Fig. 4: YAP/TAZ regulates the conserved human CRC enhancerome.

a YAP and TAZ are transcriptionally upregulated in primary tumors (n = 10) and patient-derived organoids (PDOs n = 10) compared to normal colon tissues (n = 9). Violin plots of log2 normalized gene counts. **P < 0.01, ***P < 0.001, two-sided Wilcoxon rank sum exact test. b Representative immunohistochemistry images with insets showing YAP/TAZ nuclear localization in tumor tissues (middle) and PDOs (bottom) compared to normal mucosa (top). Scale bars, 50 µm, magnification ×40. c Relative distribution of TAZ peaks around ChromHMM-defined active enhancers (n = 33,131, yellow) and promoters (red). d Genomic overview of YAP/TAZ canonical targets showing H3K4me3, H3K27ac, H3K4me1, TAZ profiles, and ChromHMM states (see Supplementary Fig. 5b and Fig. 2c, e for details on ChromHMM tracks). e TEAD binding motif enrichment around the summit of TAZ peaks. f Distribution of TAZ peaks across ChromHMM-defined functional elements. g TAZ enrichment in human CRC gained enhancers (G.E.) increases with the level of enhancer conservation across PDOs. The bar plots show the percentage of enhancers in each G.E. subset that overlap a TAZ peak or the percentage (mean ± s.d.) of TAZ-bound regions in 1000 random sets generated for each G.E. subsets: (i) all G.E., (ii) G.E. conserved in >5 patients, and (iii) G.E. conserved in >8 patients (see “Methods”). ***P < 0.001, one-sided empirical P-value. h TAZ genomic overview showing H3K4me3, H3K27ac, H3K4me1, and TAZ profiles, RNA-seq signals, ChromHMM states, and capture Hi-C promoter-enhancer interactions. i YAP/TAZ-inhibition affects patient-derived tumor organoid growth. Representative images of fully formed normal (left) and tumor (right) organoids cultured for 48 h following treatment with 1 μM of verteporfin (VP; top) or DMSO (bottom). Scale bar: 100 μm, magnification ×10. j VP treatment significantly reduces cell viability in tumor compared to normal PDOs. Viability was assessed by flow cytometry 48 h after exposure and normalized to DMSO (mean ± s.d., n: Normal = 3 and Tumor = 6 independent CRC patients; see Supplementary Fig. 5g). *P = 0.012, one-sided Mann–Whitney U exact test.