Identification of genes in HepG2 cells that respond to DNA methylation and histone deacetylation inhibitor treatment

Abstract

Previous studies have demonstrated that epigenetics has an important role in the regulation of gene expression in cancer. Epigenetics is the study of reversible, heritable changes in gene function, which occur independently from changes in the DNA sequence. DNA methylation and histone deacetylation are the two most important epigenetic modifications. DNA methylation was one of the first discovered epigenetic modifications and it may lead to changes in chromatin structure, DNA conformation and DNA stability, thereby controlling gene expression. Sample data on the HepG2 cell line from the Gene Expression Omnibus database under GSE5230 accession number were obtained and GEOquery and the limma package were then used to analyze the data and identify differentially expressed genes using Gene Otology. This was conducted in order to investigate the effect on gene expression of inhibiting DNA methylation and histone deacetylation, and to explore the potential role of epigenetics in the development and treatment of hepatic carcinoma. It was found that inhibition of DNA methylation and histone deacetylation affected not only substance metabolism, but also the immune activity in HepG2 cells. Furthermore, common target sites for transcription factors were identified in the differentially expressed genes. It may be concluded that the inhibition of DNA methylation and histone deacetylation contributes to the treatment of hepatic carcinoma and may provide a novel therapeutic strategy for the treatment of hepatic cancer.