Fig. 6: Spatial organization amongst immune cells in COVID-19 lungs.

Radial connectivity map depicting all statistically significantly co-located pairs of immune- immature neutrophil subsets (including ADJ subsets) (a) immune-monocyte subsets (b, c, separated for clarity) cells in all histopathology states (n = 10 ALV, n = 8 DAD and n = 8 OP). Anchor cells (immature neutrophil and monocyte subsets) are in smaller, inner circle. 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. These significantly co-located pairs of cells are derived from n = 479,349 single cells in all ROIs 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 (see “Methods” for 3-step mathematical algorithm for determining statistical significance of co-location). Spatial connectivity plots for Neut_CD8_ADJ (d) and Mono_CD31_ADJ (e), showing immune cells that are statistically significant co-located to proliferating alveolar epithelium (designated ‘anchor cell’) in the three histopathology states (see “Methods” for 3-step mathematical algorithm for determining statistical significance of co-location). Size of nodes (filled-in circle) represent mean cell counts for the specified cell cluster for all the ROIs in the histopathology state, 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. Thickness of line relate to value of g(r = 20) relative to each pair in the plot – the thicker the line, the higher the g(r = 20) and strength of co-location between the immune cell type and anchor cell. f Adjacency cell network (ACN) map showing contact between the Mono_CD31_ADJ cluster, Neut_CD8_ADJ cluster and proliferating alveolar epithelial. Cell segmentation masks generated by DeepCell were used to produce this spatially-embedded network in which nodes represent centres of cell types (e.g. green – Neut_CD8_ADJ cell cluster). Nodes are connected by a line if the corresponding cells in the segmentation mask share a border. g MCD image showing CD8 (green), CD15(red) and CD15 and CD8 co-staining (yellow) (representing Neut_CD8_ADJ cell clusters) amidst endothelial cells (CD31 staining in turquoise) and monocytes (CD14 staining in purple) in a lung section with DAD on histopathology analysis. Exemplar ROI is shown for (f) and (g), out of 26 ROIs stained, from 12 patients (n = 10 ALV ROI, n = 8 DAD and n = 8 OP).