Fig. 2: Analysis of B cells in GALT using imaging mass cytometry.
From: Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue
a A representative example of the 16 ROI analysed for this figure. Example is gut-associated lymphoid tissue from human colon showing key lineage marker expression, with inset of epithelium and subepithelial dome region. Cyan = CD20, magenta = CD3, yellow = CD68, orange = E-cadherin. b Segmentation of cells (grey) from same ROI as shown in (a), with cells computationally classified as B cells highlighted (red). c UMAP of B cells with assigned subtypes (DN = double negative, IEDN = intraepithelial DN, PB/PC = plasmablast/plasma cells, MZB = marginal zone B cells, MZP = marginal zone precursor, GC LZ = germinal centre light zone, GC DZ = germinal centre dark zone). d Heatmap of mean expression of markers used for dimensionality reduction for B cell subtypes. e Distance of B cell subtypes from nearest epithelial cell (in μm). Centre line = median; box limits = upper and lower quartiles; whiskers = 1.5x interquartile range. Statistics between groups were assessed by two-tailed t test: **P < 0.01, ****P < 0.0001, n = 16 ROIs. Exact p values can be found in the Source Data file. f B cell subtypes overlaid on ROI from (a, b). g Imaging mass cytometry derived image of ROI from (a), showing DN-related markers CD27 (green), IgD (red) and CD11c (magenta). Computationally derived borders of DN2 cells (white) are overlaid and show that they are found in a region that is CD27-IgD-CD11c+ near the epithelium. h Confocal microscopy image of RNAscope experiment showing the distribution of DAPI (blue), CD20 protein (red, pseudocolor) and ITGAX transcript (green) in a representative appendix follicle. CD20+ITGAX+ cells in the Follicle Associated Epithelium (FAE) are highlighted with arrows. Scalebars = 100 μm. Source data are provided as a Source Data file.
