J Korean Med Sci.  2012 Jun;27(6):594-604. 10.3346/jkms.2012.27.6.594.

Pharmacological Unmasking Microarray Approach-Based Discovery of Novel DNA Methylation Markers for Hepatocellular Carcinoma

  • 1Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea. ghkang@snu.ac.kr
  • 2Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.
  • 3Department of General Surgery, Seoul National University College of Medicine, Seoul, Korea.
  • 4Department of Pathology, Korea University School of Medicine, Seoul, Korea.


DNA methylation is one of the main epigenetic mechanisms and hypermethylation of CpG islands at tumor suppressor genes switches off these genes. To find novel DNA methylation markers in hepatocellular carcinoma (HCC), we performed pharmacological unmasking (treatment with 5-aza-2'-deoxycytidine or trichostatin A) followed by microarray analysis in HCC cell lines. Of the 239 promoter CpG island loci hypermethylated in HCC cell lines (as revealed by methylation-specific PCR), 221 loci were found to be hypermethylated in HCC or nonneoplastic liver tissues. Thirty-three loci showed a 20% higher methylation frequency in tumors than in adjacent nonneoplastic tissues. Correlation of individual cancer-related methylation markers with clinicopathological features of HCC patients (n = 95) revealed that the number of hypermethylated genes in HCC tumors was higher in older than in younger patients. Univariate and multivariate survival analysis revealed that the HIST1H2AE methylation status is closely correlated with the patient's overall survival (P = 0.022 and P = 0.010, respectively). In conclusion, we identified 221 novel DNA methylation markers for HCC. One promising prognostic marker, HIST1H2AE, should be further validated in the prognostication of HCC patients.


CpG Islands; DNA Methylation; Carcinoma, Hepatocellular; Microarray; Prognosis

MeSH Terms

Azacitidine/analogs & derivatives/pharmacology
Carcinoma, Hepatocellular/*genetics/mortality
Cell Line, Tumor
CpG Islands
DNA Methylation/*drug effects
Hep G2 Cells
Hydroxamic Acids/pharmacology
Liver Neoplasms/*genetics/mortality
Middle Aged
Oligonucleotide Array Sequence Analysis
Promoter Regions, Genetic
Survival Analysis
Tumor Markers, Biological/*genetics
Hydroxamic Acids
Tumor Markers, Biological
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