Fig. 1

Asymmetric double knockout CRISPR screen of gene pairs that affect cancer cell response to T cell killing. A Schematic overview of CADRE screen. B Schematic of CADRE library design, 61 genes with immunotherapy resistance were crossed in combinatorial fashion with 19 significantly mutated tumor suppressors to create a DKO pool. SKOs and NTCs serve for comparison and as controls. C Titration of BC3 cells, and BC3 CADRE cells co-cultured with E:T ratios ranging from 0.1 to 5. High E:T ratios demonstrated significant phenotypic differences and were therefor selected for screening (q values of 1.76e-3 and 1.19e-2 by multiple T test, 1% FDR for E:T ratios 2 and 5, respectively). *, adjusted p-value < 0.05. **, adjusted p-value < 0.01. ***, adjusted p-value < 0.001. D Principal component analysis (PCA) of the sgRNA pair read count distributions across screens, E:T ratios, technical replicates, and pre-T cell treatment controls. E Scatterplots comparing guide representation of the CADRE library in post co-culture samples averaged across all replicates, E:T ratios, and screens compared to pre-selection infected cell controls. Jak1- and Jak2-associated sgRNA pairs (either DKO or SKO) are marked in red. F Scatterplot comparing Bonferroni-adjusted p value determined by outlier test compared to Studentized residuals from linear regression analysis in Additional file 1: Fig. S3F