Fig. 3: TNFα-induced p16/p19 expression and colonic stem cell markers were associated with epigenetic remodeling. | Nature Communications

Fig. 3: TNFα-induced p16/p19 expression and colonic stem cell markers were associated with epigenetic remodeling.

From: Sleeping Beauty transposon mutagenesis identified genes and pathways involved in inflammation-associated colon tumor development

Fig. 3

a HE for the normal mouse colon, the ulcer at day 7 from DSS, and regenerating epithelia. Bars; 100 µm. b An experimental design to establish organoids from DSS-treated mice. c Quantitative PCR (qPCR) results for p16 and p19 using wt (control) and DSS organoids. Six independent samples. d A pathway analysis showing deregulated pathways in DSS organoids. Two-sided Fisher’s exact test. e A volcano plot showing the expression changes in DSS compared to control organoids. Three mice were used for control and DSS, respectively. f A picture showing the timing of cytokine addition and sample collection. g Photos of wt and wt+TNFα organoids. Bars; 200 µm. h, i qPCR showing expression changes by cytokines in wt organoids for p16 (h), p19 (i). j A pathway analysis for RNA-seq using wt and wt+TNFα organoids. Two-sided Fisher’s exact test. k RNA-seq for colonic stem cell genes29 using wt and wt+TNFα organoids. l A heatmap for the colonic stem cell genes29 obtained by RNA-seq between wt and wt+TNFα organoids. m GSEA analysis for RNA-seq. Two-sided Fisher’s exact test. n Graphs showing RNA expression of indicated genes in colonic mucosa of the healthy control (cont) and UC patients (UC) derived from the dataset. o A heatmap showing the expression of genes in the Hoxb cluster obtained by RNA-seq between wt and wt+TNFα organoids. p Venn diagram showing the number of genes identified from ChIP-seq and RNA-seq. q IGV images for ChIP-seq in indicated genetic loci. Unique peaks subtracted (sub) were shown by bold black lines. K27:H3K27me3, K4:H3K4me3. r A heatmap showing the intensity of H3K27me3 in promoters of stem cell genes with increased expression in wt+TNFα organoids. s Integrated analysis for cell clustering by scRNA-seq. t T-SNE clustering analyses showing cell populations. u Bar graphs showing % of cells double positive for a stem cell marker and senescence marker(s) in Ki67(−) cells. Data are presented as mean values +/− SD, and tested with two-sided t test for (c, e, h, i, k, n).

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