A functional map of HIV-host interactions in primary human T cells.
Joseph HiattJudd F HultquistMichael J McGregorMehdi BouhaddouRyan T LeenayLacy M SimonsJanet M YoungPaige HaasTheodore L RothVictoria R TobinJason A WojcechowskyjJonathan M WooUjjwal RathoreDevin A CaveroEric ShifrutThong T NguyenKelsey M HaasHarmit S MalikJennifer A DoudnaAndrew P MayAlexander MarsonNevan J KroganPublished in: Nature communications (2022)
Human Immunodeficiency Virus (HIV) relies on host molecular machinery for replication. Systematic attempts to genetically or biochemically define these host factors have yielded hundreds of candidates, but few have been functionally validated in primary cells. Here, we target 426 genes previously implicated in the HIV lifecycle through protein interaction studies for CRISPR-Cas9-mediated knock-out in primary human CD4+ T cells in order to systematically assess their functional roles in HIV replication. We achieve efficient knockout (>50% of alleles) in 364 of the targeted genes and identify 86 candidate host factors that alter HIV infection. 47 of these factors validate by multiplex gene editing in independent donors, including 23 factors with restrictive activity. Both gene editing efficiencies and HIV-1 phenotypes are highly concordant among independent donors. Importantly, over half of these factors have not been previously described to play a functional role in HIV replication, providing numerous novel avenues for understanding HIV biology. These data further suggest that host-pathogen protein-protein interaction datasets offer an enriched source of candidates for functional host factor discovery and provide an improved understanding of the mechanics of HIV replication in primary T cells.
Keyphrases
- human immunodeficiency virus
- antiretroviral therapy
- hiv positive
- hiv infected
- hepatitis c virus
- hiv testing
- hiv aids
- men who have sex with men
- protein protein
- crispr cas
- small molecule
- endothelial cells
- south africa
- genome wide
- high throughput
- signaling pathway
- single cell
- dna methylation
- transcription factor
- oxidative stress
- cell death
- binding protein