Cell-specific expression of lung disease risk-related genes in the human small airway epithelium

Abstract

Background: The human small airway epithelium (SAE) plays a central role in the early events in the pathogenesis of most inherited and acquired lung disorders. Little is known about the molecular phenotypes of the specific cell populations comprising the SAE in humans, and the contribution of SAE specific cell populations to the risk for lung diseases. Methods: Drop-seq single-cell RNA-sequencing was used to characterize the transcriptome of single cells from human SAE of nonsmokers and smokers by bronchoscopic brushing. Results: Eleven distinct cell populations were identified, including major and rare epithelial cells, and immune/inflammatory cells. There was cell type-specific expression of genes relevant to the risk of the inherited pulmonary disorders, genes associated with risk of chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis and (non-mutated) driver genes for lung cancers. Cigarette smoking significantly altered the cell type-specific transcriptomes and disease risk-related genes. Conclusions: This data provides new insights into the possible contribution of specific lung cells to the pathogenesis of lung disorders.

Smoking shifts human small airway epithelium club cells toward a lesser differentiated population

“…Preliminary studies suggested that not all club cell-associated markers are distributed equally amongst all club cells in the human SAE, leading to the hypothesis that club cells are composed of multiple subtypes that could represent uniquely functioning club cell subpopulations in the SAE. To test this hypothesis, single cell sequencing was used to assess SAE samples obtained by bronchoscopy from three healthy nonsmoker and three healthy smoker subjects 31 . Using unsupervised clustering analysis, club cells were identified as cells with high expression of SCGB1A1 (expressed in both intermediate and secretory cells), low expression of KRT5 (typically expressed highly in basal cells), and the absence of MUC5AC (mucous cell-specific; Fig.…”

“… a Cluster identification. SAE cell types were identified from Dropseq single cell RNA sequencing datasets from six individuals (three healthy nonsmokers and three healthy smokers) using established cell specific markers including KRT5 for basal cells, SCGB1A1 for club cells, MUC5AC for goblet cells, and FOXJ1/DNAI1 for ciliated cells 31 . Club cells were identified by the presence of SCGB1A1, low levels of the basal marker KRT5, and the absence of the differentiated goblet cell marker MUC5AC.…”

“…Based on the knowledge that club cells have a defense function, this analysis was focused on defining the biology of club cells in the healthy SAE and then understanding how this biology may be altered by the stress of cigarette smoking. Using a previously published dataset 31 , subclustering of combined nonsmoker and smoker club cell populations led to the identification of three distinct, unique club cell subpopulations (progenitor, proliferating and effector). The progenitor population was identified as a branch point leading to further differentiation of both the effector population and mucous cells.…”

Posttranscriptional Gene Regulatory Networks in Chronic Airway Inflammatory Diseases: In silico Mapping of RNA-Binding Protein Expression in Airway Epithelium

“…However, a rate-limiting factor for this validation lies in the fact that few studies have focused on transcriptomic of small airway epithelium in large number of patients. While correlation network analysis is being conducted on the transcriptome of larger COPD case/control cohorts for which lung tissue samples are available (118), other systems-biology approaches using single-cell sequencing of small airway epithelial cells are concurrently uncovering relevant biological features using brushing samples isolated in a number of COPD and control subjects equal to, or smaller than that of the study we evaluated (119,120).…”

Topography-dependent gene expression and function of common cell archetypes in large and small porcine airways

“…Whereas there is abundant literature describing the histopathology of airway disease in the small airways, less is known about the origins, function, and role in disease of small airway epithelia and their cellular components (Bhowmick and Gappa-Fahlenkamp, 2016; Hackett et al, 2012; O’Beirne et al, 2018; Okuda et al, 2019; Shamsuddin and Quinton, 2012, 2014; Tilley et al, 2011; Vucic et al, 2014; Yang et al, 2017; Zuo et al, 2020; Zuo et al, 2018). The analysis of human small airways has been limited by their poor accessibility to measurements or sampling in vivo in living subjects.…”