GSE123405
Single cell RNA-sequencing Identification of Novel Cell-specific Expression of Lung Disease-related Genes in the Human Small Airway Epithelium
The human small airway epithelium (SAE) plays a central role in the early events in the pathogenesis of most chronic inherited and acquired lung disorders. Little is known about the molecular phenotypes of the specific cell populations comprising the SAE, and the contribution of specific cell populations to the pathogenesis of human disease. There was cell type-specific expression of the genes relevant to the pathogenesis of the inherited pulmonary disorders, genes associated with risk of chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF), and (non-mutated) driver genes for lung cancers. Some unexpected observations included high expression of CFTR (cystic fibrosis) and SCNN1A and B (bronchiectasis) in ionocytes, DTNBP1 (Hermansky-Pudlak syndrome) in mast cells, FAM13A (COPD) in neuroendocrine cells, RIN3 (COPD) in mast cells, NSPA1L (IPF) in neuroendocrine cells and a variety of lung cancer-related genes expressed in different cell types that, if mutated, become driver genes. Cigarette smoking significantly altered the cell-specific transcriptome of the different cell populations. Many of the genes relevant to the hereditary and acquired disorders exhibited cell-specific modulation by cigarette smoking, including MUC5B (IPF) down-regulation specifically in intermediate, club and mucus-producing cells and SFTPB (surfactant deficiency) up-regulation in ionocytes. Overall design: Three healthy nonsmokers and three asymptomatic smokers were assessed using approved clinical protocols by Weill Cornell Medical College Institutional Review Board and the small airway epithelium (10th-12th generations of bronchi) were collected by bronchoscopic brushing.  Single cell capture and Drop-seq single-cell RNA-sequencing was performed for 11702 single-cell samples.  Using unbiased clustering on the single cell transcriptome from nonsmokers, 11 distinct cell populations were identified in the SAE brushed samples, including major (basal, intermediate, club, ciliated and mucous-producing cells) and rare epithelial cells (neuroendocrine cells, ionocytes), and immune/inflammatory cells (T cells, mast and antigen-presenting cells). We evaluated the effect of smoking on the 11 distinct nonsmoker cell populations and genes associated with lung disorders.