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Genome-wide analysis of DNA methylation identifies novel cancer-related genes in hepatocellular carcinoma

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Tumor Biology

Abstract

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.

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Acknowledgments

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).

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Authors and Affiliations

  1. First Department of Internal Medicine, Sapporo Medical University, S1, W16, Chuo-Ku, Sapporo, 060-8543, Japan

    Masahiro Shitani, Shigeru Sasaki, Noriyuki Akutsu, Hideyasu Takagi, Hiromu Suzuki, Hiroyuki Yamamoto & Yasuhisa Shinomura

  2. Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan

    Hiromu Suzuki & Minoru Toyota

  3. Department of Public Health, Sapporo Medical University, Sapporo, Japan

    Masanori Nojima

  4. Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan

    Takashi Tokino

  5. First Department of Surgery, Sapporo Medical University, Sapporo, Japan

    Koichi Hirata

  6. Division of Novel Therapy for Cancer, The Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan

    Kohzoh Imai

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  1. Masahiro Shitani
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Correspondence to Shigeru Sasaki or Yasuhisa Shinomura.

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Supplementary Table 1

Primer sequences used in this study (XLS 36 kb)

Supplementary Table 2

GO analysis of commonly methylated genes in HCC (XLS 29 kb)

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Shitani, M., Sasaki, S., Akutsu, N. et al. Genome-wide analysis of DNA methylation identifies novel cancer-related genes in hepatocellular carcinoma. Tumor Biol. 33, 1307–1317 (2012). https://doi.org/10.1007/s13277-012-0378-3

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  • DOI: https://doi.org/10.1007/s13277-012-0378-3

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