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Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication

Nature volume 463, pages 818–822 (2010)Cite this article

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Abstract

Influenza A virus, being responsible for seasonal epidemics and reoccurring pandemics, represents a worldwide threat to public health1. High mutation rates facilitate the generation of viral escape mutants, rendering vaccines and drugs directed against virus-encoded targets potentially ineffective2. In contrast, targeting host cell determinants temporarily dispensable for the host but crucial for virus replication could prevent viral escape. Here we report the discovery of 287 human host cell genes influencing influenza A virus replication in a genome-wide RNA interference (RNAi) screen. Using an independent assay we confirmed 168 hits (59%) inhibiting either the endemic H1N1 (119 hits) or the current pandemic swine-origin (121 hits) influenza A virus strains, with an overlap of 60%. Notably, a subset of these common hits was also essential for replication of a highly pathogenic avian H5N1 strain. In-depth analyses of several factors provided insights into their infection stage relevance. Notably, SON DNA binding protein (SON)3 was found to be important for normal trafficking of influenza virions to late endosomes early in infection. We also show that a small molecule inhibitor of CDC-like kinase 1 (CLK1)4 reduces influenza virus replication by more than two orders of magnitude, an effect connected with impaired splicing of the viral M2 messenger RNA. Furthermore, influenza-virus-infected p27-/- (cyclin-dependent kinase inhibitor 1B; Cdkn1b) mice accumulated significantly lower viral titres in the lung, providing in vivo evidence for the importance of this gene. Thus, our results highlight the potency of genome-wide RNAi screening for the dissection of virus–host interactions and the identification of drug targets for a broad range of influenza viruses.

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Figure 1: Genome-wide RNAi screen reveals host factors required for the influenza infectious cycle.
Figure 2: Host cell factors affect replication of a broad range of influenza virus variants.
Figure 3: Dissection of infection processes affected by host cell factors.
Figure 4: In-depth analysis of the impact of p27 and CLK1 on influenza A virus infection.

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Acknowledgements

The authors would like to thank M. Drabkina, G. Heins, D. Khalil and D. Manntz for technical support, and K. Hoffmann and the experimental animal facility, headed by U. Klemm, for supporting mouse experiments. We also thank A. Pekosz for providing the influenza luciferase reporter construct and S. Becker for the pandemic H1N1 influenza strain. This work was supported through the EU FP6 project RIGHT (LSHB-CT-2004-005276), ERA-Net Pathogenomics (grant no. 0313938A) and a grant from FCI to T.F.M., and the RiNA network Berlin to T.R. and T.F.M. T.W. acknowledges German Government support via BMG (FSI program) and BMBF (FluResearchNet). H.K. and A.A. are student fellows of the Egyptian Government and IMPRS-IDI, respectively.

Author Contributions A.K., N.M. and T.F.M. conceived the project; A.K., N.M., T.W. and T.F.M. designed experiments; A.K., N.M., Y.S., A.A., D.H., D.B., H.K. and T.W. performed experiments; A.K., N.M., K.-P.P., S.H. and A.P.M. conducted bioinformatics; N.M., E.M., T.R. and T.F.M. established the screening platform; A.K., N.M., D.H., D.B., L.A.O. and T.F.M. wrote the manuscript.

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Author notes

  1. Simone Hess, Elke Müller & Thomas Rudel

    Present address: Present addresses: Hannover Medical School, 30625 Hannover, Germany (S.H.); Exploratory Research Space, RWTH Aachen University, Templergraben 55, 52056 Aachen, Germany (E.M.); Department of Microbiology, Biocenter, University of Würzburg, 97074 Würzburg, Germany (T.R.).,

  2. Alexander Karlas and Nikolaus Machuy: These authors contributed equally to this work.

Authors and Affiliations

  1. Molecular Biology Department,,

    Alexander Karlas, Nikolaus Machuy, Yujin Shin, Anita Artarini, Dagmar Heuer, Daniel Becker, Hany Khalil, Lesley A. Ogilvie, Simone Hess, André P. Mäurer, Elke Müller, Thomas Rudel & Thomas F. Meyer

  2. Core Facility Bioinformatics, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany ,

    Klaus-Peter Pleissner

  3. Robert Koch-Institute, Nordufer 20, 13353 Berlin, Germany ,

    Thorsten Wolff

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Correspondence to Thomas F. Meyer.

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Karlas, A., Machuy, N., Shin, Y. et al. Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature 463, 818–822 (2010). https://doi.org/10.1038/nature08760

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