A Genome-Wide Knockout Screen in Human Macrophages Identified Host Factors Modulating <i>Salmonella</i> Infection

Abstract

A genome-scale CRISPR knockout library screen of THP-1 human macrophages was performed to identify loss-of-function mutations conferring resistance to <i>Salmonella</i> uptake. The screen identified 183 candidate genes, from which 14 representative genes involved in actin dynamics (<i>ACTR3</i>, <i>ARPC4</i>, <i>CAPZB</i>, <i>TOR3A</i>, <i>CYFIP2</i>, <i>CTTN</i>, and <i>NHLRC2</i>), glycosaminoglycan metabolism (<i>B3GNT1</i>), receptor signaling (<i>PDGFB</i> and <i>CD27</i>), lipid raft formation (<i>CLTCL1</i>), calcium transport (<i>ATP2A2</i> and <i>ITPR3</i>), and cholesterol metabolism (<i>HMGCR</i>) were analyzed further. For some of these pathways, known chemical inhibitors could replicate the <i>Salmonella</i> resistance phenotype, indicating their potential as targets for host-directed therapy. The screen indicated a role for the relatively uncharacterized gene <i>NHLRC2</i> in both <i>Salmonella</i> invasion and macrophage differentiation. Upon differentiation, <i>NHLRC2</i> mutant macrophages were hyperinflammatory and did not exhibit characteristics typical of macrophages, including atypical morphology and inability to interact and phagocytose bacteria/particles. Immunoprecipitation confirmed an interaction of NHLRC2 with FRYL, EIF2AK2, and KLHL13.<b>IMPORTANCE</b><i>Salmonella</i> exploits macrophages to gain access to the lymphatic system and bloodstream to lead to local and potentially systemic infections. With an increasing number of antibiotic-resistant isolates identified in humans, <i>Salmonella</i> infections have become major threats to public health. Therefore, there is an urgent need to identify alternative approaches to anti-infective therapy, including host-directed therapies. In this study, we used a simple genome-wide screen to identify 183 candidate host factors in macrophages that can confer resistance to <i>Salmonella</i> infection. These factors may be potential therapeutic targets against <i>Salmonella</i> infections.