Comprehensive Identification of Host Modulators of HIV-1 Replication using Multiple Orthologous RNAi Reagents

Jian Zhu; Teresa Davoli; Jill M. Perriera; Christopher R. Chin; Gaurav D. Gaiha; Sinu P. John; Frederic D. Sigiollot; Geng Gao; Qikai Xu; Hongjing Qu; Thomas Pertel; Jennifer S. Sims; Jennifer A. Smith; Richard E. Baker; Louise Maranda; Aylwin Ng; Stephen J. Elledge; Abraham L. Brass

doi:10.1016/j.celrep.2014.09.031

Cell Reports (Oct 2014)

Comprehensive Identification of Host Modulators of HIV-1 Replication using Multiple Orthologous RNAi Reagents

Jian Zhu,
Teresa Davoli,
Jill M. Perriera,
Christopher R. Chin,
Gaurav D. Gaiha,
Sinu P. John,
Frederic D. Sigiollot,
Geng Gao,
Qikai Xu,
Hongjing Qu,
Thomas Pertel,
Jennifer S. Sims,
Jennifer A. Smith,
Richard E. Baker,
Louise Maranda,
Aylwin Ng,
Stephen J. Elledge,
Abraham L. Brass

Affiliations

Jian Zhu: Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02127, USA
Teresa Davoli: Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02127, USA
Jill M. Perriera: Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
Christopher R. Chin: Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
Gaurav D. Gaiha: Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
Sinu P. John: Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
Frederic D. Sigiollot: Novartis Institutes for BioMedical Research, Cambridge, MA 02115, USA
Geng Gao: Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02127, USA
Qikai Xu: Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02127, USA
Hongjing Qu: Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02127, USA
Thomas Pertel: Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
Jennifer S. Sims: Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA
Jennifer A. Smith: ICCB-Longwood Screening Facility, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
Richard E. Baker: Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA
Louise Maranda: Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue, North Worcester, MA 01655, USA
Aylwin Ng: Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
Stephen J. Elledge: Department of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02127, USA
Abraham L. Brass: Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA

DOI: https://doi.org/10.1016/j.celrep.2014.09.031
Journal volume & issue: Vol. 9, no. 2
pp. 752 – 766

Abstract

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RNAi screens have implicated hundreds of host proteins as HIV-1 dependency factors (HDFs). While informative, these early studies overlap poorly due to false positives and false negatives. To ameliorate these issues, we combined information from the existing HDF screens together with new screens performed with multiple orthologous RNAi reagents (MORR). In addition to being traditionally validated, the MORR screens and the historical HDF screens were quantitatively integrated by the adaptation of an established analysis program, RIGER, for the collective interpretation of each gene’s phenotypic significance. False positives were addressed by the removal of poorly expressed candidates through gene expression filtering, as well as with GESS, which identifies off-target effects. This workflow produced a quantitatively integrated network of genes that modulate HIV-1 replication. We further investigated the roles of GOLGI49, SEC13, and COG in HIV-1 replication. Collectively, the MORR-RIGER method minimized the caveats of RNAi screening and improved our understanding of HIV-1–host cell interactions.

Published in Cell Reports

ISSN: 2211-1247 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Biology (General)
Website: http://www.cell.com/cell-reports/home

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