Fig. 5: Spatial organization of immune cells around structural cells in COVID-19 lungs.

a, b Spatial connectivity plots for proliferating alveolar epithelium, showing immune cells that are significantly co-located to proliferating alveolar epithelium (designated ‘anchor cell’) in the three histopathology states. The size of the nodes (filled-in circle) represents mean cell counts (abundance) for the specified cell cluster for all the ROIs in the histopathology state (scale shown in grey), and colour of nodes relate to histopathology state. Connecting lines indicate a statistically significant co-location between the two cell types derived from QCM and cross-PCF analyses. The thickness of the lines relates to the g(r = 20) value relative to each pair in the plot – the thicker the line, the higher the g(r = 20) and therefore greater strength of co-location between the immune cell type and anchor cell. n = 479,349 single cells from n = 12 COVID patients’ lung sections (n = 10 ROIs for ALV; n = 8 DAD; n = 8 OP); n = 144,937 cells in ALV, n = 146333 in DAD and n = 163,506 in OP. Histogram shows % of two anchor cells – proliferating alveolar epithelial (PAE) cells (c) and endothelial cells (d) that are in contact with specified immune cell type. Source data are provided in the Source Data File. e, f Cross-PCF profiles for the two most abundant co-located structure:immune cell pairs in DAD. Curves show the change in g(r) along the radius(r) from anchor cells [proliferating alveolar epithelium (prolif alv epit) and endothelial cells (endo)] for Neut-CD8_ADJ cell clusters and Mono_CD31_ADJ cell clusters respectively. Blue coloured area around curve is the 95% confidence interval for n = 8 ROIs with DAD. g. Radial connectivity map depicting all statistically significant pairs of structure:immune cells in all histopathology states; anchor cells (structural cells) are in smaller, inner circle. n = 479,349 single cells from n = 12 COVID patients’ lung sections (n = 10 ROIs for ALV; n = 8 DAD; n = 8 OP). ‘DRhi BE’ – HLADR^hi bronchial epithelium; ‘DRlo BE’ – HLA DR^lo bronchial epithelium; “Endo’- endothelial cells; ‘PAE’- ‘proliferating alveolar epithelium’, ‘PBE’ – ‘proliferating bronchial epithelium’; ‘PE’ – ‘proliferating endothelium’ ‘BV” –‘blood vessels’. Numerical values indicate g(r = 20) for that pair in that state (coloured bar), and % indicates proportion of anchor cells that are co-located with the specified immune cells. h Topographical correlation map showing distribution of the co-located Neut_CD8_ADJ cluster and proliferating alveolar epithelial cell pair (left panel) in an exemplar tissue (an ROI with DAD). Cells of type A (e.g. Neut_CD8_ADJ) are positively (\({\Gamma }_{{ab}}\gg 0\)) or negatively (\({\Gamma }_{{ab}}\ll 0\)) associated with cells of type B (e.g. Proliferating alveolar epithelium) (see Methods). i. MCD images showing Neut_CD8_ADJ clusters amidst single CD8⁺ T cells, CD15⁺ immature neutrophils and epithelial markers (EpCAM and PanCK). Couplets of CD8⁺ and CD15⁺ cells - Neut_CD8_ADJ clusters (red and green merging to form yellow cells) (arrows) are most clearly visible in DAD. Exemplar section is shown from analyses of n = 10 ALV ROIs, n = 8 DAD ROIs and n = 8 OP ROIs (n = 12 patients). Sections were stained once with 37 plex panel.