Spatial transcriptome analysis in the airway epithelium identifies an altered gene expression profile in COPD versus control tissue

Introduction: The airway epithelium is the first line of defence against pathogens and environmental particles, such as cigarette smoke, by acting as a physical barrier and by exerting immunological functions. There is evidence that the airway epithelium is altered in COPD, however spatially resolved studies are lacking on whole lung tissue sections. Spatial transcriptomics has the power to identify genes in lung-relevant region(s) and cell type(s) in tissues from different disease states. Aims: To identify an airway epithelium specific gene expression profile associated with COPD. Methods: Sections of human lung tissue were obtained from lung resection from control donors (n=3) and donors with a diagnosis of COPD (n=3). Slides were hybridised with the GeoMx Human Whole Transcriptome Atlas. Regions of interest were selected (minimum 30 cells, 3 ROI per donor), based on panCK positive fluorescent staining and by tracing around the airway epithelium, from which barcodes were collected, library prepared, and sequenced. Count files were analysed in R using the StandR package and Limma. Results: We identified a specific gene expression profile (FDR 5%) for airway epithelium in COPD tissues versus control (152 genes). Genes enriched by disease state in epithelial regions included cytokeratin genes (KRT5, 15, and 19), which were upregulated in COPD. Conclusion: Our preliminary work has identified a spatially resolved epithelial gene expression profile in COPD lung tissue, including elevated cytokeratin genes, which are major structural proteins of epithelial cells that are essential for tissue integrity.