Fig. 1: IFN-γ-induced lineage replacement of colonic epithelia upon injury.

a Single-molecule-ISH (sm-ISH) (×200 magnification) was used to assess the stem cell marker Lgr5 in healthy and acute colitis (5 days DSS treatment) colon tissue of WT and IFN-γR KO mice. b Axin2, a Wnt-target gene, was evaluated using sm-ISH as in (a). Scale bar: 100 µm. c, d Quantification of Lgr5 (c) and Axin2 (d) expression. n = 3 mice per group. e Immunofluorescence (IF) (×600 magnification) was employed to compare expression of the differentiated colonocyte marker KRT20 in healthy and acute colitis colon tissue sections of WT and IFN-γR KO mice. The length of KRT20-expressing crypts was quantified (f). Scale bar: 100 µm. n = 3 with 45 measured crypts each. Data are represented as mean ± SD. g IFN-γ activation by cell population upon DSS (acute colitis) in vivo, as measured by GSVA enrichment score of the level above the average level in control (healthy) mice from an online sc-RNAseq dataset (GSE201723). The dashed line indicates the average control level for each population. SC stem cells. TA transit-amplifying cells. n = 3 mice per group. Error bars indicate ±2 SEM. h Live-cell imaging (×200 magnification) was employed to demonstrate IFN-γ-driven cell disintegration in differentiated organoids, comparing proliferative progenitors and differentiated colonocytes with or without IFN-γ treatment for 23 h. Scale bar: 50 µm. i IF staining (×600 magnification) of KRT20 in progenitors, IFN-γ-treated progenitors, and differentiated organoids (Diff.). Scale bar: 60 µm. The experiments were repeated independently three times with similar results in (h) and (i). j mRNA expression of Krt20, assessed by RT-PCR in organoids grown in FM with or without IFN-γ treatment or in differentiation medium; n = 3 biological replicates. All p-values above were determined using one-way ANOVA (two-sided) with no adjustments for multiple comparisons. Unless otherwise indicated, data are represented as mean ± SD. Source data is provided as a Source Data file.