Extended Data Fig. 3: SARS-CoV-2 proviral signatures revealed by depleted genes in the GOF screen.
a. Protein-protein interaction network for top 100 depleted hits from the CRISPR GOF screen based on STRING analysis. Solid lines between genes indicate direct interaction, dashed lines indicate indirect connections. Nodes are color-coded by functional groups and scaled according to screen enrichment RRA score. b. Pathway analysis of top 100 depleted hits in the GOF screen indicates enriched pathways with putative antiviral roles. Circle size indicates the number of genes within each pathway, color indicates FDR of pathway enrichment. c-d. Individual guide TCID50 validation of the effect of transcriptional upregulation of the top five putative proviral hits on SARS-CoV-2 viral titer in Calu-3 cells infected at an MOI of 0.05 for 48 hours. Each gene was targeted with two sgRNAs. Dotted line indicates the limit of detection (LOD) of the assay and average titer of NTG lines tested. Significance was determined by a two-sided t-test comparing each GOF cell line to the NTG control cells, n = 3 biological replicates. e-f. Same as (c-d) but with additional proviral hits of interest. Significance was determined by a two-sided t-test comparing each GOF cell line to the NTG control cells, n = 3. Dotted line indicates the LOD of the assay and average titer of NTG lines. g. Western blot analysis of Calu-3 ACE2 GOF cells. One western blot was conducted in this experiment, then re-probed for β-actin as a loading control. For all panels: error bars denote mean ± s.e.m., significance is indicated as: n.s.=not significant, *= P < 0.05, **= P < 0.01, ***=P < 0.001, ****= P < 0.0001.
