Extended Data Fig. 6. Interferon signaling is upregulated in dysplastic Lgr5-p53^KO gastric organoids.

(a) mRNA expression of Trp53 in p53^KO, p53^WT, Lgr5-p53^KO, Lgr5-p53^WT, dys-Lgr5-p53^KO and dys-Lgr5-p53^WT gastric organoids. Data presented as mean ± s.d. of n = 2 (nondysplastic) and n = 3 (dysplastic) cell culture replicates.

(b) mRNA expression levels of Csf3, Cxcl10, and Ccl5 in p53^KO, p53^WT, Lgr5-p53^KO, Lgr5-p53^WT, dys-Lgr5-p53^KO and dys-Lgr5-p53^WT gastric organoids by RT-PCR. Data presented as mean ± s.d. of n = 3 cell culture replicates.

(c) Volcano plot of differential expressed gene-sets in p53^KO gastric organoids plotted as normalized enrichment scores (NES) by -log10(p-value), where p-values for gene set enrichment scores were determined by randomly permuting genes (n=100,000 permutations). Individual inflammation gene sets are described with corresponding NES.

(d) Scatter plot of single sample GSEA (ssGSEA) of interferon pathway and Ccl5 mRNA expression in gastric cancer cell lines annotated by TP53 mutation status (n = 26 for TP53 mutant and n = 10 for TP53 wildtype). Gray shaded region represents 95% confidence interval of the linear regression fit. Pearson’s correlation value R = 0.6 and p-value computed based on a two-sided t-distribution.

(e) Schematic of proposed vicious feedback cycle in gastric premalignancy: chronic inflammation and carcinogen exposure selects for p53 mutant gastric cells, which in turn stimulate inflammatory cytokines, particularly Csf3, Cxcl10, Ccl5