Nanog promoter methylation and chromatin modification in different cancer cells

Abstract

Cancers possess the ability to grow indefinitely and hence it is proposed that some of the cancer cells may have stem cell properties. One of the similar characteristics between cancer cells and stem cells is that cancer cells have genetic or epigenetic signature of stem cells: a subset of stem cell associated genes has been found transcriptional activated in poorly differentiated human tumors; and the epigenetic reprogramming induced pluripotent stem cells are prone to generate tumors. We investigated the methylation states of the upstream region of Nanog (18 CpGs between -1449 and +31 from the TSS) in several cancer cell lines using bisulfite genomic sequencing. Normal peripheral blood mononuclear cells (PBMC) showed hypermethylation. In contrast, Hela (cervix adenocarcinoma) and 97L (hepatocellular carcinoma) were hypomethylated with the percentage of CpG methylated being 27% and 16% respectively; from site -1449 to -952 being only 18%, and 8% respectively, although AGS (gastric adenocarcinoma) and HCT116 (colorectal carcinoma) cancer lines displayed a hypermethylation. By ChIP-qPCR analysis, Nanog promoter contained high level of H3K4me3 in 97L cells but low level of H3K4me3 in HCT116 cells, which corresponded to the gene methylation states, suggesting differential Nanog methylation and chromatin modification in different cancer cells. Moreover, 97L showed a reduced methylation (41%) of Oct4 at promoter region and hypomethylation (6%) of c-Myc at exon 3. Thus, hypomethylation of three pluripotent stem cell genes Nanog, Oct4, and c-Myc in liver cancer 97L cells indicate an epigenetic stem cell signature.