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. [Display omitted] •Multiple orthologous RNAi reagents were used to elucidate HIV-host interactions•Screens were traditionally validated and quantitatively phenotyped•All screen data sets were integrated to quantify each gene’s role in HIV-1 replication•Roles of GOLGI49, SEC13, COG, and THOC in HIV-1 replication were investigated RNAi screens have implicated hundreds of host proteins as HIV-1 dependency factors. While informative, these studies overlap poorly. Zhu et al. now combine data from previous work with a screen using multiple orthologous RNAi reagents to produce a quantitatively integrated network of genes that modulate HIV-1 replication.