Fig. 1: CRISPR genome-wide screens in human Calu-3 cells identify host factors important for infection by wild-type SARS-CoV-2 and variants of concern. | Nature Communications

Fig. 1: CRISPR genome-wide screens in human Calu-3 cells identify host factors important for infection by wild-type SARS-CoV-2 and variants of concern.

From: Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2

Fig. 1: CRISPR genome-wide screens in human Calu-3 cells identify host factors important for infection by wild-type SARS-CoV-2 and variants of concern.The alternative text for this image may have been generated using AI.

a Schematic of genome-wide CRISPR screening workflow for the identification of SARS-CoV-2-host factors. Calu-3 cells were transduced with the Brunello CRISPR library, selected with puromycin and infected with WT-SARS-CoV-2, Alpha or Beta VOCs. Surviving cells were harvested 7–9 days post-infection (dpi). The abundance of each sgRNA in the mock controls and selected population was determined by high-throughput sequencing and a gene enrichment analysis was performed. The figure was created with BioRender.com. b Performance in the screens of example sgRNAs. The density across the screens is plotted for the full library (top) and for the 4 sgRNAs targeting top resistance hits, top sensitization hits and the non-targeting control sgRNA. c Volcano plot showing top genes conferring resistance and sensitivity to SARS-CoV-2. d Gene enrichment score for CRISPR screens of WT-SARS-CoV-2 and VOCs infection. Enrichment scores were determined by MaGECK. e Real-time PCR quantification of WT-SARS-CoV-2 levels in wild-type and CRISPR-edited Calu-3 cells. A non-targeting (NT) sgRNA was used as control. Cells were infected using MOI = 0.002 for 48 h. Data were analyzed from three biologically independent experiments by one-way ANOVA with two-sided Tukey’s multiple comparison test. Shown are means ± SD. *p < 0.05; **p < 0.005; ***p < 0.0001. f Cell viability assay of wild-type and individual CRISPR-edited Calu-3 cells infected with SARS-CoV-2 at MOI of 0.002 for 48 h, and stained with crystal violet. One of three repetitions is shown. g Histograms of mRNA levels in Calu-3, Vero-E6, and A549 cells66,67,68, normalized to transcripts per million (TPM). Red, green, and blue lines represent the levels of GATA6, CUL5, and IRF6, respectively, in each dataset. IRF6 is below threshold in A549 and Vero-E6 cells. h Comparative analysis of previously reported SARS-CoV-2 knockout screens performed in the Calu-3 cell line21,62. Top proviral candidates identified in our screens are displayed. Source data are provided as a Source Data file.

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