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

Author

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, and Abraham L. Brass

Subjects
Biology (General), QH301-705.5
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.

Published
2014
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2. Comprehensive Identification of Host Modulators of HIV-1 Replication using Multiple Orthologous RNAi Reagents

Author

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

Subjects
False positives and false negatives, Cell Cycle Proteins, Biology, Virus Replication, General Biochemistry, Genetics and Molecular Biology, Article, Jurkat Cells, Cog, RNA interference, False positive paradox, Humans, Gene, lcsh:QH301-705.5, Genetics, HEK 293 cells, Nuclear Proteins, RNA-Binding Proteins, Phenotype, 3. Good health, High-Throughput Screening Assays, DNA-Binding Proteins, Adaptor Proteins, Vesicular Transport, HEK293 Cells, Viral replication, lcsh:Biology (General), Host-Pathogen Interactions, HIV-1, RNA Interference, Carrier Proteins, Algorithms, HeLa Cells
Abstract

SUMMARY 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., Graphical Abstract

Published
2014

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