TMPRSS2 promotes SARS-CoV-2 evasion from NCOA7-mediated restriction

Abstract

Interferons play a critical role in regulating host immune responses to SARS-CoV-2, but the interferon (IFN)-stimulated gene (ISG) effectors that inhibit SARS-CoV-2 are not well characterized. The IFN-inducible short isoform of human nuclear receptor coactivator 7 (NCOA7) inhibits endocytic virus entry, interacts with the vacuolar ATPase, and promotes endo-lysosomal vesicle acidification and lysosomal protease activity. Here, we used ectopic expression and gene knockout to demonstrate that NCOA7 inhibits infection by SARS-CoV-2 as well as by lentivirus particles pseudotyped with SARS-CoV-2 Spike in lung epithelial cells. Infection with the highly pathogenic, SARS-CoV-1 and MERS-CoV, or seasonal, HCoV-229E and HCoV-NL63, coronavirus Spike-pseudotyped viruses was also inhibited by NCOA7. Importantly, either overexpression of TMPRSS2, which promotes plasma membrane fusion versus endosomal fusion of SARS-CoV-2, or removal of Spike’s polybasic furin cleavage site rendered SARS-CoV-2 less sensitive to NCOA7 restriction. Collectively, our data indicate that furin cleavage sensitizes SARS-CoV-2 Spike to the antiviral consequences of endosomal acidification by NCOA7, and suggest that the acquisition of furin cleavage may have favoured the co-option of cell surface TMPRSS proteases as a strategy to evade the suppressive effects of IFN-induced endo-lysosomal dysregulation on virus infection. IFNs play a critical role in regulating host immune responses to virus infections. In cultured cell systems, SARS-CoV-2 can trigger robust IFN and innate immune responses through activation of cytoplasmic RNA sensors, and is also highly sensitive to inhibition by IFN treatment. Consistent with this, ISGs are induced in patients with COVID-19, and inborn errors in the IFN system are associated with severe COVID-19. Our understanding of the repertoire and mechanisms of action of the ISGs that impact SARS-CoV-2 is currently incomplete. In this study, we demonstrate that the IFN-inducible short isoform of NCOA7 is a potent inhibitor of SARS-CoV-2 infection. Our data support the presence of two distinct pathways of SARS-CoV-2 entry and reveal that only the pH-dependent endo-lysosomal pathway is efficiently inhibited by NCOA7. Unravelling the biological significance of the polybasic furin cleavage site in the viral Spike protein, and the concomitant use of TMPRSS2 for cell surface fusion is an area of intense research. Our findings suggest that the acquisition of the polybasic furin cleavage site in Spike may have driven the co-option of the cell surface TMPRSS2 protease to evade the antiviral effects of NCOA7-mediated perturbation of the endo-lysosomal system.