Fig. 4: IL-11⁺ fibroblasts express genes associated with cell proliferation and tissue repair.

Il11-Egfp mice were treated with DSS. On day 7 after DSS treatment, cells were isolated from colons of Il11-Egfp reporter mice, and IL-11⁺ cells (EGFP⁺) and IL-11⁻ (EGFP⁻) cells among Ter119⁻ CD45⁻ CD31⁻ EpCAM⁻ cell populations were sorted by flow cytometry. We isolated mRNA from IL-11⁻ and from IL-11⁺ cells and analyzed both using RNA-seq (n = 3 mice). a Verification of enrichment of IL-11⁺ cells by flow cytometry. Expression of Il11 and Egfp mRNAs was determined by qPCR. Results are mean ± SEM (n = 5 mice). b Volcano plot of whole genes. The horizontal line indicates genes differentially regulated in IL-11⁺ cells compared with IL-11⁻ cells, shown in log₂. The vertical line indicates p-values, shown in −log₁₀. Significantly upregulated and downregulated genes are indicated by red and blue dots, respectively. Several upregulated genes are plotted. c Gene ontology (GO) terms that were significantly enriched in IL-11⁺ cells compared with IL-11⁻ cells. GO enrichment analysis of differentially expressed genes were performed using the DAVID Bioinformatics Resources. d Heat map of enriched genes in IL-11⁺ fibroblasts compared with IL-11⁻ fibroblasts. Color code for heatmap indicates Z-score of gene expression. e Expression of I111ra is not different between IL-11⁺ and IL-11⁻ fibroblasts. Expression of Il11ra mRNA was determined by qPCR. Results are mean ± SEM (n = 5 mice). f Gene set enrichment analysis of IAFs-related genes in IL-11⁺ and IL-11⁻ fibroblasts. FDR false discovery rate, NES normalized enrichment score. Statistical significance was determined by using the two-tailed unpaired Student’s t-test (a, e) or two-tailed Kolmogorov-Smirnov test (f). The estimation of logFC and adjusted p-value were calculated using edgeR package in R (b, c).