Hepatitis C Virus-induced Differential Transcriptional Traits in Host Cells After Persistent Infection Elimination by Direct-Acting Antivirals In Cell Culture

Chronic hepatitis C virus infection (HCV) causes liver inflammation and fibrosis, leading to development of severe liver disease, such as cirrhosis or hepatocellular carcinoma (HCC). Approval of direct acting antiviral (DAA) drug combinations has revolutionized chronic HCV therapy, with virus eradication in >98% of the treated patients. The efficacy of these treatments is such that it is formally possible for cured patients to carry formerly infected cells that display irreversible transcriptional alterations directly caused by chronic HCV Infection. Combining differential transcriptomes from two different persistent infection models, we observed a major reversion of infection-related transcripts after complete infection elimination. However, a small number of transcripts were abnormally expressed in formerly infected cells. Comparison of the results obtained in proliferating and growth-arrested cell culture models suggest that permanent transcriptional alterations may be established by several mechanisms. Interestingly, some of these alterations were also observed in the liver biopsies of virologically cured patients. Overall, our data suggest a direct and permanent impact of persistent HCV infection on the host cell transcriptome even after virus elimination, possibly contributing to development of HCC. To determine the impact of direct-acting antiviral (DAA) treatment on the reversal of persistent hepatitis C virus (HCV) infection-induced host cell transcriptional alterations, human hepatoma cells were persisitently infected in cell culture with recombinant HCV viruses. Persistent infection was maintained for weeks before infection elimination by DAA treatment. Experiments were performed in two experimental models: one in proliferating cell cultures and a second model in quiescent, partially-differentiated human hepatoma cells. Four biological replicates from mock, infected and the corresponding DAA-treated samples were analyzed by RNAseq in the proliferating cell culture model (Huh7pro). Three biological replicates from mock, infected and the corresponding DAA-treated samples were analyzed by RNAseq in the partially-differentiated cell culture model (Huh7DMSO).