Host cell factors in HIV replication: Meta-analysis of genome-wide studies

Frederic D. Bushman; Nirav Malani; Jason Fernandes; Iván D'Orso; Gerard Cagney; Tracy L. Diamond; Honglin Zhou; Daria J. Hazuda; Amy S. Espeseth; Renate König; Sourav Bandyopadhyay; Trey Ideker; Stephen P. Goff; Nevan J. Krogan; Alan D. Frankel; John A T Young; Sumit K. Chanda

doi:10.1371/journal.ppat.1000437

Host cell factors in HIV replication: Meta-analysis of genome-wide studies

Frederic D. Bushman, Nirav Malani, Jason Fernandes, Iván D'Orso, Gerard Cagney, Tracy L. Diamond, Honglin Zhou, Daria J. Hazuda, Amy S. Espeseth, Renate König, Sourav Bandyopadhyay, Trey Ideker, Stephen P. Goff, Nevan J. Krogan, Alan D. Frankel, John A T Young, Sumit K. Chanda

Research output: Contribution to journal › Review article › peer-review

373 Scopus citations

Abstract

We have analyzed host cell genes linked to HIV replication that were identified in nine genome-wide studies, including three independent siRNA screens. Overlaps among the siRNA screens were very modest (<7% for any pairwise combination), and similarly, only modest overlaps were seen in pairwise comparisons with other types of genome-wide studies. Combining all genes from the genome-wide studies together with genes reported in the literature to affect HIV yields 2,410 protein-coding genes, or fully 9.5% of all human genes (though of course some of these are false positive calls). Here we report an "encyclopedia" of all overlaps between studies (available at http://www.hostpathogen.org), which yielded a more extensively corroborated set of host factors assisting HIV replication. We used these genes to calculate refined networks that specify cellular subsystems recruited by HIV to assist in replication, and present additional analysis specifying host cell genes that are attractive as potential therapeutic targets.

Original language	English (US)
Article number	e1000437
Journal	PLoS pathogens
Volume	5
Issue number	5
DOIs	https://doi.org/10.1371/journal.ppat.1000437
State	Published - May 2009

ASJC Scopus subject areas

Parasitology
Microbiology
Immunology
Molecular Biology
Genetics
Virology

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Bushman, F. D., Malani, N., Fernandes, J., D'Orso, I., Cagney, G., Diamond, T. L., Zhou, H., Hazuda, D. J., Espeseth, A. S., König, R., Bandyopadhyay, S., Ideker, T., Goff, S. P., Krogan, N. J., Frankel, A. D., Young, J. A. T., & Chanda, S. K. (2009). Host cell factors in HIV replication: Meta-analysis of genome-wide studies. PLoS pathogens, 5(5), Article e1000437. https://doi.org/10.1371/journal.ppat.1000437

Bushman, FD, Malani, N, Fernandes, J, D'Orso, I, Cagney, G, Diamond, TL, Zhou, H, Hazuda, DJ, Espeseth, AS, König, R, Bandyopadhyay, S, Ideker, T, Goff, SP, Krogan, NJ, Frankel, AD, Young, JAT & Chanda, SK 2009, 'Host cell factors in HIV replication: Meta-analysis of genome-wide studies', PLoS pathogens, vol. 5, no. 5, e1000437. https://doi.org/10.1371/journal.ppat.1000437

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AU - Zhou, Honglin

AU - Hazuda, Daria J.

AU - Espeseth, Amy S.

AU - König, Renate

AU - Bandyopadhyay, Sourav

AU - Ideker, Trey

AU - Goff, Stephen P.

AU - Krogan, Nevan J.

AU - Frankel, Alan D.

AU - Young, John A T

AU - Chanda, Sumit K.

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Host cell factors in HIV replication: Meta-analysis of genome-wide studies

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