A Functional Genomic Screen Identifies Cellular Cofactors of Hepatitis C Virus Replication

Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
Cell host & microbe (Impact Factor: 12.33). 04/2009; 5(3):298-307. DOI: 10.1016/j.chom.2009.02.001
Source: PubMed


Hepatitis C virus (HCV) chronically infects 3% of the world's population, and complications from HCV are the leading indication for liver transplantation. Given the need for better anti-HCV therapies, one strategy is to identify and target cellular cofactors of the virus lifecycle. Using a genome-wide siRNA library, we identified 96 human genes that support HCV replication, with a significant number of them being involved in vesicle organization and biogenesis. Phosphatidylinositol 4-kinase PI4KA and multiple subunits of the COPI vesicle coat complex were among the genes identified. Consistent with this, pharmacologic inhibitors of COPI and PI4KA blocked HCV replication. Targeting hepcidin, a peptide critical for iron homeostasis, also affected HCV replication, which may explain the known dysregulation of iron homeostasis in HCV infection. The host cofactors for HCV replication identified in this study should serve as a useful resource in delineating new targets for anti-HCV therapies.

Download full-text


Available from: Andrew W. Tai, Apr 04, 2014
  • Source
    • "Statins Inhibition of HMG-CoA reductase Kim et al. (2007) Chlorocylizinehydrocholoride Inhibition of entry He et al. (2015) approaches (Tai et al., 2009; Li et al., 2009; Li et al., 2014). Finally, the phenotypic effects of siRNAs may be unrelated to the intended target, as " off-target " effects can result from partial complementarity to multiple mRNAs at the seed region of nucleotides 2–8 (Franceschini et al., 2014). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Hepatitis C virus (HCV) remains a major global health burden, with more than 130 million individuals chronically infected and at risk for the development of hepatocellular carcinoma (HCC). The recent clinical licensing of direct-acting antivirals enables viral cure. However, limited access to therapy and treatment failure in patient subgroups warrants a continuing effort to develop complementary antiviral strategies. Furthermore, once fibrosis is established, curing HCV infection does not eliminate the risk for HCC. High-throughput approaches and screens have enabled the investigation of virus-host interactions on a genome-wide scale. Gain- and loss-of-function screens have identified essential host-dependency factors in the HCV viral life cycle, such as host cell entry factors or regulatory factors for viral replication and assembly. Network analyses of systems-scale data sets provided a comprehensive view of the cellular state following HCV infection, thus improving our understanding of the virus-induced responses of the target cell. Interactome, metabolomics and gene expression studies identified dysregulated cellular processes potentially contributing to HCV pathogenesis and HCC. Drug screens using chemical libraries led to the discovery of novel antivirals. Here, we review the contribution of high-throughput approaches for the investigation of virus-host interactions, viral pathogenesis and drug discovery.
    Virus Research 09/2015; DOI:10.1016/j.virusres.2015.09.013 · 2.32 Impact Factor
  • Source
    • "If these host proteins are indispensable for pathogens during infections, but not essential for host cells, they may serve as antimicrobial therapeutic targets to fight drug resistance. In parallel with the increase in the amount of PHI data, several genome-wide RNAi screening studies to identify cellular host factors were performed within the last decade (Ng et al., 2007; Brass et al., 2008; Hao et al., 2008; König et al., 2008, 2010; Krishnan et al., 2008; Zhou et al., 2008; Bushman et al., 2009; Li et al., 2009; Sessions et al., 2009; Tai et al., 2009; Karlas et al., 2010; Kumar et al., 2010; Murali et al., 2011; Moser et al., 2013; Lee et al., 2014). The detailed knowledge about mechanisms of the relationships between these host factors and their targeting pathogens is required urgently to develop new and more effective antimicrobial therapeutics, necessitating a computational systems biology approach to PHIs. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Pathogens manipulate the cellular mechanisms of host organisms via pathogen-host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein-protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature.
    Frontiers in Microbiology 04/2015; 6. DOI:10.3389/fmicb.2015.00235 · 3.99 Impact Factor
  • Source
    • "Genome-scale siRNA screens have been carried out for many viruses other than VACV, including HIV-1 [41]–[43], West Nile Virus (WNV) [44], Hepatitis C Virus (HCV) [30], [45], Vesicular Stomatitis Virus (VSV) [29], Borna Disease Virus [46], enteroviruses [27], Dengue virus [28], herpes simplex virus 1 (HSV-1) [33] and influenza A virus [26], [31], [47]. Host factors common to two or more of these screens could represent broadly acting cellular proteins with a generalised effect on viral replication. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Vaccinia virus (VACV) is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics.
    PLoS ONE 06/2014; 9(6):e98431. DOI:10.1371/journal.pone.0098431 · 3.23 Impact Factor
Show more