Fig. 4: Tipe0^−/− enterocytes have decreased differentiation markers and the intestine is shifted towards a less differentiated state.

All enteroid IF images representative of >3 d7 enteroids per genotypes, and three independent replicates were performed. a Alkaline phosphatase in intestinal tissue (purple, bars = 110 µm); images representative of mean staining seen in 4 WT and 5 Tipe0^−/− mice. b Keratin-20 staining and F-actin staining in enteroids (IF, bars = 20 µm) with atypical symmetry in Tipe0^−/− enteroids and dedifferentiated buds only seen in the WT (outlined with white dashed line). Images representative of >10 enteroids per group per experiment, with three independent experiments performed. c Alcian blue staining, bars = 20 µm, with quantification (d p = 0.0022). Image representative of mean staining for 6 mice/group. e, f Paneth cell staining in ileal tissue and enteroids. e Paneth cells/crypt (N = 4 mice/group, 7 crypts/mouse, pooled) as determined by lysozyme staining in intestinal tissue (f); images representative of mean staining seen in each group. Staining also performed in enteroids (f, lower row). White circles indicate proliferative crypt foci as indicated by lysozyme staining in the enteroids. Bars = 130 µm for tissue, 20 µm for enteroids; counterstains (in red) as indicated. For enteroids, images representative of >4 enteroids per group in each of 3 independent experiments. g–i Single cell RNASeq of enterocytes, N = 3 mice/genotype. WT = 3402 isolated cells, Tipe0^−/− = 2006 isolated cells. Analysis of group populations by two-tailed t-test. g t-SNE plots by genetically defined cell populations with bar graphs and tabulated percentages of the major lineages (h). Blue circles indicate areas where fetal-like stem cells were found, while the red circles indicate the regions where Lgr5⁺ stem cells were found. These specific, rare populations are highlighted separately in i. For all graphs, **p < 0.01; p < 0.001; ****p < 0.0001 vs WT, or as indicated; error bars show mean ± SEM. Analyses done by two-tailed Mann–Whitney U test unless otherwise specified. Source data are provided as a source data file.