Changes in intrahepatic gene expression profiles from chronic hepatitis to hepatocellular carcinoma in patients with hepatitis C virus infection

Aim:  DNA microarray technology has enabled genome-wide analysis of gene transcript levels, which has yielded insight into the molecular nature of hepatitis C virus infection. However, little insight into the molecular nature of the early to advanced stages of chronic liver disease has as yet been obtained. Methods:  We compared the gene expression profiles of liver biopsy specimens from 14 patients at different stages of chronic hepatitis C. We also evaluated the liver tissue of hepatocellular carcinoma and its surrounding region obtained surgically in seven patients with hepatitis C virus infection. Results:  Of 21 073 genes, 582 genes showed significant changes in expression levels across the disease group. Twenty-eight samples from six disease groups clustered according to the histological classification except for 4 samples. A heat map produced by hierarchical clustering revealed nine clusters where gene expression profiles were changed in abundance. Among 44 genes which changed twofold or more in transcript abundance, transcripts from chronic hepatitis tended to be upregulated, and gradually downregulated according to disease progression toward hepatocellular carcinoma in five of nine clusters. In chronic hepatitis, transcripts relating to metabolism and immune response were upregulated, while in hepatocellular carcinoma, transcripts associated with cell cycle, growth, proliferation, apoptosis and signaling pathway were upregulated. Conclusion:  Disease progression in hepatitis C virus-infected patients appeared to be associated with changes in gene expression profiles in the liver consistent with plausible functional categories, although we should confirm these findings using larger samples.