Fig. 3

The molecular characteristics of colorectal adenoma are preserved in organoid cultures. A Clustered heatmap of log2-transformed RPKMs showed the 3511 differentially expressed genes in adenomas, CA organoids, and normal mucosae originated from four patients (P1, P2, P4, P5). Stem genes were marked. M, mucosa; A, adenoma; O, organoid. B Gene set enrichment analysis (GSEA) indicated a gene list containing the upregulated genes in adenoma compared with normal mucosa. NES, normalized enrichment score. FDR, false discovery rate. C Immunohistochemical staining displayed the expression of OLFM4 in CA organoid and corresponding primary adenoma and normal mucosa. A representative result of three independent experiments was shown. Scale bar, 100 μm. D Clustered heatmap of log2-transformed RPKMs showed the expression of indicated stem genes between adenoma and normal mucosa. E Adenoma and normal mucosa were harvested to verify expression of c-Myc, LGR5, OLFM4, CD44, CD166– and CD133 using qRT-PCR. All data were presented as mean ± SD (n = 7) and subjected to Student’s t-test in E. *** indicates P < 0.001 versus mucosa. * indicates P < 0.05. ns indicates no significant difference. F Clustered heatmap of normalized RPKMs showed the 2689 differentially expressed genes in CA organoids originated from four patients (P1, P2, P4, P5) and four representative colorectal adenocarcinoma organoids labeled as P17.2, P19b.1, P20.11, and P31.12 from GSE65253. O, CA organoids; C, colorectal adenocarcinoma organoids