and prognostication. To facilitate clinical application of DNA methylation diagnosis, a scaled-down device that allows quick and accurate analysis, even in small hospitals and clinics, is now being developed. One therapeutic strategy against HCC proliferation could involve a combination of epigenetic modifiers, such as a DNA methylation inhibitor, a histone deacetylase inhibitor and an S-adenosylhomocysteine hydrolase inhibitor, to sensitize cancer cells to conventional chemotherapies, in addition to eradication of hepatitis viruses for personalized and/or pre-emptive medical care.

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References

  1. Arai E, Kanai Y (2010) DNA methylation profiles in precancerous tissue and cancers: carcinogenetic risk estimation and prognostication based on DNA methylation status. Epigenomics 2:467–481

    Article  CAS  PubMed  Google Scholar 

  2. Arai E, Ushijima S, Gotoh M, Ojima H, Kosuge T, Hosoda F, Shibata T, Kondo T, Yokoi S, Imoto I, Inazawa J, Hirohashi S, Kanai Y (2009) Genome-wide DNA methylation profiles in liver tissue at the precancerous stage and in hepatocellular carcinoma. Int J Cancer 125:2854–2862

    Article  CAS  PubMed  Google Scholar 

  3. Arai E, Chiku S, Mori T, Gotoh M, Nakagawa T, Fujimoto H, Kanai Y (2012) Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas. Carcinogenesis 33:1487–1493

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Armeanu S, Pathil A, Venturelli S, Mascagni P, Weiss TS, Göttlicher M, Gregor M, Lauer UM, Bitzer M (2005) Apoptosis on hepatoma cells but not on primary hepatocytes by histone deacetylase inhibitors valproate and ITF2357. J Hepatol 42:210–217

    Article  CAS  PubMed  Google Scholar 

  5. Asrih M, Jornayvaz FR (2015) Metabolic syndrome and nonalcoholic fatty liver disease: is insulin resistance the link? Mol Cell Endocrinol 418(Pt 1):55–65

    Article  CAS  PubMed  Google Scholar 

  6. Bae HJ, Jung KH, Eun JW, Shen Q, Kim HS, Park SJ, Shin WC, Yang HD, Park WS, Lee JY, Nam SW (2015) MicroRNA-221 governs tumor suppressor HDAC6 to potentiate malignant progression of liver cancer. J Hepatol 63:408–419

    Article  CAS  PubMed  Google Scholar 

  7. Belloni L, Allweiss L, Guerrieri F, Pediconi N, Volz T, Pollicino T, Petersen J, Raimondo G, Dandri M, Levrero M (2012) IFN-α inhibits HBV transcription and replication in cell culture and in humanized mice by targeting the epigenetic regulation of the nuclear cccDNA minichromosome. J Clin Invest 122:529–537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R (2011) High density DNA methylation array with single CpG site resolution. Genomics 98:288–295

    Article  CAS  PubMed  Google Scholar 

  9. Buurman R, Sandbothe M, Schlegelberger B, Skawran B (2016) HDAC inhibition activates the apoptosome via Apaf1 upregulation in hepatocellular carcinoma. Eur J Med Res 21:26

    Article  PubMed  PubMed Central  Google Scholar 

  10. Buzzanco A, Gomez A, Rodriguez E, French BA, Tillman BA, Chang S, Ganapathy E, Junrungsee S, Zarrinpar A, Agopian VG, Naini BV, French SW Jr, French SW Sr (2014) Digital quantitation of HCC-associated stem cell markers and protein quality control factors using tissue arrays of human liver sections. Exp Mol Pathol 97:399–410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Chen J, Wu M, Zhang X, Zhang W, Zhang Z, Chen L, He J, Zheng Y, Chen C, Wang F, Hu Y, Zhou X, Wang C, Xu Y, Lu M, Yuan Z (2013) Hepatitis B virus polymerase impairs interferon-α-induced STA T activation through inhibition of importin-α5 and protein kinase C-δ. Hepatology 57:470–482

    Article  CAS  PubMed  Google Scholar 

  12. Chiba T, Suzuki E, Negishi M, Saraya A, Miyagi S, Konuma T, Tanaka S, Tada M, Kanai F, Imazeki F, Iwama A, Yokosuka O (2012) 3-Deazaneplanocin A is a promising therapeutic agent for the eradication of tumor-initiating hepatocellular carcinoma cells. Int J Cancer 130:2557–2567

    Article  CAS  PubMed  Google Scholar 

  13. Claycombe KJ, Brissette CA, Ghribi O (2015) Epigenetics of inflammation, maternal infection, and nutrition. J Nutr 145:1109S–1115S

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R (2003) Sensitive and quantitative universal pyrosequencing methylation analysis of CpG sites. BioTechniques 35:146–150

    CAS  PubMed  Google Scholar 

  15. Ding ZY, Jin GN, Wang W, Chen WX, Wu YH, Ai X, Chen L, Zhang WG, Liang HF, Laurence A, Zhang MZ, Datta PK, Zhang B, Chen XP (2014) Reduced expression of transcriptional intermediary factor 1 gamma promotes metastasis and indicates poor prognosis of hepatocellular carcinoma. Hepatology 60:1620–1636

    Article  CAS  PubMed  Google Scholar 

  16. Fan J, Lou B, Chen W, Zhang J, Lin S, Lv FF, Chen Y (2014) Down-regulation of HDAC5 inhibits growth of human hepatocellular carcinoma by induction of apoptosis and cell cycle arrest. Tumour Biol 35:11523–11532

    Article  CAS  PubMed  Google Scholar 

  17. Fasano M, Theise ND, Nalesnik M, Goswami S (1998) Garcia de Davila MT, Finegold MJ, Greco MA. Immunohistochemical evaluation of hepatoblastomas with use of the hepatocyte-specific marker, hepatocyte paraffin 1, and the polyclonal anti-carcinoembryonic antigen. Mod Pathol 11:934–938

    CAS  PubMed  Google Scholar 

  18. Fei Q, Shang K, Zhang J, Chuai S, Kong D, Zhou T, Fu S, Liang Y, Li C, Chen Z, Zhao Y, Yu Z, Huang Z, Hu M, Ying H, Chen Z, Zhang Y, Xing F, Zhu J, Xu H, Zhao K, Lu C, Atadja P, Xiao ZX, Li E, Shou J (2015) Histone methyltransferase SETDB1 regulates liver cancer cell growth through methylation of p53. Nat Commun 6:8651

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark SJ (2006) Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet 38:540–549

    Article  CAS  PubMed  Google Scholar 

  20. Fu Y, Feng MX, Yu J, Ma MZ, Liu XJ, Li J, Yang XM, Wang YH, Zhang YL, Ao JP, Xue F, Qin W, Gu J, Xia Q, Zhang ZG (2014) DNA methylation-mediated silencing of matricellular protein dermatopontin promotes hepatocellular carcinoma metastasis by α3β1 integrin-Rho GTPase signaling. Oncotarget 5:6701–6715

    Article  PubMed  PubMed Central  Google Scholar 

  21. Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, Nakagawa H (2012) Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet 44:760–764

    Article  CAS  PubMed  Google Scholar 

  22. Gahr S, Mayr C, Kiesslich T, Illig R, Neureiter D, Alinger B, Ganslmayer M, Wissniowski T, Fazio PD, Montalbano R, Ficker JH, Ocker M, Quint K (2015) The pan–deacetylase inhibitor panobinostat affects angiogenesis in hepatocellular carcinoma models via modulation of CTGF expression. Int J Oncol 47:963–970

    CAS  PubMed  Google Scholar 

  23. Gardner KE, Allis CD, Strahl BD (2011) Operating on chromatin, a colorful language where context matters. J Mol Biol 409:36–46

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Hansen RS, Wijmenga C, Luo P, Stanek AM, Canfield TK, Weemaes CM, Gartler SM (1999) The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci U S A 96:14412–14417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Herman JG, Graff JR, Myöhänen S, Nelkin BD, Baylin SB (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A 93:9821–9826

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Hermann A, Gowher H, Jeltsch A (2004) Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 61:2571–2587

    Article  CAS  PubMed  Google Scholar 

  27. Hernandez-Vargas H, Lambert MP, Le Calvez-Kelm F, Gouysse G, McKay-Chopin S, Tavtigian SV, Scoazec JY, Herceg Z (2010) Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors. PLoS One 5:e9749

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Hirohashi S (1991) Pathology and molecular mechanisms of multistage human hepatocarcinogenesis. Princess Takamatsu Symp 22:87–93

    CAS  PubMed  Google Scholar 

  29. Huang J, Deng Q, Wang Q, Li KY, Dai JH, Li N, Zhu ZD, Zhou B, Liu XY, Liu RF, Fei QL, Chen H, Cai B, Zhou B, Xiao HS, Qin LX, Han ZG (2012) Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat Genet 44:1117–1121

    Article  CAS  PubMed  Google Scholar 

  30. Inazawa J, Inoue J, Imoto I (2004) Comparative genomic hybridization (CGH)-arrays pave the way for identification of novel cancer-related genes. Cancer Sci 95:559–563

    Article  CAS  PubMed  Google Scholar 

  31. Iwata N, Yamamoto H, Sasaki S, Itoh F, Suzuki H, Kikuchi T, Kaneto H, Iku S, Ozeki I, Karino Y, Satoh T, Toyota J, Satoh M, Endo T, Imai K (2000) Frequent hypermethylation of CpG islands and loss of expression of the 14-3-3 sigma gene in human hepatocellular carcinoma. Oncogene 19:5298–5302

    Article  CAS  PubMed  Google Scholar 

  32. Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl:245–254

    Article  PubMed  CAS  Google Scholar 

  33. Jones PA, Issa J-P, Baylin S (2016) Targeting the cancer epigenome for therapy. Nat Rev Genet 17:630–641

    Article  CAS  PubMed  Google Scholar 

  34. Jurinke C, Denissenko MF, Oeth P, Ehrich M, van den Boom D, Cantor CR (2005) A single nucleotide polymorphism based approach for the identification and characterization of gene expression modulation using MassARRAY. Mutat Res 573:83–95

    Article  CAS  PubMed  Google Scholar 

  35. Kanai Y (2010) Genome-wide DNA methylation profiles in precancerous conditions and cancers. Cancer Sci 101:36–45

    Article  CAS  PubMed  Google Scholar 

  36. Kanai Y, Arai E (2014) Multilayer-omics analyses of human cancers: exploration of biomarkers and drug targets based on the activities of the International Human Epigenome Consortium. Front Genet 5:24

    PubMed  PubMed Central  Google Scholar 

  37. Kanai Y, Ushijima S, Tsuda H, Sakamoto M, Sugimura T, Hirohashi S (1996) Aberrant DNA methylation on chromosome 16 is an early event in hepatocarcinogenesis. Jpn J Cancer Res 87:1210–1217

    Article  CAS  PubMed  Google Scholar 

  38. Kanai Y, Ushijima S, Hui AM, Ochiai A, Tsuda H, Sakamoto M, Hirohashi S (1997) The E-cadherin gene is silenced by CpG methylation in human hepatocellular carcinomas. Int J Cancer 71:355–359

    Article  CAS  PubMed  Google Scholar 

  39. Kanai Y, Ushijima S, Nakanishi Y, Sakamoto M, Hirohashi S (2003) Mutation of the DNA methyltransferase (DNMT) 1 gene in human colorectal cancers. Cancer Lett 192:75–82

    Article  CAS  PubMed  Google Scholar 

  40. Kanai Y, Saito Y, Ushijima S, Hirohashi S (2004) Alterations in gene expression associated with the overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, during human hepatocarcinogenesis. J Cancer Res Clin Oncol 130:636–644

    Article  CAS  PubMed  Google Scholar 

  41. Kanda M, Sugimoto H, Nomoto S, Oya H, Shimizu D, Takami H, Hashimoto R, Sonohara F, Okamura Y, Yamada S, Fujii T, Nakayama G, Koike M, Fujiwara M, Kodera Y (2014) Clinical utility of PDSS2 expression to stratify patients at risk for recurrence of hepatocellular carcinoma. Int J Oncol 45:2005–2012

    Article  CAS  PubMed  Google Scholar 

  42. Keating ST, El-Osta A (2015) Epigenetics and metabolism. Circ Res 116:715–736

    Article  CAS  PubMed  Google Scholar 

  43. Khan FS, Ali I, Afridi UK, Ishtiaq M, Mehmood R (2016) Epigenetic mechanisms regulating the developmentof hepatocellular carcinoma and their promise for therapeutics. Hepatol Int. doi:10.1007/s12072-016-9743-4

  44. Kim TY, Jong HS, Song SH, Dimtchev A, Jeong SJ, Lee JW, Kim TY, Kim NK, Jung M, Bang YJ (2003) Transcriptional silencing of the DLC-1 tumor suppressor gene by epigenetic mechanism in gastric cancer cells. Oncogene 22:3943–3951

    Article  CAS  PubMed  Google Scholar 

  45. Kondo Y, Kanai Y, Sakamoto M, Mizokami M, Ueda R, Hirohashi S (2000) Genetic instability and aberrant DNA methylation in chronic hepatitis and cirrhosis – a comprehensive study of loss of heterozygosity and microsatellite instability at 39 loci and DNA hypermethylation on 8 CpG islands in microdissected specimens from patients with hepatocellular carcinoma. Hepatology 32:970–979

    Article  CAS  PubMed  Google Scholar 

  46. Kubo T, Yamamoto J, Shikauchi Y, Niwa Y, Matsubara K, Yoshikawa H (2004) Apoptotic speck protein-like, a highly homologous protein to apoptotic speck protein in the pyrin domain, is silenced by DNA methylation and induces apoptosis in human hepatocellular carcinoma. Cancer Res 64:5172–5177

    Article  CAS  PubMed  Google Scholar 

  47. Lachenmayer A, Toffanin S, Cabellos L, Alsinet C, Hoshida Y, Villanueva A, Minguez B, Tsai HW, Ward SC, Thung S, Friedman SL, Llovet JM (2012) Combination therapy for hepatocellular carcinoma: additive preclinical efficacy of the HDAC inhibitor panobinostat with sorafenib. J Hepatol 56:1343–1350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Li GM, Wang YG, Pan Q, Wang J, Fan JG, Sun C (2014) RNAi screening with shRNAs against histone methylation-related genes reveals determinants of sorafenib sensitivity in hepatocellular carcinoma cells. Int J Clin Exp Pathol 7:1085–1092

    PubMed  PubMed Central  Google Scholar 

  49. Li XY, Feng XZ, Tang JZ, Dong K, Wang JF, Meng CC, Wang J, Mo YW, Sun ZW (2016a) MicroRNA-200b inhibits the proliferation of hepatocellular carcinoma by targeting DNA methyltransferase 3a. Mol Med Rep 13:3929–3935

    Article  CAS  PubMed  Google Scholar 

  50. Li CP, Cai MY, Jiang LJ, Mai SJ, Chen JW, Wang FW, Liao YJ, Chen WH, Jin XH, Pei XQ, Guan XY, Zeng MS, Xie D (2016b) CLDN14 is epigenetically silenced by EZH2-mediated H3K27ME3 and is a novel prognostic biomarker in hepatocellular carcinoma. Carcinogenesis 37:557–566

    Article  CAS  PubMed  Google Scholar 

  51. Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Liu JB, Zhang YX, Zhou SH, Shi MX, Cai J, Liu Y, Chen KP, Qiang FL (2011) CpG island methylator phenotype in plasma is associated with hepatocellular carcinoma prognosis. World J Gastroenterol 17:4718–4724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Liu C, Liu L, Chen X, Shen J, Shan J, Xu Y, Yang Z, Wu L, Xia F, Bie P, Cui Y, Bian XW, Qian C (2013) Decrease of 5-hydroxymethylcytosine is associated with progression of hepatocellular carcinoma through downregulation of TET1. PLoS One 8:e62828

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Matsuda Y, Ichida T, Matsuzawa J, Sugimura K, Asakura H (1999) p16(INK4) is inactivated by extensive CpG methylation in human hepatocellular carcinoma. Gastroenterology 116:394–400

    Article  CAS  PubMed  Google Scholar 

  55. Matsuda Y, Wakai T, Kubota M, Osawa M, Hirose Y, Sakata J, Kobayashi T, Fujimaki S, Takamura M, Yamagiwa S, Aoyagi Y (2014) Valproic acid overcomes transforming growth factor-β-mediated sorafenib resistance in hepatocellular carcinoma. Int J Clin Exp Pathol 7:1299–1313

    PubMed  PubMed Central  Google Scholar 

  56. Matsukura S, Soejima H, Nakagawachi T, Yakushiji H, Ogawa A, Fukuhara M, Miyazaki K, Nakabeppu Y, Sekiguchi M, Mukai T (2003) CpG methylation of MGMT and hMLH1 promoter in hepatocellular carcinoma associated with hepatitis viral infection. Br J Cancer 88:521–529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Matsumura S, Imoto I, Kozaki K, Matsui T, Muramatsu T, Furuta M, Tanaka S, Sakamoto M, Arii S, Inazawa J (2012) Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor suppressor in hepatocellular carcinoma. Clin Cancer Res 18:3541–3551

    Article  CAS  PubMed  Google Scholar 

  58. Matsuno Y, Hirohashi S, Furuya S, Sakamoto M, Mukai K, Shimosato Y (1990) Heterogeneity of proliferative activity in nodule-in-nodule lesions of small hepatocellular carcinoma. Jpn J Cancer Res 81:1137–1140

    Article  CAS  PubMed  Google Scholar 

  59. Miura F, Enomoto Y, Dairiki R, Ito T (2012) Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res 40:e136

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Miyagawa K, Sakakura C, Nakashima S, Yoshikawa T, Kin S, Nakase Y, Ito K, Yamagishi H, Ida H, Yazumi S, Chiba T, Ito Y, Hagiwara A (2006) Down-regulation of RUNX1, RUNX3 and CBFbeta in hepatocellular carcinomas in an early stage of hepatocarcinogenesis. Anticancer Res 26:3633–3643

    CAS  PubMed  Google Scholar 

  61. Mori T, Nomoto S, Koshikawa K, Fujii T, Sakai M, Nishikawa Y, Inoue S, Takeda S, Kaneko T, Nakao A (2005) Decreased expression and frequent allelic inactivation of the RUNX3 gene at 1p36 in human hepatocellular carcinoma. Liver Int 25:380–388

    Article  CAS  PubMed  Google Scholar 

  62. Mottamal M, Zheng S, Huang TL, Wang G (2015) Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents. Molecules 20:3898–3941

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Nagashio R, Arai E, Ojima H, Kosuge T, Kondo Y, Kanai Y (2011) Carcinogenetic risk estimation based on quantification of DNA methylation levels in liver tissue at the precancerous stage. Int J Cancer 129:1170–1179

    Article  CAS  PubMed  Google Scholar 

  64. Neumann O, Kesselmeier M, Geffers R, Pellegrino R, Radlwimmer B, Hoffmann K, Ehemann V, Schemmer P, Schirmacher P, Lorenzo Bermejo J, Longerich T (2012) Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors. Hepatology 56:1817–1827

    Article  CAS  PubMed  Google Scholar 

  65. Noh JH, Jung KH, Kim JK, Eun JW, Bae HJ, Xie HJ, Chang YG, Kim MG, Park WS, Lee JY, Nam SW (2011) Aberrant regulation of HDAC2 mediates proliferation of hepatocellular carcinoma cells by deregulating expression of G1/S cell cycle proteins. PLoS One 6:e28103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Okochi O, Hibi K, Sakai M, Inoue S, Takeda S, Kaneko T, Nakao A (2003) Methylation-mediated silencing of SOCS-1 gene in hepatocellular carcinoma derived from cirrhosis. Clin Cancer Res 9:5295–5298

    CAS  PubMed  Google Scholar 

  67. Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ (2001) A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 11:483–496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Oya H, Kanda M, Sugimoto H, Shimizu D, Takami H, Hibino S, Hashimoto R, Okamura Y, Yamada S, Fujii T, Nakayama G, Koike M, Nomoto S, Fujiwara M, Kodera Y (2015) Dihydropyrimidinaselike 3 is a putative hepatocellular carcinoma tumor suppressor. J Gastroenterol 50:590–600

    Article  CAS  PubMed  Google Scholar 

  69. Park ES, Park YK, Shin CY, Park SH, Ahn SH, Kim DH, Lim KH, Kwon SY, Kim KP, Yang SI, Seong BL, Kim KH (2013) Hepatitis B virus inhibits liver regeneration via epigenetic regulation of urokinase-type plasminogen activator. Hepatology 58:762–776

    Article  CAS  PubMed  Google Scholar 

  70. Revill K, Wang T, Lachenmayer A, Kojima K, Harrington A, Li J, Hoshida Y, Llovet JM, Powers S (2013) Genome-wide methylation analysis and epigenetic unmasking identify tumor suppressor genes in hepatocellular carcinoma. Gastroenterology 145:1424–1435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Saito Y, Kanai Y, Sakamoto M, Saito H, Ishii H, Hirohashi S (2001) 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. Hepatology 33:561–568

    Article  CAS  PubMed  Google Scholar 

  72. Saito Y, Kanai Y, Sakamoto M, Saito H, Ishii H, Hirohashi S (2002) Overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, associated with DNA hypomethylation on pericentromeric satellite regions during human hepatocarcinogenesis. Proc Natl Acad Sci U S A 99:10060–10065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Saito Y, Kanai Y, Nakagawa T, Sakamoto M, Saito H, Ishii H, Hirohashi S (2003) Increased protein expression of DNA methyltransferase (DNMT) 1 is significantly correlated with the malignant potential and poor prognosis of human hepatocellular carcinomas. Int J Cancer 105:527–532

    Article  CAS  PubMed  Google Scholar 

  74. Sakamoto A, Hino S, Nagaoka K, Anan K, Takase R, Matsumori H, Ojima H, Kanai Y, Arita K, Nakao M (2015) Lysine Demethylase LSD1 coordinates glycolytic and mitochondrial metabolism in hepatocellular carcinoma cells. Cancer Res 75:1445–1456

    Article  CAS  PubMed  Google Scholar 

  75. Sato T, Arai E, Kohno T, Tsuta K, Watanabe S, Soejima K, Betsuyaku T, Kanai Y (2013) DNA methylation profiles at precancerous stages associated with recurrence of lung adenocarcinoma. PLoS One 8:e59444

    Article  PubMed  PubMed Central  Google Scholar 

  76. Schagdarsurengin U, Wilkens L, Steinemann D, Flemming P, Kreipe HH, Pfeifer GP, Schlegelberger B, Dammann R (2003) Frequent epigenetic inactivation of the RASSF1A gene in hepatocellular carcinoma. Oncogene 22:1866–1871

    Article  CAS  PubMed  Google Scholar 

  77. Shen J, Wang S, Zhang YJ, Kappil M, Wu HC, Kibriya MG, Wang Q, Jasmine F, Ahsan H, Lee PH, Yu MW, Chen CJ, Santella RM (2012a) Genome-wide DNA methylation profiles in hepatocellular carcinoma. Hepatology 55:1799–1808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Shen J, Wang S, Zhang YJ, Kappil MA, Wu HC, Kibriya MG, Wang Q, Jasmine F, Ahsan H, Lee PH, Yu MW, Chen CJ, Santella RM (2012b) Genome-wide aberrant DNA methylation of microRNA host genes in hepatocellular carcinoma. Epigenetics 7:1230–1237

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Song MA, Tiirikainen M, Kwee S, Okimoto G, Yu H, Wong LL (2013) Elucidating the landscape of aberrant DNA methylation in hepatocellular carcinoma. PLoS One 8:e55761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Sun L, Hui AM, Kanai Y, Sakamoto M, Hirohashi S (1997) Increased DNA methyltransferase expression is associated with an early stage of human hepatocarcinogenesis. Jpn J Cancer Res 88:1165–1170

    Article  CAS  PubMed  Google Scholar 

  81. Susanto JM, Colvin EK, Pinese M, Chang DK, Pajic M, Mawson A, Caldon CE, Musgrove EA, Henshall SM, Sutherland RL, Biankin AV, Scarlett CJ (2015) The epigenetic agents suberoylanilide hydroxamic acid and 5-AZA-2′ deoxycytidine decrease cell proliferation, induce cell death and delay the growth of MiaPaCa2 pancreatic cancer cells in vivo. Int J Oncol 46:2223–2230

    Article  CAS  PubMed  Google Scholar 

  82. Suva ML, Riggi N, Janiszewska M, Radovanovic I, Provero P et al (2009) EZH2 is essential for glioblastoma cancer stem cell maintenance. Cancer Res 69:9211–9218

    Article  CAS  PubMed  Google Scholar 

  83. Tan J, Yang X, Zhuang L, Jiang X, Chen W, Lee PL, Karuturi RK, Tan PB, Liu ET, Yu Q (2007) Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev 21:1050–1063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Tao R, Li J, Xin J, Wu J, Guo J, Zhang L, Jiang L, Zhang W, Yang Z, Li L (2011) Methylation profile of single hepatocytes derived from hepatitis B virus-related hepatocellular carcinoma. PLoS One 6:e19862

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Tian Y, Wong VW, Wong GL, Yang W, Sun H, Shen J, Tong JH, Go MY, Cheung YS, Lai PB, Zhou M, Xu G, Huang TH, Yu J, To KF, Cheng AS, Chan HL (2015) Histone deacetylase HDAC8 promotes insulin resistance and β-catenin activation in NAFLD-associated hepatocellular carcinoma. Cancer Res 75:4803–4816

    Article  CAS  PubMed  Google Scholar 

  86. Tsuda H, Zhang WD, Shimosato Y, Yokota J, Terada M, Sugimura T, Miyamura T, Hirohashi S (1990) Allele loss on chromosome 16 associated with progression of human hepatocellular carcinoma. Proc Natl Acad Sci U S A 87:6791–6794

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Vivekanandan P, Daniel HD, Kannangai R, Martinez-Murillo F, Torbenson M (2010) Hepatitis B virus vreplication induces methylation of both host and viral DNA. J Virol 84:4321–4329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Wang S, Zhu Y, He H, Liu J, Xu L, Zhang H, Liu H, Liu W, Liu Y, Pan D, Chen L, Wu Q, Xu J, Gu J (2013) Sorafenib suppresses growth and survival of hepatoma cells by accelerating degradation of enhancer of zeste homolog 2. Cancer Sci 104:750–759

    Article  CAS  PubMed  Google Scholar 

  89. Wang DY, Zou LP, Liu XJ, Zhu HG, Zhu R (2015) Hepatitis B virus X protein induces the histone H3 lysine 9 trimethylation on the promoter of p16 gene in hepatocarcinogenesis. Exp Mol Pathol 99:399–408

    Article  CAS  PubMed  Google Scholar 

  90. Waterland RA (2006) AssessingtheeffectsofhighmethionineintakeonDNA methylation. J Nutr 136:1706S–1710S

    CAS  PubMed  Google Scholar 

  91. Wong IH, Lo YM, Yeo W, Lau WY, Johnson PJ (2000) Frequent p15 promoter methylation in tumor and peripheral blood from hepatocellular carcinoma patients. Clin Cancer Res 6:3516–3521

    CAS  PubMed  Google Scholar 

  92. Wong N, Lam WC, Lai PB, Pang E, Lau WY, Johnson PJ (2001) Hypomethylation of chromosome 1 heterochromatin DNA correlates with q-arm copy gain in human hepatocellular carcinoma. Am J Pathol 159:465–471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Wong CM, Lee JM, Ching YP, Jin DY, Ng IO (2003) Genetic and epigenetic alterations of DLC-1 gene in hepatocellular carcinoma. Cancer Res 63:7646–7651

    CAS  PubMed  Google Scholar 

  94. Wu J, Du C, Lv Z, Ding C, Cheng J, Xie H, Zhou L, Zheng S (2013) The up-regulation of histone deacetylase 8 promotes proliferation and inhibits apoptosis in hepatocellular carcinoma. Dig Dis Sci 58:3545–3553

    Article  CAS  PubMed  Google Scholar 

  95. Xie HJ, Noh JH, Kim JK, Jung KH, Eun JW, Bae HJ, Kim MG, Chang YG, Lee JY, Park H, Nam SW (2012) HDAC1 inactivation induces mitotic defect and caspase-independent autophagic cell death in liver cancer. PLoS One 7:e34265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Xiong Z, Laird PW (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25:2532–2534

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Yao JY, Zhang L, Zhang X, He ZY, Ma Y, Hui LJ, Wang X, Hu YP (2010) H3K27 trimethylation is an early epigenetic event of p16INK4a silencing for regaining tumorigenesis in fusion reprogrammed hepatoma cells. J Biol Chem 285:18828–18837

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Yeo W, Chung HC, Chan SL, Wang LZ, Lim R, Picus J, Boyer M, Mo FK, Koh J, Rha SY, Hui EP, Jeung HC, Roh JK, Yu SC, To KF, Tao Q, Ma BB, Chan AW, Tong JH, Erlichman C, Chan AT, Goh BC (2012) Epigenetic therapy using belinostat for patients with unresectable hepatocellular carcinoma: a multicenter phase I/II study with biomarker and pharmacokinetic analysis of tumors from patients in the Mayo Phase II Consortium and the Cancer Therapeutics Research Group. J Clin Oncol 30:3361–3367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Yoshiura K, Kanai Y, Ochiai A, Shimoyama Y, Sugimura T, Hirohashi S (1995) Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas. Proc Natl Acad Sci U S A 92:7416–7419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Yu J, Ni M, Xu J, Zhang H, Gao B, Gu J, Chen J, Zhang L, Wu M, Zhen S, Zhu J (2002) Methylation profiling of twenty promoter-CpG islands of genes which may contribute to hepatocellular carcinogenesis. BMC Cancer 2:29

    Article  PubMed  PubMed Central  Google Scholar 

  101. Yuan BZ, Miller MJ, Keck CL, Zimonjic DB, Thorgeirsson SS, Popescu NC (1998) Cloning, characterization, and chromosomal localization of a gene frequently deleted in human liver cancer (DLC-1) homologous to rat RhoGAP. Cancer Res 58:2196–2199

    CAS  PubMed  Google Scholar 

  102. Zheng DL, Zhang L, Cheng N, Xu X, Deng Q, Teng XM, Wang KS, Zhang X, Huang J, Han ZG (2009) Epigenetic modification induced by hepatitis B virus X protein via interaction with de novo DNA methyltransferase DNMT3A. J Hepatol 50:377–387

    Article  CAS  PubMed  Google Scholar 

  103. Zhu C, Utsunomiya T, Ikemoto T, Yamada S, Morine Y, Imura S, Arakawa Y, Takasu C, Ishikawa D, Imoto I, Shimada M (2014) Hypomethylation of long interspersed nuclear element-1 (LINE-1) is associated with poor prognosis via activation of c-MET in hepatocellular carcinoma. Ann Surg Oncol 21(Suppl 4):S729–S735

    Article  PubMed  Google Scholar 

  104. Zucman-Rossi J, Villanueva A, Nault JC, Llovet JM (2015) Genetic landscape and biomarkers of hepatocellular carcinoma. Gastroenterology 149:1226–1239

    Article  CAS  PubMed  Google Scholar 

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Arai, E., Yotani, T., Kanai, Y. (2017). DNA and Histone Methylation in Liver Cancer. In: Kaneda, A., Tsukada, Yi. (eds) DNA and Histone Methylation as Cancer Targets. Cancer Drug Discovery and Development. Humana Press, Cham. https://doi.org/10.1007/978-3-319-59786-7_16

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