Fig. 5: Cell type and neighborhood changes in COPD.

A Box plot of the cell type numbers in healthy and COPD (mean ± standard error, with individual values). Significant differences are highlighted with asterisk (**, adjusted P = 0.0087), according to unpaired parametric two-sided multiple t-test (20) of logit-transformed data with Holm-Sidak correction. Individual data points demonstrate samples from different donors and patients, n = 3. The direct cell type comparison without the correction also revealed significant differences between healthy and COPD samples in the following cell types: AT0 (P = 0.0004), AT1 (P = 0.0127), AT1-AT2 (P = 0.0090), basal cells (P = 0.0295), T lymphocytes (P = 0.0088), labeled by asterisks at the cell type name. B Representative (from three biological replicates) maps of alveolar epithelial cell types detected in healthy and COPD samples, nuclei: gray. Scale bar 200 µm. C UMAP plots of analyzed cells labeled according to their cellular neighborhoods (left) and their corresponding condition (right). Neighborhood annotations: Cap-Alv capillary-enriched alveoli, AT2-Alv AT2-enriched alveoli, AT0-Alv AT0-enriched alveoli, C-Epi club-enriched epithelium, G-Epi goblet-enriched epithelium, T-Epi secretory TRB-enriched epithelium, B-Epi basal cell-enriched epithelium, Imm-Par immune cell-enriched parenchyma, Str-Par stromal cell-enriched parenchyma, SM smooth muscle, SMG submucosal gland, SMG-serous serous cell-enriched submucosal gland, TRB terminal respiratory bronchiole. Arrows indicate the clusters that are predominantly composed of COPD-derived cells. D Heatmap exploring the cell type composition of each neighborhood, with cells (vertical lines) grouped by their assigned neighborhood cluster (x-axis) represented in Fig. 5C (left). Bar color represents the ratio of neighborhood enrichment with each cell type for each cell. E Maps of cell type neighborhoods in healthy and COPD samples in alveolar region with large and small airway and respiratory bronchioles. Color code as in C (left). Scale bar 200 µm. Simple arrows: AT0-enriched alveolar neighborhood, dashed arrows – immune-enriched parenchyma, double-line arrows – secretory TRB-enriched epithelium. Source data are provided as a Source Data file.