Spatial transcriptomics (ST) of cigarette smoke (CS)-induced experimental COPD

Background: COPD is the 3^rd leading cause of death worldwide and CS inhalation is the main causative factor. There are no effective therapies, as the mechanisms of COPD pathogenesis are yet to be elucidated. Transcriptomics has been applied to study COPD pathogenesis in the lungs, however, spatial information is lost during tissue dissociation in bulk RNA sequencing. We used unbiased ST to study the pathophysiology of CS-induced experimental COPD in mouse lungs. Methods: Wild-type mice were exposed to CS for 8-12 weeks (n=6) to induce COPD, or were normal air (n=2) exposed controls. Lungs were harvested and sectioned. Visium ST technology was used to map the whole transcriptomes in each barcoded spot on the lung tissue sections with spatial context. The ST dataset was integrated with a single-cell transcriptomics dataset of lung samples from the same experiment. Results: ST detected 12,796 genes in 1,067 spots on each lung slice. Four clusters were anatomically resolved, including airway, airway smooth muscle, blood vessel and lobe edge. We found macrophage-enriched regions to be more abundant in COPD compared to air-exposed lungs. Pathway analysis of these regions showed a unique pattern of macrophage activation and suppressed major histocompatibility complex activity. Spatial signalling analysis revealed a model with unique gene crosstalk in COPD lungs, notably a neighbouring co-expression of inflammatory regulators of macrophages in areas with macrophage enrichment. Conclusions: In this study, ST revealed spatially resolved transcriptional landscapes in experimental COPD lungs, particularly inflammatory macrophage programs, which provides new insights into the understanding of COPD pathogenesis.