Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens

Existing antibiotics are inadequate to defeat tuberculosis (TB), a leading cause of death worldwide. We sought potential targets for host-directed therapies (HDTs) by investigating the host immune response to mycobacterial infection. We used high-throughput CRISPR knockout and CRISPR interference (CRISPRi) screens to identify perturbations that improve the survival of human phagocytic cells infected with Mycobacterium bovis BCG (Bacillus Calmette-Guérin), as a proxy for Mycobacterium tuberculosis (Mtb). Many of these perturbations constrained the growth of intracellular mycobacteria. We identified over 100 genes associated with diverse biological pathways as potential HDT targets. We validated key components of the type I interferon and aryl hydrocarbon receptor signaling pathways that respond to the small-molecule inhibitors cerdulatinib and CH223191, respectively; these inhibitors enhanced human macrophage survival and limited the intracellular growth of Mtb. Thus, high-throughput functional genomic screens, by elucidating highly complex host-pathogen interactions, can serve to identify HDTs to potentially improve TB treatment. [Display omitted] •High-throughput functional genomic screens elucidate host-pathogen interactions•Screens find over 100 host targets inhibiting intracellular bacterial pathogenesis•AHR/ARNT pathway inhibition blocks bacterial pathogenesis via oxylipin metabolism•Cerdulatinib and CH223191 are potential host-directed therapies for TB Lai et al. approach tuberculosis (TB) intervention from the point of view of the host by establishing large-scale CRISPR screen platforms in human innate immune cells. By either knocking out or reducing the expression of individual genes, the authors determine how human cells respond, on the genetic level, to intracellular mycobacteria, which cause TB. Specifically, they find which genes promote or suppress bacterial survival. On this basis, the authors identify potential targets for host-directed therapies.