A genome-wide genetic screen for host factors required for hepatitis C virus propagation

Abstract

Hepatitis C virus (HCV) infection is a major cause of end-stage liver disease and a leading indication for liver transplantation. Current therapy fails in many instances and is associated with significant side effects. HCV encodes only a few proteins and depends heavily on host factors for propagation. Each of these host dependencies is a potential therapeutic target. To find host factors required by HCV, we completed a genome-wide small interfering RNA (siRNA) screen using an infectious HCV cell culture system. We applied a two-part screening protocol to allow identification of host factors involved in the complete viral lifecycle. The candidate genes found included known or previously identified factors, and also implicate many additional host cell proteins in HCV infection. To create a more comprehensive view of HCV and host cell interactions, we performed a bioinformatic meta-analysis that integrates our data with those of previous functional and proteomic studies. The identification of host factors participating in the complete HCV lifecycle will both advance our understanding of HCV pathogenesis and illuminate therapeutic targets.HCV ͉ RNA interference ͉ viral host factors ͉ functional genomics ͉ viral lifecycle

Entry and replication of recombinant hepatitis C viruses in cell culture

“…Reporter viruses make such assays adaptable to high-throughput screening, with obvious advantages for antiviral research [76,126,[129][130][131]. Figure 4 illustrates a possible assay setup based on a dual reporter system, typically the Gaussia/Renilla and firefly luciferases.…”

Hepatitis c virus and host cell lipids: An intimate connection

“…132 The importance of PI4K-IIIα for HCV replication is well established, because this kinase has been identified in several siRNA-based screens as one of the top hits, regardless of the viral genotype and the experimental system. [133][134][135][136][137][138] In contrast, the role of the Golgi-resident PIK4-IIIβ is still controversially debated; it appears to contribute to replication of genotype 1 replicons, but not to replication of the JFH-1 genotype 2a isolate. 131,135,136 Nevertheless, the two isoforms of the kinase are believed to perform complementary, non-redundant tasks, because silencing of each gene decreases the levels of PI(4)P in HCV replicon cells, 81 and because the inhibitory effect mediated by PI4K-IIIα knockdown on HCV replication cannot be rescued by overexpression of PIK4-IIIβ.…”

RNAi screening reveals requirement for host cell secretory pathway in infection by diverse families of negative-strand RNA viruses

“…The advent of siRNA technology and the availability of genome-wide siRNA libraries have been useful in identifying host factors required for influenza virus, an NS RNA virus, and several positive-strand RNA viruses, as well as HIV (10)(11)(12)(13)(14)(15)(16)(17)(18)(19). The lack of similar studies with other NS RNA viruses has limited the understanding of the role of host cell factors in replication of these viruses.…”