Hypomorphic Rag1 ^R972W/R972W ( W/W ) mutant mouse model recapitulates the human phenotype with architectural distortion and T cell infiltrates in colonic tissue. (A) Immunohistochemical analysis of colon biopsy isolated from a wild-type (+/+) and a Rag1^w/w (W/W) mouse at 12 wk of age showing H&E staining (4× magnification, scale bar: 500 μm) and CD3 staining (20× magnification, scale bar: 100 μm). (B) Colitis score based on immunohistochemical analysis of 12-wk-old +/+ littermate mice (n = 13), and 3-wk-old (n = 4), 5-wk-old (n = 4), and 12-wk-old W/W mice (n = 10). Bars show the mean with SEM. (C) RNAscope analysis of the colon biopsy from a wild-type and a Rag1^w/w mouse at 12 wk of age, showing the expression of Ifng and Cxcl9 transcripts (10× magnification, scale bar: 100 μm). (D) Bar plot shows absolute counts of total TCRβ⁺ T cells isolated from the LP of 3-wk-old littermate +/+ and W/W mice (n = 4/group), and 12-wk-old littermate +/+ and W/W mice (n = 8/group). Bars show the mean with SEM. (E and F) (E) Representative contour plots of cytokine production by Th cells after restimulation and subset distribution (F) of CD4⁺ T cells isolated from the LP of littermate +/+ and W/W mice at 3 and 12 wk of age. (G) Total cell number of colonic LP IL-17A– and IFN-γ–producing Th cells. In E–G, all flow plots were gated on live CD45⁺CD90.2⁺TCRβ⁺CD4⁺Foxp3⁻ cells. Data are from at least three independent experiments. Groups were compared using a Kruskal–Wallis test with Dunn’s multiple comparisons correction (B, D, and G). **P < 0.01, ***P < 0.001, ****P < 0.0001.