Figure 4. Altered mucosal immunity in Lyz1^−/− mice is microbiota-dependent.

(A) Goblet cell numbers (counted from 50 villi per field of vision per mouse) in WT or Lyz1^−/− mice based on Alcian blue staining of ileal sections of 14 day-old WT and Lyz1^−/− mice (N=4 for each genotype from 2 independent experiments). (B) The effect of genotype and IL-13 treatment on goblet cell maturation (Muc2⁺ cells in green) in ileal entroids from WT and Lyz1^−/− mice. (C-D) qPCR analysis of mRNA expression of goblet- and tuft cell-specific genes in ileal WT and Lyz1^−/− enteroids. (E) GSEA analysis of genes related to type 2 immune response in the ileum of untreated or Abx-treated Lyz1^−/− mice (N=3–4, bulk RNAseq). (F) Differential expression of IL-13-responsive genes in the ileum of untreated or Abx-treated Lyz1^−/− mice. (G-H) GSEA analysis of goblet and tuft cell gene signatures in the ileum of untreated or Abx-treated Lyz1^−/− mice. (I) The effects of genotyope and Abx treatment on DCLK1⁺ tuft cell numbers (counted from 50 villi per field of vision per mouse; N=4–5 for each condition). (J) Representative alcian blue staining of the ileum of untreated or Abx-treated Lyz1^−/− mice. (K) Goblet cell numbers (counted from 50 villi per field of vision per mouse) in WT or Lyz1^−/− mice treated with regular water, or water with ampicillin, vancomycin, or an Abx cocktail (N=2–4 in each group). (L) Unaltered NLR signaling gene signature in untreated or Abx-treated Lyz1^−/− mice by GSEA analysis. (M) Schematic of the experimental design for panels N-O. (N-O) Representative H&E images of distal colon and colitis activitivity scores in WT and Lyz1^−/− mice treated as in panel M (N=3–7 in each group). All bar graphs display mean ± SEM from at least two independent experiments. See also Figure S4.