Lentiviral ShRNA Vectors Non-specifically Inhibited Hepatitis C Virus Propagation By Disrupting The MicroRNA Profile

RNA interference (RNAi) is widely used in gene-knockdown analysis and as a tool to screen host genes involved in viral infection. Due to the limitation of transducing cells with synthetic small interfering RNAs(siRNA), lentiviral short-hairpin RNA (shRNA) vectors are more widely used. We found that stable, but not transient, transduction with the same dose of lentiviral shRNA vectors non-specifically inhibited Hepatitis C virus (HCV) infection in hepatoma cells by disrupting host microRNA (miRNA) biogenesis; we determined that this disruption was caused by the high level of integrated shRNA vectors in stably transfected cells. As shRNA sequences and integration loci might also influence the miRNA expression profile, we performed miRNA microarray analysis and identified three miRNA previously reported to be involved in HCV infection. Another miRNA, miR-1246, was found to influence HCV propagation in this study. While our findings raise concerns about non-specific off-target effects of stable-transduction with lentiviral shRNA vectors, our studies reveal that the shRNA-regulated miRNA identified in the microarrays might provide new therapies for HCV infection.