Extended Data Fig. 4: IL-22–inducible genes are differentially upregulated in different regions of the intestines.

a-b, Mid-distal colon IECs from d8 C.r-GFP-infected mice were stained for EpCAM1, Ly6G, and CD45 and either a) analyzed by flow cytometry or b) sorted on EpCAM1⁺ (red) C.r-GFP⁺ (green) cells, cytospun, and stained with DAPI (blue). Scale bar = 10 μm. 3 mice per group and n = 2 independent experiments. c, scRNA-seq was performed on epithelial cells from mid-distal colon of naïve BL/6 mice (n = 2). Violin plots of Il22ra1 and Il10rb genes. Dots denote gene expression per individual cell. d, IECs from naïve (open symbol) and d8 C.r mice (closed symbol) were sorted from distal ileum (green), proximal colon (blue) and distal colon (red) and mRNA expression was analyzed by RT-PCR. One-way ANOVA with Tukey’s multiple comparison test; *p≤0.05, and ***p≤0.001 comparing naïve and infected mice; and ^øøøp≤0.001 comparing infected samples from different tissue regions; and ^##p≤0.01, and ^###p≤0.001 comparing naïve samples from different tissue regions. 2-3 mice pooled per sample; n = 2 independent experiments. Data are represented as mean ± SEM. IEC=intestinal epithelial cell; PCC=proximal colonocyte; DCC=distal colonocyte; DCS=deep crypt secretory cell; TA=transit-amplifying cell; CBC=crypt base columnar cell. The components of the IL-22R (IL-22Ra1 and IL-10Rβ) were found to be highly expressed by mature colonocytes, with no significant difference in IL-22R expression between mature PCCs and mature DCCs. S100a8/9 antimicrobial peptide, and the Cxcl2 and Cxcl5 chemokines are highly expressed by mature colonocytes of the DCC lineage and are heightened in the presence of IL-22–producing CD4 T cells suggesting they may play important roles in bacterial clearance during the late phase of C.r infection.