Fig. 6: Mice with intestinal epithelial TGFβ signalling mimic transcriptional features of human born to be bad pT1 tumours. | Nature Communications

Fig. 6: Mice with intestinal epithelial TGFβ signalling mimic transcriptional features of human born to be bad pT1 tumours.

From: Epithelial TGFβ engages growth-factor signalling to circumvent apoptosis and drive intestinal tumourigenesis with aggressive features

Fig. 6

a Heatmap of 60 genes with predictive value obtained from prediction analysis for microarrays (PAMR) using data from VilCreER;Alk5CA (ALK5CA-like) and non-TGFβ/Alk5-activated (WT-like) mice 4 days post-tamoxifen. n = 3 mice per genotype. b Proportion of relapse and non-relapse pT1 patients enriched with ALK5CA-like (red) or WT-like (blue) signature. Two-sided Fisher’s exact test using fisher.test function in stats R package. c Pseudocolour overlay images of representative patient tumours from each cluster stained for p-S6, p-mTOR, 4EBP1 and TGFβ1. Marker expression was assessed using multiplexed immunofluorescence and single-cell staining of epithelial tumour cells within a cohort of stage II CRC (n = 282). Scale bar, 200 µm. d Proteins (p-S6, 4EBP1, TGFβ1 and p-mTOR) associated with relapse in the pT1 cohort were used to stratify stage II CRC patients into two groups, high (red) and low (blue) expression (P = 0.003; log-rank test). e, f GSEA of TGFβ (e) and KRAS and mTORC1 (f) signatures on shrunken log expression ratio of VilCreER;Apcfl/fl;KrasG12D/+;Alk5CA (AKACA; n = 7) vs wild type (WT; n = 3) intestinal tissue 3 days post-tamoxifen using fgsea method. g CRIS-B subtype enrichment analysis on mice described in e. h Group-wise GSEA performed using fgsea R package on the log expression ratio of AKACA vs WT mouse intestinal tissue to assess enrichment of CMS/CRIS subtypes. X-axis shows normalised enrichment score (NES), and the adjusted p value is indicated on the colour bar, from red (significant) to blue (not significant). padj adjusted p value (computed and corrected for multiple testing using the Benjamini–Hochberg procedure). i CRIS-B signature single-sample GSEA analysis on VilCreER;Apcfl/fl;KrasG12D/+ (AK, green), VilCreER;Apcfl/fl;KrasG12D/+;Alk5CA (AKACA, grey) and VilCreER;Apcfl/fl;KrasG12D/+;Alk5fl/fl (AKAKO, purple) tissue 3 days post-tamoxifen. AK, AKAKO n = 3 mice, AKACA n = 7 mice. Statistical significance determined by two-sided t-test using t.test function in stats R package (4.2.0). Horizontal line represents median values, boxes indicate the inter-quartile range and bars denote the maximum and minimum values. ***p ≤ 0.001; **p ≤ 0.01; *p ≤ 0.05. j Heatmap of genes associated with growth-factor and TGFβ signalling differentially expressed in intestinal tissue harvested 3 days post-tamoxifen injection from mice of the indicated genotypes. Wild-type (WT, n = 3, mustard), VilCreER;Apcfl/fl (A, n = 6, lavender), VilCreER;Apcfl/fl;KrasG12D/+ (AK, n = 3, green), VilCreER;Alk5CA (Alk5CA, n = 7, aqua), VilCreER;Apcfl/fl;Alk5CA (AACA, n = 6, blue), VilCreER;Apcfl/fl;KrasG12D/+;Alk5CA (AKACA, n = 7, grey), VilCreER;Apcfl/fl;KrasG12D/+;Alk5CA;Smad4fl/fl (AKACAS, n = 3, brown) and VilCreER;Apcfl/fl;KrasG12D/+;Alk5fl/fl (AKAKO, n = 3, purple).

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