Rare Cells Play Central Roles in Airway Maintenance

Abstract

The lung’s airways purify inhaled air and are the primary sites of asthma and cystic fibrosis disease. Principal airway epithelium functions are attributed to its abundant cell types: basal stem cells self-renew and produce club cell progenitors, which, in turn, produce antimicrobial secretions and terminally differentiated ciliated cells that clear mucus and debris. In contrast, far less is known about the lineage and functions of rare tuft, neuroendocrine, and goblet cells. We used single cell RNA-sequencing (scRNA-seq) to study the cellular composition of the murine tracheal epithelium and validated putative transcriptional cell types by establishing their distinct tissue organization. We discovered a novel rare cell type that we termed the pulmonary ionocyte; a distinct transition zone of high-turnover squamous epithelial structures that we term ‘hillocks’; disease-relevant subsets of tuft and goblet cells; and functional variations in club cells based on their location. We computationally detected subsets of basal-like progenitors in tuft cells, neuroendocrine cells, and ionocytes, leading us to hypothesize a new lineage hierarchy model in which these cell types are direct progeny of basal stem cells rather than club cell progenitors. We developed a method to test our lineage predictions; ‘pulse-seq’ combines scRNA-seq with in vivo genetic lineage tracing and simultaneously detects both the lineage status and kinetics of the generation of every cellular subset. Using pulse-seq we validated our lineage hierarchy model, and found that hillock club cells are generated more rapidly than any other cell type in the airway. We inspected pulmonary ionocytes in mouse and human airways and found that they have a spoked morphology, uniquely express FOXI1, and are the predominant source of the cystic fibrosis transmembrane conductance regulator (CFTR). Knockout of Foxi1 in mice causes the loss of airway Cftr expression, alteration of epithelial bioelectric properties, and disrupts airway fluid and mucus physiology, all phenotypes that are characteristic of cystic fibrosis. Finally, we associated cell-type-specific expression programs with key asthma genes, linking the functions of various cell types to specific roles in asthma disease etiologies. By considering both Mendelian and complex diseases, we establish the basis for a new cellular narrative for airways disease.