Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium.

Background In spite of the wealth of literature available, the mechanistic determinants of SARS-CoV-2-mediated host-cell hijacking that results in massive infection of the human airway epithelium are still poorly understood. While ciliated cells have been identified as a major target and sink of SARS-CoV-2 during COVID-19 pathogenesis, the contribution of other airway epithelial components and the specific host factors hijacked that maintain their pro-infective cell state remains unclear. Limitations have been in part due to overreliance on single-cell gene expression profiling which may not reflect the protein activation status and analyses biased toward downstream effects rather than in actual determinants of infection. These ultimately have hampered progress in the understanding of the hijacking mechanisms implemented by SARS-CoV-2 in different cell types and in the identification of compounds to effectively counteract these host factors. Methods Here we used a human airway organotypic culture system known to model the cellular diversity of the airway epithelium, and a network-based platform to identify master regulator (MR) proteins that facilitate SARS-CoV-2 reprogramming of key airway epithelial cell types at different stages of infection. The analysis was coupled to a large-scale drug perturbation screen in these organotypic cultures using a library of FDA-approved compounds to identify drugs able to the invert SARS-CoV-2-induced activities in these cells. Results The identification of top MR differentially activated by SARS-CoV-2 in ciliated (NCOR, HDAC1), secretory (KAT2B), or basal/ciliated (MED21/MED7) cells suggested distinct host cell reprogramming mechanisms. Notably, the identification of crucial proviral factors required for SARS-CoV-2 infection (USP33, CUL5, SNX27 and PBRM1) collectively activated in all 3 main cell types revealed a potential mechanism of viral propagation common to both basal and luminal airway compartments. The perturbation assay identified 11 drugs able to invert the entire MR signature activated by SARS-CoV-2 in these cell types, with 9 of these targeting recognized proviral MR factors. Conclusions Leveraging MR analysis and drug perturbational profiles of human primary cells represents a relevant mechanism-based platform for investigation of disease pathogenesis and drug discovery in conditions affecting the airway epithelium.