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Cell Rep. 2014 Oct 23;9(2):752-66. doi: 10.1016/j.celrep.2014.09.031. Epub 2014 Oct 16.

Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents.

Author information

  • 1Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA.
  • 2Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA.
  • 3Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA.
  • 4Novartis Institutes for BioMedical Research, Cambridge, MA 02115, USA.
  • 5ICCB-Longwood Screening Facility, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.
  • 6Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue, North Worcester, MA 01655, USA.
  • 7Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
  • 8Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: selledge@genetics.med.harvard.edu.
  • 9Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA. Electronic address: abraham.brass@umassmed.edu.

Abstract

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.

PMID:
25373910
PMCID:
PMC4926641
DOI:
10.1016/j.celrep.2014.09.031
[PubMed - indexed for MEDLINE]
Free PMC Article
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