Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection

Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 and identified known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-β signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.

Competing Interest Statement

Yale University (CBW) has a patent pending related to this work entitled: 'Compounds and Compositions for Treating, Ameliorating, and/or Preventing SARS-CoV-2 Infection and/or Complications Thereof.' Yale University has committed to rapidly executable non-exclusive royalty-free licenses to intellectual property rights for the purpose of making and distributing products to prevent, diagnose and treat COVID-19 infection during the pandemic and for a short period thereafter. JGD consults for Foghorn Therapeutics, Maze Therapeutics, Merck, Agios, and Pfizer; JGD consults for and has equity in Tango Therapeutics.

Genome-wide CRISPR screen identifies genes critical for SARS-CoV-2-induced cell death. (A) Schematic of pooledscreen. Vero-E6 cells expressing Cas9 were transduced with the genome-wide C. sabaeus library via lentivirus. The transduced cellpopulation then either received a mock treatment or was challenged with SARS-CoV-2 under various culture conditions. Survivingcells from each condition were isolated and the sgRNA sequences were amplified by PCR and sequenced. (B) Volcano plot showingtop genes conferring resistance and sensitivity to SARS-CoV-2. The gene-level z-score and -log10(FDR) were both calculated usingthe mean of the five Cas9-v2 conditions. Non-targeting control sgRNAs were randomly grouped into sets of 4 to serve as “dummy”genes and are shown in green. (C) Performance of individual guide RNAs targeting ACE2, SMARCA4, CTSL, and TMPRSS2. Themean residual across the five Cas9-v2 conditions is plotted for the full library (top) and for the 4 guide RNAs targeting each gene. (D)Heatmaps of the top 25 gene hits for resistance and sensitivity, ranked by mean z-score in the Cas9-v2 conditions.Genes that areincluded in one of the gene sets labeled in (Fig 2A) are colored accordingly. Condition a: Cas9v2 D5 2.5e6 Hi-MOI; b: Cas9v2 D5 5e6Hi-MOI; c: Cas9v2 D2 5e6 Hi-MOI; d: Cas9v2 D10 5e6 Hi-MOI; e: Cas9v2 D5 2.5e6 Lo-MOI.

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