Cellular heterogeneity and patterning strategies as revealed by upper respiratory epithelium single cell atlas

The upper respiratory tract, spanning the pharyngolaryngeal to tracheobronchial regions, enables breathing, vocalization, and frontline defense against airborne insults. We generated a cellular and molecular atlas of the mouse upper respiratory epithelium from pharynx/larynx to tracheobronchial carina by combining single-cell RNA sequencing with spatial validation. Our analysis revealed 18 epithelial cell types, organized into three spatially distinct compartments: Tmprss11a+ pharyngolaryngeal, Nkx2-1+ tracheobronchial, and Dmbt1+ submucosal glands. Stratified squamous pharyngolaryngeal zones displayed extensive and region-specific Keratin codes. Within the pseudostratified tracheobronchial epithelium, diverse luminal cells, including multiple varieties of club cells, exhibit marker-expression gradients along the proximal-distal axes. Lastly, analysis of the submucosal gland epithelium -which contains various cell types, including distinctive myoepithelial cells- revealed extensive diversity both among and within its cellular populations. This spatially resolved transcriptomic atlas elucidates how epithelial identity varies along the upper respiratory axes and will guide investigations into cellular dynamics in health and disease.