Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents.
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.
Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA.
Jian
J
Zhu
Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA.
Teresa
T
Davoli
Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA.
Jill M
JM
Perriera
Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA.
Christopher R
CR
Chin
Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA.
Gaurav D
GD
Gaiha
Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA.
Sinu P
SP
John
Novartis Institutes for BioMedical Research, Cambridge, MA 02115, USA.
Frederic D
FD
Sigiollot
Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA.
Geng
G
Gao
Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA.
Qikai
Q
Xu
Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02127, USA.
Hongjing
H
Qu
Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA.
Thomas
T
Pertel
Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Charlestown, MA 02129, USA.
Jennifer S
JS
Sims
ICCB-Longwood Screening Facility, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.
Jennifer A
JA
Smith
Microbiology and Physiological Systems (MaPS) Department, University of Massachusetts Medical School, Worcester, MA 01655, USA.
Richard E
RE
Baker
Department of Quantitative Health Sciences, University of Massachusetts Medical School, 55 Lake Avenue, North Worcester, MA 01655, USA.
Louise
L
Maranda
Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
Aylwin
A
Ng
Department 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.
Stephen J
SJ
Elledge
Microbiology 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.
Abraham L
AL
Brass
D033942:Adaptor Proteins, Vesicular Transport / Q000235:genetics / Q000378:metabolism; D000465:Algorithms; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins; D057809:HEK293 Cells; D015497:HIV-1 / Q000502:physiology*; D006367:HeLa Cells; D057166:High-Throughput Screening Assays / Q000379:methods*; D054884:Host-Pathogen Interactions; D006801:Humans; D019169:Jurkat Cells; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D016601:RNA-Binding Proteins; D014779:Virus Replication
D033942:Adaptor Proteins, Vesicular Transport; D002352:Carrier Proteins; D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D016601:RNA-Binding Proteins; C507456:SEC13 protein, human; C400546:THOC1 protein, human