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

Zhao, Hong; Lin, Wenyu; Kumthip, Kattareeya; Cheng, Du; Fusco, Dahlene N.; Hofmann, Oliver; Jilg, Nikolaus; Tai, Andrew W.; Goto, Kaku; Zhang, Leiliang; Hide, Winston; Jang, Jae Young; Peng, Lee F.; Chung, Raymond T.

doi:10.1016/j.jhep.2011.07.026

« Previous Next »Journal of Hepatology
Volume 56, Issue 2 , Pages 326-333, February 2012

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

Hong Zhao
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- These authors contributed equally to this work.
Wenyu Lin
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- These authors contributed equally to this work.
Kattareeya Kumthip
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Du Cheng
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Dahlene N. Fusco
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Oliver Hofmann
- Bioinformatics Core, Harvard School of Public Health, Boston, MA 02115, USA
Nikolaus Jilg
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Andrew W. Tai
- Department of Medicine, Gastroenterology, University of Michigan Health System Ann Arbor, MI 48105, USA
Kaku Goto
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Leiliang Zhang
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Winston Hide
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
Jae Young Jang
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Lee F. Peng
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
Raymond T. Chung
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Corresponding author. Address: Gastrointestinal Unit, Department of Medicine, Warren 1007, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA. Tel.: +1 (617) 724 7562; fax: +1 (617) 643 0446.

Received 30 January 2011; received in revised form 28 June 2011; accepted 12 July 2011. published online 02 September 2011.

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.

Abbreviations: HCV, hepatitis C virus, IFN-α, interferon-α, siRNA, small interfering RNA, SART1, squamous cell carcinoma antigen recognized by T cells, U4/U6.U5 tri-snRNP, U4/U6.U5 tri-small nuclear ribonucleoproteins