Persistent epigenetic alterations in transcription factors after a sustained virological response in hepatocellular carcinoma

Abstract

Background and Aim The risk of hepatocellular carcinoma (HCC) persists in a condition of sustained virologic response (SVR) after hepatitis C virus (HCV) eradication. Comprehensive molecular analyses were performed to test the hypothesis that epigenetic abnormalities present after an SVR play a role in hepatocarcinogenesis. Methods Whole‐genome methylome and RNA sequencing were performed on HCV, SVR, and healthy liver tissue. Integrated analysis of the sequencing data focused on expression changes in transcription factors and their target genes, commonly found in HCV and SVR. Identified expression changes were validated in demethylated cultured HCC cell lines and an independent validation cohort. Results The coincidence rates of the differentially methylated regions between the HCV and SVR groups were 91% in the hypomethylated and 71% in the hypermethylated regions in tumorous tissues, and 37% in the hypomethylated and 36% in the hypermethylated regions in non‐tumorous tissues. These results indicate that many epigenomic abnormalities persist even after an SVR was achieved. Integrated analysis identified 61 transcription factors and 379 other genes that had methylation abnormalities and gene expression changes in both groups. Validation cohort specified gene expression changes for 14 genes, and gene ontology pathway analysis revealed apoptotic signaling and inflammatory response were associated with these genes. Conclusion This study demonstrates that DNA methylation abnormalities, retained after HCV eradication, affect the expression of transcription factors and their target genes. These findings suggest that DNA methylation in SVR patients may be functionally important in carcinogenesis, and could serve as biomarkers to predict HCC occurrence.

Unmet needs in the post-direct-acting antivirals era: The risk and molecular mechanisms of hepatocellular carcinoma after hepatitis C virus eradication

“…Viruses can impose epigenetic changes that alter host transcription programs, thereby promoting their own propagation, and may contribute to cancer occurrence. We and others have recently shown that the altered epigenetic state associated with HCV infection persists, to some extent, even after cure following DAAs and IFN-based treatments [ 63 - 67 ]. This observation is consistent in various HCV infection models, including immortalized human liver and hepatoma cells, a human liver chimeric mouse model, and post-SVR human liver samples.…”

“…Moreover, HCV was shown to persistently suppress innate immune pathways, including TLR3 activity, via epigenetic changes [ 66 ]. The effect of DNA methylation on transcription factors that regulate gene expression was also recently evaluated pre- and post-SVR, which remain dysregulated after HCV eradication [ 67 ].…”

“…HCV infection induces changes in host cell epigenetics and gene expression related to pathways that may be required for the virus life cycle but also contribute to carcinogenesis. Gene signatures associated with increased risk for HCC were found to intersect with epigenetic and gene expression scars [ 63 , 64 , 67 ]. These persistently altered genes and pathways are summarized in Table 3 .…”