Figure 3. Tissue-wide regulation of immune homeostasis and immune responses in the TM by the IFN-γ-EGC signalling axis.

(a) Genotypes and experimental treatment of mice (color-coded) used for scRNAseq of the TM. (b, c) UMAP of TM cells from naïve Ifngr2^CTRL (b) and Ifngr2^ΔEGC (c) mice. Identity of cell clusters is indicated (left). (d) Quantification of differentially expressed genes in clusters from naïve Ifngr2^CTRL versus Ifngr2^ΔEGC mice. (e) GSEA showing selected significant hallmark list terms for inflammatory pathways in the indicated cell clusters from naïve Ifngr2^CTRL and Ifngr2^ΔEGC mice. (f-h) Violin plot quantification of selected differentially expressed genes in mesothelial cells (f), fibroblasts (g) and muscularis macrophages (h) from naïve Ifngr2^CTRL and Ifngr2^ΔEGC mice. (i, j) UMAP of TM cells from H. poly-infected Ifngr2^CTRL (i) and Ifngr2^ΔEGC (j) mice. (k) Quantification of differentially expressed genes in cell clusters from H. poly-infected Ifngr2^CTRL versus Ifngr2^ΔEGC mice. (l) Violin plot quantification of expression of Arg1, Retnla and Chil3 in muscularis macrophages from naïve and H. poly-infected Ifngr2^CTRL and Ifngr2^ΔEGC mice. (m) GSEA showing selected significant hallmark list term for IFN-γ response in the indicated cell clusters from H. poly-infected Ifngr2^CTRL and Ifngr2^ΔEGC mice. (n, o) Violin plot of mean scaled expression of IFN-γ response-associated genes (from the GO term “response to IFN-γ”; n) and Stat1 (o) across all UMAP clusters. (p) qRT-PCR of Ifng in H. poly-infected TM (7 dpi). Mean±SEM. n=8, two experiments. Wilcoxon test (f, g, h, l, n, o), two-tailed Mann-Whitney test (p).