Transcriptomic Analysis of Air–Liquid Interface Culture in Human Lung Organoids Reveals Regulators of Epithelial Differentiation

Abstract

To develop in vitro respiratory models, it is crucial to identify the factors involved in epithelial cell differentiation. In this study, we comprehensively analyzed the effects of air–liquid interface (ALI) culture on epithelial cell differentiation using single-cell RNA sequencing (scRNA-seq). ALI culture induced a pronounced shift in cell composition, marked by a fivefold increase in ciliated cells and a reduction of more than half in basal cells. Transcriptional signatures associated with epithelial cell differentiation, analyzed using iPathwayGuide software, revealed the downregulation of VEGFA and upregulation of CDKN1A as key signals for epithelial differentiation. Our findings highlight the efficacy of the ALI culture for replicating the human lung airway epithelium and provide valuable insights into the crucial factors that influence human ciliated cell differentiation.