Fig. 3: Spatial co-location between aberrant regenerating alveolar epithelial cells and immune cells.

a Work flow and findings for each step of spatial analysis b Heat map showing g(r = 20) values for all structural vs all immune cell types. Red rectangular outline indicates g(r = 20) for alveolar epithelial vs immune cell types. Broken white circles and red triangles indicate alveolar epithelial - immune cell pairs with g(r = 20) > 1. Black squares - no co-location above complete spatial randomness [g(r = 20) < 1]. Full spatial data in Source Data File (tab for Figs. 3b, 4a–b, 5). c g(r) plots for the 5 co-locating alveolar epithelial-immune cell pairs from r = 0-300 μm. g_max = peak g(r) value in area around cell centroid of specifiied cell type from r = 0-300um; g(r = 20) = g(r) at 20 μm. d–f Cell centroid maps for CD206^hi macrophage-ABI_b-DC ADJ pairs across the three disease stages, with their topographical correlation map (TCM). TCM visualises how the spatial correlation between two cell types changes across an ROI (here, ABI_b-DC ADJ and CD206^hi macrophages). \({\Gamma }_{{ab}}\) scale indicates spatial proximity of cell type B to cell type A within a radius of r (in this case 100μm). High positive values indicate closer spatial proximity compared to complete spatial randomness. g, h Output for Neighbourhood Correlation Function (NCF) which interrogates co-location of 3 (rather than 2) cell types. Here, triplets of ABI_b-DC ADJ, ABI_a, CD206^hi macrophages, CD206^mid macrophages and CD103⁺ CD4 T cells (selected due to their co-location as pairs) are tested. Graphs shows N\(C{F}_{{C}_{1}{C}_{2}{C}_{3}}\left(r\right)\) for all triplet (C₁C₂C₃) combinations of ABI (ABI_b-DC ADJ and ABI_a) to immune cells (CD206^hi macrophages, CD103⁺ CD4 T cells) at MEC radius of 20 μm (G) and 30 μm (H). Green pane – triplets containing CD103⁺ CD4 T cells; blue pane – triplets without CD103⁺ CD4 T cells. Error bars correspond to the 95% confidence interval around median, derived by bootstrapping for each displayed NCFc₁,c₂,c₃(r = 30), based on the number of MECs at the 5^th and 95^th centile. n = 53 ROIs from 7 patients. i–k Individual \(NC{F}_{{C}_{1}{C}_{2}{C}_{3}}\left(r\right)\) plots for r = 0 to 150 μm for triplets that are most strongly spatially associated with each other compared to one which did not show association (k). Source data are available in Source Date File.