DNA cytosine methylation profile in various cancer-related genes is altered in cultured rat hepatocyte cell lines as compared with primary hepatocytes

Abstract

We determined the DNA cytosine methylation status in the promoter CpG islands of eight cancer-related genes (p16, Socs-1, Rassf1A, Hic-1, Dlc-1, Timp-1, Timp-2, and Timp-3) in five rat hepatocyte cell lines, including normal cell lines (Clone 9 and CWSV-1) and tumor cell lines (H4-II-E-C3, MH1C1, and McA-RH7777). The experimental methods used to assess the methylation profile were methylation-specific PCR (MSP) and methylation-sensitive digestion combined with PCR. The results were compared with the methylation status of rat primary hepatocytes. To evaluate methylation-mediated gene induction/silencing, the expression of gene transcripts was semi-quantitatively assessed using RT-PCR. In primary cells, the CpG islands of all genes tested were unmethylated. In contrast, there was at least one hypermethylated gene in the cultured cell lines. Three genes (p16, Socs-1 and Rassf1A) were hypermethylated in Clone 9 cells; among the other five genes, three genes (Hic-1, Timp-1 and Timp-3) were hypermethylated in the CWSV-1 cell lines and two genes (Dlc-1 and Timp-2) were hypermethylated only in the tumor cell lines. The methylation status in some of the tested genes was altered at an early stage of cell culture as compared to primary cells. It is also noteworthy that hypermethylation in Socs-1, Rassf1, Hic-1, and Timp-3 was widespread among the cell lines tested, but not in the primary cells and Clone 9 cells. This study suggests that a cautious approach is required when cell lines are utilized to study methylation-related carcinogenic, metastatic or tumoricidal mechanisms.