Extended Data Fig. 5: CAFs elicit transcriptomic rearrangements in CRC cells.
From: Patient-derived mini-colons enable long-term modeling of tumor–microenvironment complexity
a, Volcano plot showing the differentially-expressed genes in patient #MS CRC mini-colons cultured with autologous CAFs. Statistically significant up- and down-regulation events are highlighted in red and blue, respectively. Specific genes mentioned in the main text are indicated. b, Heatmap showing the overlapping differential expression events in patient #MS CRC mini-colons cultured with autologous CAFs and CAF-conditioned medium (CM). The number of differentially expressed genes and the z-score are indicated. c, Venn diagrams showing the overlap in positively (top panel) and negatively (bottom panel) enriched hallmark gene signatures in patient #MS CRC mini-colons cultured with autologous CAFs and CAF-conditioned medium. d, Expression distribution of the indicated genes across mono- and co-cultures of patient #MS CRC cells and CAFs. Cell-type labels can be found in Fig. 3h. e, Single-sample GSEA of the CAF-induced CRC signature in healthy and cancer samples from the TCGA CRC cohort. ***P < 0.0001 (two-tailed Mann–Whitney test; n = 51 and 592 for healthy and CRC samples, respectively). Violins represent data distribution, median and quartiles.
