Fig. 2: Ablation of DHX9 results in aberrant ISCs and intestinal secretory cells.

a Gene ontology analysis revealing the down-regulated expressed genes in IECs of Dhx9^ΔIEC mice compared to Dhx9^fl//fl mice (P < 0.05; right-tailed Fischer’s exact t-test). b Heat map analysis of the RNA-seq dataset displaying marker genes for intestinal epithelial cell lines in Dhx9^ΔIEC mice versus Dhx9^fl//fl mice. c Volcano plot analysis of the RNA-seq dataset illustrating the top upregulated and downregulated genes in IECs of Dhx9^ΔIEC mice compared to Dhx9^fl//fl mice (P < 0.05; right-tailed Fischer’s exact t-test). d Gene set enrichment analysis (GSEA) comparing the gene expression profiles of intestinal cells based on RNA-seq data in Dhx9^ΔIEC compared to Dhx9^fl//fl IECs. Two-tailed t-test with the Benjamini–Hochberg correction for an adjusted P-value. e Single-cell RNA sequencing of IECs from Dhx9^ΔIECand their Dhx9^fl//fl littermates. Visualized as a Uniform Manifold Approximation and Projection (UMAP) plot, categorizing 30,252 cells from the small intestine into 15 distinct clusters based on their gene expression profiles. f Graphical representation of the proportion of each identified cell cluster relative to the total population in the analyzed samples. g–j Littermate 8 week-old male Dhx9^fl//fl and Dhx9^ΔIEC mice were subjected to immunofluorescence staining. Representative staining of Ki67 in colon (upper panel) and ileum (lower panel) sections (at least 30 crypt-villus axes were counted, colon of Dhx9^fl//fl, n = 32; colon of Dhx9^ΔIEC, n = 31; ileum of Dhx9^fl//fl, n = 33; ileum of Dhx9^ΔIEC, n = 31) (g); Lysozyme and E-cadherin in ileum sections (at least 30 crypt-villus axes were counted, Dhx9^fl//fl, n = 30; Dhx9^ΔIEC, n = 34) (h); Muc2 and E-cadherin in colon sections (at least 30 crypt axes were counted, Dhx9^fl//fl, n = 35; Dhx9^ΔIEC, n = 32) (i); Muc2 and E-cadherin in ileum sections (at least 30 crypt-villus axes were counted, Dhx9^fl//fl, n = 31; Dhx9^ΔIEC, n = 32) (j). Scale bars represent 100 μm. Each experiment was performed on n = 3 mice individually, with similar results. Error bars show means ± SEM. Statistical analyses were performed by two-tailed unpaired Student’s t-test. Source data are provided as a Source Data file.