Single cell and population transcriptomics reveal epithelial remodeling in type 2-high asthma

BACKGROUND: The type 2 cytokine-high asthma endotype (T2H) is characterized by IL-13-driven mucus obstruction of the airways. To investigate this poorly understood pathobiology, we characterized IL-13 effects on human airway epithelial cultures using single cell RNA-sequencing, finding that IL-13 generated a novel transcriptional state for each cell type. Specifically, we discovered a mucus secretory program induced by IL-13 in all cell types which converted both mucus and defense secretory cells into a metaplastic state with emergent mucin production and secretion, while leading to ER stress and cell death in ciliated cells. The IL-13-remodeled epithelium secreted a pathologic, mucin-imbalanced, and innate immunity-depleted proteome that arrested mucociliary motion. Signatures of IL-13-induced cellular remodeling were mirrored by transcriptional signatures characteristic of the nasal airway epithelium within T2H versus T2-low asthmatic children. Our results reveal the epithelium-wide scope of T2H asthma and present novel therapeutic targets for restoring normal epithelial function. Single cell transcriptomics was carried out for experiments involving either acute (48 hours) or chronic (11 days) stimulation with IL-13 (or mock stimulation with BSA) of air-liquid interface (ALI) cultures grown from epithelial cells taken from two tracheal donors. For the acute stimulation experiment, we sequenced a total of 2,385 cells, plus positive and negative controls (1,894 remaining after QC). For the chronic stimulation experiment, we sequenced a total of 802 single cells (756 remaining after QC and batch correction).