Whole transcriptome analysis of chemically induced hepatocellular carcinoma using RNA-sequencing analysis.

RNA-sequencing (RNA-Seq) is a useful method to explore the molecular events in cells and tissues at the transcriptional level. However, comprehensive transcriptome analysis of hepatocarcinogenesis and progression is lacking. In this study, we aimed to characterize a dimethylnitrosamine (DEN) and carbon tetrachloride (CCl(4) ; DEN+CCl(4) )-induced hepatocellular carcinoma (HCC) mouse model by RNA-Seq. In total, 2033 genes were up-regulated and 841 genes were down-regulated after DEN and CCl(4) stimulation. The differentially expressed genes were highly enriched for the Gene Ontology terms oxoacid metabolic process, carboxylic acid metabolic process, and organic acid metabolic process. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the top five significantly overrepresented pathways were metabolic pathways, chemical carcinogenesis, steroid hormone biosynthesis, retinol metabolism and metabolism of xenobiotics by cytochrome P450. Moreover, a protein-protein interaction network analysis indicated that Rous sarcoma oncogene (Src) may play a key role in DEN+CCl(4) -induced HCC. These results provide a comprehensive overview of transcriptome events in DEN+CCl(4) -induced HCC.