Background: Although hepatocellular carcinoma (HCC) is one of the commonest cancers worldwide, the underlying molecular mechanisms contributing to hepatocarcinogenesis are still not clear.
Methods: In this study, we performed double array analysis, consisting of both expression profiling and karyotyping analysis using single-nucleotide polymorphism (SNP) array, of the same HCC sample from a 68-year-old woman with chronic hepatitis type C, and attempted to find a novel tumor-suppressor gene as a prognostic marker for HCC.
Results: According to the results of expression array, EFEMP1 gene, which has a role as an angiostatic molecule, showed decreased expression in tumor tissue. The copy number of chromosome 2, where EFEMP1 exists, 2p16, did not show chromosomal deletion. We found many CpG islands in the promoter region of EFEMP1 gene. Reactivation of EFEMP1 expression was seen on 5-aza-2'-deoxycytidine (5-aza-dC) treatment using HCC cell lines, and 24 of 48 (50%) HCC samples showed promoter hypermethylation. In the 24 methylated cases, most of the values of EFEMP1 gene expression examined by real-time reverse-transcription polymerase chain reaction (RT-PCR) in tumor tissues were significantly decreased (P = 0.0004). Intriguingly, EFEMP1 hypermethylation was significantly correlated with worse prognosis (P = 0.0271).
Conclusion: Double array analysis revealed a novel tumor-suppressor gene, EFEMP1, for hepatocellular carcinoma. The mechanism for downregulation of EFEMP1 expression was closely associated with promoter hypermethylation. Promoter methylation of EFEMP1 gene was a marker of a worse prognosis in hepatocellular carcinoma.