Extended Data Fig. 8: SOX2 overexpression induces IFN activation and promotes ADAR1 dependency.
From: Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence
a-c, ADAR1 dependency from genome-wide CRISPR screening in (a) 608 SOX2 amplified cell lines versus 16 non SOX2 amplified cell lines (b) 65 SCCs versus 246 adenocarcinoma cell lines (c) 10 SOX2 amplified SCC versus 55 non SOX2 amplified SCC cell lines. Box and whisker plots show the median (center line), interquartile range (box), 1.5 x interquartile range (whiskers), and outliers (points). Two-sided Mann-Whitney U tests were performed to assess significant differences in ADAR1 dependency, which are defined using CERES scores from the Dependency Map’s 19Q3 data release. SOX2 amplified lines are defined as those with log2(copy ratio) > 1. d, Representative images of crystal violet staining from noted human ESCC cell lines grown for two weeks treatment with or without doxycycline induction of indicated ADAR1 shRNA. Two biological replicates were performed. e, Tumor volume of 2 × 106 KYSE70 cells transduced with indicated inducible ADAR1 shRNA injected into flanks of nude mice and provided doxycycline-containing food (625 ppm). Representative images of tumors from panel. Scale bar is 2 cm. 4–8 tumors per group. f, Immunoblots of Adar1 depletion in CPP and SCPP organoids following transduction with indicated Adar1 sgRNA and with transfection of control, dsRNA (poly IC) and dsDNA (poly dAdT). (This experiment was repeated once with similar results). g, mRNA expression of Mx1, Cxcl10 and Isg15 in CPP and SCPP by quantitative-PCR. Three biological replicates were performed for each organoid. Data are shown as mean ± SD, p-value calculated by two-sided unpaired t-tests. h, Gene-Set Enrichment Analysis (GSEA) of pathways upregulated in SCPP compared with CPP organoids. (FDR-adjusted q-value calculated using the GSEA package) i, Enrichment scores (ES) plots for the interferon alpha and gamma gene sets in comparison of mRNA profiles of SCPP compared to CPP organoids. (Left, two-sided FDR-adjusted q-value=0.024; nominal p = 0.008 calculated using the GSEA package) (Right, two-sided FDR-adjusted q-value=0.015; nominal p = 0.034 calculated using the GSEA package) j, The most statistically enriched pathway identified from significant upregulation gained super-enhancer related genes in the comparison of SCPP vs Normal organoids (nominal p-value calculated using the GSEA package).
