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Tumor Biology

, Volume 33, Issue 5, pp 1307–1317 | Cite as

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

  • Masahiro Shitani
  • Shigeru Sasaki
  • Noriyuki Akutsu
  • Hideyasu Takagi
  • Hiromu Suzuki
  • Masanori Nojima
  • Hiroyuki Yamamoto
  • Takashi Tokino
  • Koichi Hirata
  • Kohzoh Imai
  • Minoru Toyota
  • Yasuhisa Shinomura
Research Article

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.

Keywords

Hepatocellular carcinoma DNA methylation CpG island LINE-1 Biomarker 

Notes

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).

Conflicts of interest

None

Supplementary material

13277_2012_378_MOESM1_ESM.xls (36 kb)
Supplementary Table 1 Primer sequences used in this study (XLS 36 kb)
13277_2012_378_MOESM2_ESM.xls (29 kb)
Supplementary Table 2 GO analysis of commonly methylated genes in HCC (XLS 29 kb)
13277_2012_378_MOESM3_ESM.pdf (936 kb)
ESM 1 (PDF 936 kb)

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Copyright information

© International Society of Oncology and BioMarkers (ISOBM) 2012

Authors and Affiliations

  • Masahiro Shitani
    • 1
  • Shigeru Sasaki
    • 1
  • Noriyuki Akutsu
    • 1
  • Hideyasu Takagi
    • 1
  • Hiromu Suzuki
    • 1
    • 2
  • Masanori Nojima
    • 3
  • Hiroyuki Yamamoto
    • 1
  • Takashi Tokino
    • 4
  • Koichi Hirata
    • 5
  • Kohzoh Imai
    • 6
  • Minoru Toyota
    • 2
  • Yasuhisa Shinomura
    • 1
  1. 1.First Department of Internal MedicineSapporo Medical UniversitySapporoJapan
  2. 2.Department of Molecular BiologySapporo Medical UniversitySapporoJapan
  3. 3.Department of Public HealthSapporo Medical UniversitySapporoJapan
  4. 4.Medical Genome Science, Research Institute for Frontier MedicineSapporo Medical University School of MedicineSapporoJapan
  5. 5.First Department of SurgerySapporo Medical UniversitySapporoJapan
  6. 6.Division of Novel Therapy for Cancer, The Advanced Clinical Research Center, The Institute of Medical ScienceThe University of TokyoTokyoJapan

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