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RNA interference screen for human genes associated with West Nile virus infection

Nature volume 455, pages 242–245 (2008)Cite this article

Abstract

West Nile virus (WNV), and related flaviviruses such as tick-borne encephalitis, Japanese encephalitis, yellow fever and dengue viruses, constitute a significant global human health problem1. However, our understanding of the molecular interaction of such flaviviruses with mammalian host cells is limited1. WNV encodes only 10 proteins, implying that it may use many cellular proteins for infection1. WNV enters the cytoplasm through pH-dependent endocytosis, undergoes cycles of translation and replication, assembles progeny virions in association with endoplasmic reticulum, and exits along the secretory pathway1,2,3. RNA interference (RNAi) presents a powerful forward genetics approach to dissect virus–host cell interactions4,5,6. Here we report the identification of 305 host proteins that affect WNV infection, using a human-genome-wide RNAi screen. Functional clustering of the genes revealed a complex dependence of this virus on host cell physiology, requiring a wide variety of molecules and cellular pathways for successful infection. We further demonstrate a requirement for the ubiquitin ligase CBLL1 in WNV internalization, a post-entry role for the endoplasmic-reticulum-associated degradation pathway in viral infection, and the monocarboxylic acid transporter MCT4 as a viral replication resistance factor. By extending this study to dengue virus, we show that flaviviruses have both overlapping and unique interaction strategies with host cells. This study provides a comprehensive molecular portrait of WNV–human cell interactions that forms a model for understanding single plus-stranded RNA virus infection, and reveals potential antiviral targets.

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Figure 1: RNAi screen and bioinformatics.
Figure 2: CBLL1 and ERAD silencing reduces West Nile virus (WNV) infection.
Figure 3: MCT4 silencing enhances WNV replication.
Figure 4: Interaction of West Nile virus (WNV) and dengue virus (DENV) with host cells.

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Acknowledgements

The human genome RNAi library was made available through the support of the New England Regional Center of Excellence in Biodefense and Emerging Infectious Disease (U54AI057159). The screening was performed at the ICCB-Longwood screening facility (Harvard Medical School). We thank B. Lindenbach for suggestions and Y. Benita for illustrations. We thank L2 Diagnostics for providing the anti-WNV antibody. This work was supported by the NIH. A.N. is supported by a fellowship award from the Crohn’s and Colitis Foundation of America. R.J.X. is supported by the NIH (AI062773) and by CCIB development funds. F.D.G was supported by an NIH training grant in Emerging and Tropical Infectious Diseases (AI07526); portions of this work were supported by a grant from NIAID to P.W.M. through the WRCE (NIH U54 AI057156). E.F. and S.J.E. are Investigators of the Howard Hughes Medical Institute.

Author Contributions M.N.K., H.A. and E.F. designed the experiments; M.N.K., B.S., E.F. and R.A. performed the screen; M.N.K., B.S., R.A.K., A.L.B., S.J.E. and H.A. analysed the data; M.N.K. and H.S. performed validations; P.D.U. designed microscopy; F.D.G. and P.W.M. designed replicon experiments; S.L. provided PITPNM2 cDNA; A.N. and R.J.X. performed bioinformatics analyses; and M.N.K., H.A., A.N., R.J.X. and E.F. co-wrote the paper.

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Author notes

  1. Ramnik J. Xavier, Herve Agaisse and Erol Fikrig: These authors contributed equally to this work.

Authors and Affiliations

  1. Section of Infectious Diseases,,

    Manoj N. Krishnan, Bindu Sukumaran, Hameeda Sultana & Erol Fikrig

  2. Department of Internal Medicine,, Section of Rheumatology,

    Feng Qian & Ruth R. Montgomery

  3. Section for Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticutt 06520-8031, USA ,

    Pradeep D. Uchil, Rachel Adametz & Herve Agaisse

  4. Center for Computational and Integrative Biology, and Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA ,

    Aylwin Ng & Ramnik J. Xavier

  5. Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA,

    Felicia D. Gilfoy & Peter W. Mason

  6. Department of Systems Biology,,

    Melody Tsui

  7. Department of Genetics, Center for Genetics and Genomics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA,

    Abraham L. Brass & Stephen J. Elledge

  8. Department of Neurobiology, Weizmann Institute of Science, Israel

    Sima Lev

  9. L2 Diagnostics, 300 George Street, New Haven, Connecticutt 06511, USA ,

    Raymond A. Koski

  10. Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA ,

    Stephen J. Elledge & Erol Fikrig

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  1. Manoj N. Krishnan
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Corresponding author

Correspondence to Erol Fikrig.

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Krishnan, M., Ng, A., Sukumaran, B. et al. RNA interference screen for human genes associated with West Nile virus infection. Nature 455, 242–245 (2008). https://doi.org/10.1038/nature07207

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