OBJECTIVETo profile the methylation alterations of CpG islands in hetpatocellular carcinoma cell lines.

METHODSA global analysis of DNA methylation using the Human CpG-island 12K Array (HCGI12K) from Canada University Health Network was performed on nine human hepatocellular carcinoma (HCC) cell lines (Hep3B, HepG2, PLC/RPF/5/RPF/5, SMMC-7721, BEL-7402, MHCC97-H, MHCC97-L, HCCLM3, HCCLM6) and a control cell line Chang's liver. Metastatic potential related alterations were also screened in MHCC97 series cell lines (MHCC97-H, MHCC97-L, HCCLM3, HCCLM6), using MHCC97-L, a cell line with low metastatic potential, as control. To screen the key genes which are hypermethylation or hypomethylation in the HCC cell lines compared with the normal liver cell line by normalization processing and cluster analysis of microarray data. Two randomly selected genes was analyzed by methylation specific PCR to verify the chip results.

RESULTSBy a standard of methylation alteration ratio > or = 2 or < or = 0.5, fifty-eight CpG island cloning sites and sixty-six upstream or downstream tumor-related genes were identified. The genes were oncogenes, tumour suppressor genes and their ligand genes, apoptosis-related genes, cell proliferation and differentiation genes, cell cycle-related gene and cell signaling pathway key genes such as Wnt, ras, and FGF pathway-related genes. The methylation specific PCR results were consistent with those obtained by chips.

CONCLUSIONThe results of this study demonstrate that there are a series of CpG island methylation alterations in HCC cell lines. The expression of many oncogenes, tumor suppressor genes and other key genes may be up- or down-regulated, respectively, because of their CpG island hypomethylation or hypermethylation accordingly. It may provide a basis for screening HCC biological markers by CpG island methylation profilling.