Fig. 2: AMP-mediated regional immune surveillance in the intestine.

a Combined visualization of three UMAP embeddings of prenatal and postnatal human intestinal epithelium and human organoids. b UMAP embedding overlay showing the regional subsets of pre- and postnatal epithelial cells. c, d Dot plot showing the regional and cellular specificity of AMPs in human (c) and mouse (d). e The trajectory dendrogram of duodenum epithelial cells highlighting the expression of SI-specific AMPs (DEFA5, DEFA6, PRSS2, REG3A, REG3G, ITLN2) correlates positively with LGR5. f Bar plot depicting the proportion of stem cells and Paneth cells in the epithelium of duodenum, jejunum and ileum in scRNA-seq data. g RNAScope in situ hybridization of DEFA5 (red), LGR5 (green), and DAPI (blue) in bowel sections from the human ileum. Scale bars, 10 μm. Staining repeated on two participants. h Bowel sections from the human intestine were immunofluorescent stained for DEFA5 (red), LGR5 (green), and DAPI (blue). Scale bars, 50 μm. Staining repeated on three participants. i Expression of DEFA5 in histological sections (n = 3 for each region). Scale bars, 100 or 20 µm. j Bar plot depicting the proportion of DEFA5+ cells from T/ILCs, B/Plasma, Myeloid, Megakaryocytes/Mast cell compartments are different between proximal SI, distal SI, and LI. k Feature plots showing expression of T cell markers, SI-specific AMPs, and epithelial markers in T/ILCs compartment. l Bowel sections from the human ileum were immunofluorescent stained for DEFA5 (red), CD3 (green), and DAPI (blue). Arrows point to T cells expressing DEFA5. Scale bars, 10 μm. Staining repeated on two participants. Source data underlying Fig. 2f and j are provided as a Source Data file.