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Integrated multi-omics analyses identify key anti-viral host factors and pathways controlling SARS-CoV-2 infection

ABSTRACT: Anti-viral host factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill this gap, we performed a genome-wide CRISPR dropout screen and integrated analyses of the multi-omics data of the CRISPR screen, genome-wide association studies, single-cell RNA-seq, and host-host/viral protein-protein/RNA interactome. We identified many anti-viral host genes that were missed by previous studies, including the components of V-ATPases, ESCRT, and N-glycosylation pathways that inhibited viral entry/replication. We also identified the cohesin complex as a novel antiviral pathway, supporting an important role of three-dimensional chromatin organization in mediating host-viral interaction. Furthermore, we discovered an anti-viral transcription factor KLF5, a regulator of sphingolipid metabolism, which was up-regulated and harbored genetic variations linked to COVID-19 patients with severe symptoms. Our analyses provide a resource for understanding the host antiviral network for combating SARS-CoV-2 and may help develop new therapeutic strategies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE209750 | GEO | 2023/08/08

REPOSITORIES: GEO

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