A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors

Abstract

Host proteins are essential for entry and replication of HIV and provide important non-viral therapeutic targets. Large-scale RNAi-based screens have identified nearly a thousand candidate host factors, but with little agreement among studies and few validated factors. Here, we demonstrate that a genome-wide CRISPR-based screen identifies bona fide host factors in a physiologically relevant cell system. We identify five factors, including CD4 and CCR5, that are required for HIV infection yet dispensable for cellular proliferation and viability. TPST2 and SLC35B2 act in a common pathway to sulfate CCR5 on extracellular tyrosine residues, facilitating recognition by HIV envelope. ALCAM mediates cell aggregation, which is required for cell-to-cell HIV transmission. We validate these pathways in primary human CD4+ T cells through Cas9-mediated knockout and antibody blockade. Our findings indicate that HIV infection and replication rely on a limited set of host-dispensable genes and suggest focusing on these pathways for therapeutic intervention.

Arrayed CRISPR screen with image-based assay reliably uncovers host genes required for coxsackievirus infection

“…Our arrayed screens are compatible with these screening platforms. Currently, most CRIPSR screens are conducted in a pooled format, using the lentiviral system to identify viral host factors (Ma et al 2015;Marceau et al 2016;Savidis et al 2016;Zhang et al 2016;Kim et al 2017;Park et al 2017). Although these screens have been used successfully, only a few significant factors were selected, even though a genome-wide sgRNA library covering over 10,000 genes was used.…”

New Connections: Cell-to-Cell HIV-1 Transmission, Resistance to Broadly Neutralizing Antibodies, and an Envelope Sorting Motif

“…The presence of cells that harbor multiple copies of HIV-1 from infected patients supports the concept that this phenomenon occurs during in vivo HIV-1 infection (20)(21)(22). Further support for the idea of the importance of cell-to-cell contact in vivo comes from the recent identification of a cell aggregation factor, activated leukocyte cell adhesion molecule (ALCAM), as a host dependency genetic marker of HIV-1 infection (23). Interestingly, that study also demonstrated that knockdown of ALCAM protected cells in vitro from cellassociated infection but not from cell-free infection.…”

Elucidation of host–pathogen protein–protein interactions to uncover mechanisms of host cell rewiring

“…To do so, interaction studies can be coupled to endogenous host interaction maps [81,82] or to functional genomic screens to measure the fitness cost upon disruptions of either pathogenic or host molecular components [21], as was done for the HCV interactome [33]. By measuring sets of phenotypes such as pathogenic replication or host cell death, functional studies have the benefice of being able to simultaneously identify the positive, negative or neutral impact on the infection of targeted bacterial [83] or host factors [74,84]. Altogether, interaction studies, biochemical characterizations and functional screens may not only identify host – pathogen interactions, but also inform us on their phenotypic impacts and their molecular mechanisms for bacterial or viral pathogenicity.…”