A functional genomic screen reveals novel host genes that mediate interferon-alpha's effects against hepatitis C virus

J Hepatol. 2012 Feb;56(2):326-33. doi: 10.1016/j.jhep.2011.07.026. Epub 2011 Aug 31.


Background & aims: The precise mechanisms by which IFN exerts its antiviral effect against HCV have not yet been elucidated. We sought to identify host genes that mediate the antiviral effect of IFN-α by conducting a whole-genome siRNA library screen.

Methods: High throughput screening was performed using an HCV genotype 1b replicon, pRep-Feo. Those pools with replicate robust Z scores ≥2.0 entered secondary validation in full-length OR6 replicon cells. Huh7.5.1 cells infected with JFH1 were then used to validate the rescue efficacy of selected genes for HCV replication under IFN-α treatment.

Results: We identified and confirmed 93 human genes involved in the IFN-α anti-HCV effect using a whole-genome siRNA library. Gene ontology analysis revealed that mRNA processing (23 genes, p=2.756e-22), translation initiation (nine genes, p=2.42e-6), and IFN signaling (five genes, p=1.00e-3) were the most enriched functional groups. Nine genes were components of U4/U6.U5 tri-snRNP. We confirmed that silencing squamous cell carcinoma antigen recognized by T cells (SART1), a specific factor of tri-snRNP, abrogates IFN-α's suppressive effects against HCV in both replicon cells and JFH1 infectious cells. We further found that SART1 was not IFN-α inducible, and its anti-HCV effector in the JFH1 infectious model was through regulation of interferon stimulated genes (ISGs) with or without IFN-α.

Conclusions: We identified 93 genes that mediate the anti-HCV effect of IFN-α through genome-wide siRNA screening; 23 and nine genes were involved in mRNA processing and translation initiation, respectively. These findings reveal an unexpected role for mRNA processing in generation of the antiviral state, and suggest a new avenue for therapeutic development in HCV.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, Neoplasm / genetics
  • Antiviral Agents / pharmacology*
  • Cell Line
  • Computational Biology
  • Genome, Human
  • Genomics
  • Hepacivirus / drug effects*
  • Hepacivirus / genetics
  • Hepacivirus / physiology
  • Hepatitis C, Chronic / drug therapy*
  • Hepatitis C, Chronic / genetics*
  • Hepatitis C, Chronic / virology
  • High-Throughput Screening Assays
  • Host-Pathogen Interactions / genetics*
  • Humans
  • Interferon-alpha / pharmacology*
  • Pharmacogenetics
  • RNA, Small Interfering / genetics
  • Receptor, Interferon alpha-beta / genetics
  • Replicon
  • Ribonucleoproteins, Small Nuclear / genetics


  • Antigens, Neoplasm
  • Antiviral Agents
  • IFNAR1 protein, human
  • Interferon-alpha
  • RNA, Small Interfering
  • Ribonucleoproteins, Small Nuclear
  • SART1 protein, human
  • Receptor, Interferon alpha-beta