Genome-wide analysis of DNA methylation identifies novel cancer-related genes in hepatocellular carcinoma
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Aberrant DNA methylation has been implicated in the development of hepatocellular carcinoma (HCC). Our aim was to clarify its molecular mechanism and to identify useful biomarkers by screening for DNA methylation in HCC. Methylated CpG island amplification coupled with CpG island microarray (MCAM) analysis was carried out to screen for methylated genes in primary HCC specimens [hepatitis B virus (HBV)-positive, n = 4; hepatitis C virus (HCV)-positive, n = 5; HBV/HCV-negative, n = 7]. Bisulfite pyrosequencing was used to analyze the methylation of selected genes and long interspersed nuclear element (LINE)-1 in HCC tissue (n = 57) and noncancerous liver tissue (n = 50) from HCC patients and in HCC cell lines (n = 10). MCAM analysis identified 332, 342, and 259 genes that were methylated in HBV-positive, HCV-positive, and HBV/HCV-negative HCC tissues, respectively. Among these genes, methylation of KLHL35, PAX5, PENK, and SPDYA was significantly higher in HCC tissue than in noncancerous liver tissue, irrespective of the hepatitis virus status. LINE-1 hypomethylation was also prevalent in HCC and correlated positively with KLHL35 and SPDYA methylation. Receiver operating characteristic curve analysis revealed that methylation of the four genes and LINE-1 strongly discriminated between HCC tissue and noncancerous liver tissue. Our data suggest that aberrant hyper- and hypomethylation may contribute to a common pathogenesis mechanism in HCC. Hypermethylation of KLHL35, PAX, PENK, and SDPYA and hypomethylation of LINE-1 could be useful biomarkers for the detection of HCC.
KeywordsHepatocellular carcinoma DNA methylation CpG island LINE-1 Biomarker
We thank Dr. Yutaka Kondo for technical advice on MCAM analysis and Masami Ashida for technical assistance. This study was supported in part by a Grant-in-Aid for Scientific Research (B) from the Japan Society for Promotion of Science (Y. Shinomura), a Grant-in-Aid for the Third-term Comprehensive 10-year Strategy for Cancer Control (M. Toyota and H. Suzuki), and a Grant-in-Aid for Cancer Research from the Ministry of Health, Labor, and Welfare, Japan (M. Toyota and H. Suzuki).
Conflicts of interest
- 10.Kaneto H, Sasaki S, Yamamoto H, Itoh F, Toyota M, Suzuki H, Ozeki I, Iwata N, Ohmura T, Satoh T, Karino Y, Toyota J, Satoh M, Endo T, Omata M, Imai K. Detection of hypermethylation of the p16(ink4a) gene promoter in chronic hepatitis and cirrhosis associated with hepatitis B or C virus. Gut. 2001;48:372–7.CrossRefPubMedPubMedCentralGoogle Scholar
- 14.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. Genome-wide DNA methylation profiles in liver tissue at the precancerous stage and in hepatocellular carcinoma. Int J Cancer. 2009;125:2854–62.CrossRefPubMedGoogle Scholar
- 16.Goto Y, Shinjo K, Kondo Y, Shen L, Toyota M, Suzuki H, Gao W, An B, Fujii M, Murakami H, Osada H, Taniguchi T, Usami N, Kondo M, Hasegawa Y, Shimokata K, Matsuo K, Hida T, Fujimoto N, Kishimoto T, Issa JP, Sekido Y. Epigenetic profiles distinguish malignant pleural mesothelioma from lung adenocarcinoma. Cancer Res. 2009;69:9073–82.CrossRefPubMedGoogle Scholar
- 17.Suzuki H, Yamamoto E, Nojima M, Kai M, Yamano HO, Yoshikawa K, Kimura T, Kudo T, Harada E, Sugai T, Takamaru H, Niinuma T, Maruyama R, Yamamoto H, Tokino T, Imai K, Toyota M, Shinomura Y. Methylation-associated silencing of microrna-34b/c in gastric cancer and its involvement in an epigenetic field defect. Carcinogenesis. 2010;31:2066–73.CrossRefPubMedGoogle Scholar
- 23.Lazzi S, Bellan C, Onnis A, De Falco G, Sayed S, Kostopoulos I, Onorati M, D’Amuri A, Santopietro R, Vindigni C, Fabbri A, Righi S, Pileri S, Tosi P, Leoncini L. Rare lymphoid neoplasms coexpressing B- and T-cell antigens. The role of pax-5 gene methylation in their pathogenesis. Hum Pathol. 2009;40:1252–61.CrossRefPubMedGoogle Scholar
- 25.Li X, Cheung KF, Ma X, Tian L, Zhao J, Go MY, Shen B, Cheng AS, Ying J, Tao Q, Sung JJ, Kung HF, Yu J. Epigenetic inactivation of paired box gene 5, a novel tumor suppressor gene, through direct upregulation of p53 is associated with prognosis in gastric cancer patients. Oncogene. 2011. doi: 10.1038/onc.2011.511.
- 26.Morris MR, Ricketts CJ, Gentle D, McRonald F, Carli N, Khalili H, Brown M, Kishida T, Yao M, Banks RE, Clarke N, Latif F, Maher ER. Genome-wide methylation analysis identifies epigenetically inactivated candidate tumour suppressor genes in renal cell carcinoma. Oncogene. 2011;30:1390–401.CrossRefPubMedGoogle Scholar
- 31.Kishida Y, Natsume A, Kondo Y, Takeuchi I, An B, Okamoto Y, Shinjo K, Saito K, Ando H, Ohka F, Sekido Y, Wakabayashi T. Epigenetic subclassification of meningiomas based on genome-wide DNA methylation analyses. Carcinogenesis. 2012;33:436–41.Google Scholar
- 34.Zucchi I, Mento E, Kuznetsov VA, Scotti M, Valsecchi V, Simionati B, Vicinanza E, Valle G, Pilotti S, Reinbold R, Vezzoni P, Albertini A, Dulbecco R. Gene expression profiles of epithelial cells microscopically isolated from a breast-invasive ductal carcinoma and a nodal metastasis. Proc Natl Acad Sci U S A. 2004;101:18147–52.CrossRefPubMedPubMedCentralGoogle Scholar
- 39.Calvisi DF, Simile MM, Ladu S, Pellegrino R, De Murtas V, Pinna F, Tomasi ML, Frau M, Virdis P, De Miglio MR, Muroni MR, Pascale RM, Feo F. Altered methionine metabolism and global DNA methylation in liver cancer: relationship with genomic instability and prognosis. Int J Cancer. 2007;121:2410–20.CrossRefPubMedGoogle Scholar