Comparison of genome-scale DNA methylation profiles in hepatocellular carcinoma by viral status

Reference

• McGlynn KA, Petrick JL, London WT. Global epidemiology of hepatocellular carcinoma: an emphasis on demographic and regional variability. Clin liver Dis 2015; 19:223-38; PMID:25921660; http://dx.doi.org/10.1016/j.cld.2015.01.001
   PubMed Web of Science ®Google Scholar
• Siegel RL, Miller KD, Jemal A. Cancer statistics, 2015. CA Cancer J Clin 2015; 65:5-29; PMID:25559415; http://dx.doi.org/10.3322/caac.21254
   PubMed Web of Science ®Google Scholar
• Shitani M, Sasaki S, Akutsu N, Takagi H, Suzuki H, Nojima M, Yamamoto H, Tokino T, Hirata K, Imai K, et al. Genome-wide analysis of DNA methylation identifies novel cancer-related genes in hepatocellular carcinoma. Tumour Biol 2012; 33:1307-17; PMID:22457049; http://dx.doi.org/10.1007/s13277-012-0378-3
   PubMed Web of Science ®Google Scholar
• Shen J, Wang S, Zhang YJ, Wu HC, Kibriya MG, Jasmine F, Ahsan H, Wu DP, Siegel AB, Remotti H, et al. Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips. Epigenetics 2013; 8:34-43; http://dx.doi.org/10.4161/epi.23062
   PubMed Web of Science ®Google Scholar
• El-Serag HB. Hepatocellular carcinoma. N Engl J Med 2011; 365:1118-27; PMID:21992124; http://dx.doi.org/10.1056/NEJMra1001683
   PubMed Web of Science ®Google Scholar
• Stuver SO, Boschi-Pinto C, Trichopoulos D. Infection with hepatitis B and C viruses, social class and cancer. IARC Sci Publ 1997:319-24; PMID:9353672
   PubMedGoogle Scholar
• Zhong S, Tang MW, Yeo W, Liu C, Lo YM, Johnson PJ. Silencing of GSTP1 gene by CpG island DNA hypermethylation in HBV-associated hepatocellular carcinomas. Clin Cancer Res 2002; 8:1087-92; PMID:11948118
   PubMed Web of Science ®Google Scholar
• Moribe T, Iizuka N, Miura T, Kimura N, Tamatsukuri S, Ishitsuka H, Hamamoto Y, Sakamoto K, Tamesa T, Oka M. Methylation of multiple genes as molecular markers for diagnosis of a small, well-differentiated hepatocellular carcinoma. Int J Cancer J Int du Cancer 2009; 125:388-97; PMID:19384946; http://dx.doi.org/10.1002/ijc.24394
   PubMed Web of Science ®Google Scholar
• Tao R, Li J, Xin J, Wu J, Guo J, Zhang L, Jiang L, Zhang W, Yang Z, Li L. Methylation profile of single hepatocytes derived from hepatitis B virus-related hepatocellular carcinoma. PloS one 2011; 6:e19862; PMID:21625442; http://dx.doi.org/10.1371/journal.pone.0019862
   Google Scholar
• Song MA, Tiirikainen M, Kwee S, Okimoto G, Yu H, Wong LL. Elucidating the landscape of aberrant DNA methylation in hepatocellular carcinoma. PloS one 2013; 8:e55761; PMID:23437062; http://dx.doi.org/10.1371/journal.pone.0055761
   PubMed Web of Science ®Google Scholar
• Shen J, Wang S, Zhang YJ, Kappil M, Wu HC, Kibriya MG, Wang Q, Jasmine F, Ahsan H, Lee PH, et al. Genome-wide DNA methylation profiles in hepatocellular carcinoma. Hepatology 2012; 55:1799-808; PMID:22234943; http://dx.doi.org/10.1002/hep.25569
   PubMed Web of Science ®Google Scholar
• Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, Lin SM. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC bioinformatics 2010; 11:587; PMID:21118553; http://dx.doi.org/10.1186/1471-2105-11-587
   PubMed Web of Science ®Google Scholar
• Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV, Cho RJ, Chen RO, Brownstein BH, Cobb JP, Tschoeke SK, et al. A network-based analysis of systemic inflammation in humans. Nature 2005; 437:1032-7; PMID:16136080; http://dx.doi.org/10.1038/nature03985
   PubMed Web of Science ®Google Scholar
• Quackenbush J. Computational analysis of microarray data. Nat Rev Genet 2001; 2:418-27; PMID:11389458; http://dx.doi.org/10.1038/35076576
   PubMed Web of Science ®Google Scholar
• Zhao Y, Xue F, Sun J, Guo S, Zhang H, Qiu B, Geng J, Gu J, Zhou X, Wang W, et al. Genome-wide methylation profiling of the different stages of hepatitis B virus-related hepatocellular carcinoma development in plasma cell-free DNA reveals potential biomarkers for early detection and high-risk monitoring of hepatocellular carcinoma. Clinical epigenetics 2014; 6:30; PMID:25859288; http://dx.doi.org/10.1186/1868-7083-6-30
   PubMed Web of Science ®Google Scholar
• Lambert MP, Paliwal A, Vaissiere T, Chemin I, Zoulim F, Tommasino M, Hainaut P, Sylla B, Scoazec JY, Tost J, et al. Aberrant DNA methylation distinguishes hepatocellular carcinoma associated with HBV and HCV infection and alcohol intake. J Hepatol 2011; 54:705-15; PMID:21146512; http://dx.doi.org/10.1016/j.jhep.2010.07.027
   PubMed Web of Science ®Google Scholar
• Arzumanyan A, Reis HM, Feitelson MA. Pathogenic mechanisms in HBV- and HCV-associated hepatocellular carcinoma. Nat Rev Cancer 2013; 13:123-35; PMID:23344543; http://dx.doi.org/10.1038/nrc3449
   PubMed Web of Science ®Google Scholar
• Brechot C. Pathogenesis of hepatitis B virus-related hepatocellular carcinoma: old and new paradigms. Gastroenterology 2004; 127:S56-61; PMID:15508104; http://dx.doi.org/10.1053/j.gastro.2004.09.016
   PubMed Web of Science ®Google Scholar
• Di Bisceglie AM. Hepatitis B and hepatocellular carcinoma. Hepatology 2009; 49:S56-60; PMID:19399807; http://dx.doi.org/10.1002/hep.22962
   PubMed Web of Science ®Google Scholar
• Moradpour D, Penin F, Rice CM. Replication of hepatitis C virus. Nat Rev Microbiol 2007; 5:453-63; PMID:17487147; http://dx.doi.org/10.1038/nrmicro1645
   PubMed Web of Science ®Google Scholar
• Bartosch B. Hepatitis B and C viruses and hepatocellular carcinoma. Viruses 2010; 2:1504-9; PMID:21994691; http://dx.doi.org/10.3390/v2081504
   PubMed Web of Science ®Google Scholar
• Deng YB, Nagae G, Midorikawa Y, Yagi K, Tsutsumi S, Yamamoto S, Hasegawa K, Kokudo N, Aburatani H, Kaneda A. Identification of genes preferentially methylated in hepatitis C virus-related hepatocellular carcinoma. Cancer science 2010; 101:1501-10; PMID:20345479; http://dx.doi.org/10.1111/j.1349-7006.2010.01549.x
   PubMed Web of Science ®Google Scholar
• Yang B, Guo M, Herman JG, Clark DP. Aberrant promoter methylation profiles of tumor suppressor genes in hepatocellular carcinoma. Am J Pathol 2003; 163:1101-7; PMID:12937151; http://dx.doi.org/10.1016/S0002-9440(10)63469-4
   PubMed Web of Science ®Google Scholar
• Nishida N, Nagasaka T, Nishimura T, Ikai I, Boland CR, Goel A. Aberrant methylation of multiple tumor suppressor genes in aging liver, chronic hepatitis, and hepatocellular carcinoma. Hepatology 2008; 47:908-18; PMID:18161048; http://dx.doi.org/10.1002/hep.22110
   PubMed Web of Science ®Google Scholar
• Aran D, Sabato S, Hellman A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Gen Biol 2013; 14:R21; PMID:23497655; http://dx.doi.org/10.1186/gb-2013-14-3-r21
   PubMed Web of Science ®Google Scholar
• Deaton AM, Bird A. CpG islands and the regulation of transcription. Gen Dev 2011; 25:1010-22; PMID:21576262; http://dx.doi.org/10.1101/gad.2037511
   PubMed Web of Science ®Google Scholar
• Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13:484-92; PMID:22641018; http://dx.doi.org/10.1038/nrg3230
   PubMed Web of Science ®Google Scholar
• Lucia Radici MB, Rita Crinelli, Mauro Magnani Ubiquitin C gene: Structure, function, and transcriptional regulation. Adv Biosci Biotechnol 2013; 4:1057-62; http://dx.doi.org/10.4236/abb.2013.412141
   Google Scholar
• Gui T, Dong X, Li R, Li Y, Wang Z. Identification of hepatocellular carcinoma-related genes with a machine learning and network analysis. J Comput Biol 2015; 22:63-71; PMID:25247452; http://dx.doi.org/10.1089/cmb.2014.0122
   PubMed Web of Science ®Google Scholar
• Dhillon AS, Hagan S, Rath O, Kolch W. MAP kinase signalling pathways in cancer. Oncogene 2007; 26:3279-90; PMID:17496922; http://dx.doi.org/10.1038/sj.onc.1210421
   PubMed Web of Science ®Google Scholar
• Avila MA, Berasain C, Sangro B, Prieto J. New therapies for hepatocellular carcinoma. Oncogene 2006; 25:3866-84; PMID:16799628; http://dx.doi.org/10.1038/sj.onc.1209550
   PubMed Web of Science ®Google Scholar
• Yoshida T, Hisamoto T, Akiba J, Koga H, Nakamura K, Tokunaga Y, Hanada S, Kumemura H, Maeyama M, Harada M, et al. Spreds, inhibitors of the Ras/ERK signal transduction, are dysregulated in human hepatocellular carcinoma and linked to the malignant phenotype of tumors. Oncogene 2006; 25:6056-66; PMID:16652141; http://dx.doi.org/10.1038/sj.onc.1209635
   PubMed Web of Science ®Google Scholar
• Tsuboi Y, Ichida T, Sugitani S, Genda T, Inayoshi J, Takamura M, Matsuda Y, Nomoto M, Aoyagi Y. Overexpression of extracellular signal-regulated protein kinase and its correlation with proliferation in human hepatocellular carcinoma. Liver Int 2004; 24:432-6; PMID:15482339; http://dx.doi.org/10.1111/j.1478-3231.2004.0940.x
   PubMed Web of Science ®Google Scholar
• Deng R, Zhao X, Qu Y, Chen C, Zhu C, Zhang H, Yuan H, Jin H, Liu X, Wang Y, et al. Shp2 SUMOylation promotes ERK activation and hepatocellular carcinoma development. Oncotarget 2015; 6:9355-69; PMID:25823821; http://dx.doi.org/10.18632/oncotarget.3323
   PubMed Web of Science ®Google Scholar
• Wang YH, Dong YY, Wang WM, Xie XY, Wang ZM, Chen RX, Chen J, Gao DM, Cui JF, Ren ZG. Vascular endothelial cells facilitated HCC invasion and metastasis through the Akt and NF-kappaB pathways induced by paracrine cytokines. J Exp Clin Cancer Res 2013; 32:51; http://dx.doi.org/10.1186/1756-9966-32-51
   PubMed Web of Science ®Google Scholar
• Steelman LS, Chappell WH, Abrams SL, Kempf RC, Long J, Laidler P, Mijatovic S, Maksimovic-Ivanic D, Stivala F, Mazzarino MC, et al. Roles of the Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR pathways in controlling growth and sensitivity to therapy-implications for cancer and aging. Aging 2011; 3:192-222; PMID:21422497; http://dx.doi.org/10.1371/journal.pone.0019862
   PubMedGoogle Scholar
• Jang CW, Shibata Y, Starmer J, Yee D, Magnuson T. Histone H3.3 maintains genome integrity during mammalian development. Gen Dev 2015; 29:1377-92; PMID:26159997; http://dx.doi.org/10.1101/gad.264150.115
   PubMed Web of Science ®Google Scholar
• Quan H, Zhou F, Nie D, Chen Q, Cai X, Shan X, Zhou Z, Chen K, Huang A, Li S, et al. Hepatitis C virus core protein epigenetically silences SFRP1 and enhances HCC aggressiveness by inducing epithelial-mesenchymal transition. Oncogene 2014; 33:2826-35; PMID:23770846; http://dx.doi.org/10.1038/onc.2013.225
   PubMed Web of Science ®Google Scholar