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Expression data from surface airway epithelial basal cells, ciliated cells, and club cells.

ABSTRACT: To identify key genes that define surface airway epithelial (SAE) basal cells, we FACS isolated basal, ciliated, and club cell populations as previously reported (Zhao et al., 2014; PMID: 25043474) and performed microarray analysis on isolated mRNA. For fractionating SAE into basal, club, and ciliated populations, cells were stained with EpCAM-PECy7 (eBiosciences), GSIβ4-FITC (Sigma), SSEA1-Alexa Fluor® 647 (BioLegend), and CD24-PE (BD Pharmingen) for 30 minutes on ice as previously described (Zhao et al., 2014), prior to FACS. Basal cells were considered EpCAM+ and GSIβ4+. Secretory cells were considered EpCAM+ and SSEA1+. Ciliated cells were considered EpCAM+, GSIβ4- and CD24+. Primary SAE cells were harvested from C57BL/6 mice and sorted into basal, ciliated, and club cell populations for the purpose of identifying enrichment of transcripts specific to each cell type population.

ORGANISM(S): Mus musculus

PROVIDER: GSE111557 | GEO | 2018/04/30

REPOSITORIES: GEO

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Project description:The club cell, a small airway epithelial (SAE) secretory cell that uniquely expresses SCGB1A1, plays a central role in host defense in the human lung. Based on data demonstrating that ~50% of club cells express MUC5B, a secretory mucin critical for mucociliary clearance, we hypothesized that subpopulations of club cells with distinct functions may exist. To evaluate this, the SAE of normal nonsmokers and healthy cigarette smokers was sampled by bronchoscopy and brushing followed by single cell sequencing using Drop-seq technology. Subpopulations of SCGCB1A1+KRT5loMUC5AC- club cells were assessed by unsupervised clustering to evaluate club cell subpopulations. Immunostaining of SAE in lung sections, brushed SAE cells, and in vitro air-liquid interface culture was utilized to confirm the transcriptomic-based observations. Unsupervised clustering of SCGCB1A1+KRT5loMUC5AC‾ club cells in the SAE identified 3 unique club cell populations that differed by differentiation state and function, including: (1) progenitor; (2) proliferating; and (3) effector subpopulations. The progenitor club cell population was energetically active with high expression of mitochondrial and ribosomal proteins and the highest KRT5 levels vs other club cell populations. The proliferating population, defined by high expression of cyclins and proliferation markers, was the smallest, representing 2% of club cells. The effector club cell cluster expressed transcripts for host defense genes, xenobiotic metabo-lism, and barrier functions commonly associated with club cell function. Comparison of the club cell subpopulations in smokers vs nonsmokers demonstrated that the proportion of the club cell effector population was significantly decreased in smokers with a concomitant significant in-crease in the proliferating cell population. These observations provide novel insights into both the makeup of human SAE club cell subpopulations and smoking-induced changes in club cell biology.

Project description:The small airway epithelium (SAE) the pseudostratified epithelium that covers the majority of the human airway surface from the 6th generation to the alveoli, is the major site of lung disease caused by smoking, and the cell population that exhibits the earliest manifestations of smoking-induced disease. The focus of this study is to use RNA-Seq (massive parallel sequencing technology) to sequence all polyA+ mRNAs expressed by the SAE of healthy nonsmokers to gain new insights into the biology of the SAE, and how these cells respond to cigarette smoke. Taking advantage of RNA-Seq providing quantitative mRNA levels, that data demonstrates that while the SAE shares its transcriptome with many cell types, it has unique characteristics that are enriched in this cell population, with the mostly highly expressed genes (SCGB1A1) characteristics of Clara cells, an airway epithelial cell unique to the human small airways. Among other genes expressed by the SAE are those characteristic of ciliated and mucin-producing cells, basal cells and neuroendocrine cells. The RNA-Seq data includes identification of the highly expressed SAE transcription factors, transmembrane receptors, signaling ligands and growth factors. RNA-Seq permitted quantification of expression of highly homologous gene families, the absolute smoking-induced changes in SAE gene expression, including genes expressed at low levels, and assessment of the effect of smoking on SAE gene splicing. Together, these observations can serve as the baseline for assessment of the dysregulation of SAE gene expression in human airway disease. The small airway epithelium (SAE) is the major site of lung disease caused by smoking, and the cell population that exhibits the earliest manifestations of smoking-induced disease. This study used RNA-Seq to sequence all polyA+ mRNAs expressed by the SAE of 5 healthy nonsmokers to gain new insights into the biology of the SAE, and evaluate how these cells respond to cigarette smoke using 6 healthy smoker samples (SRA029282.1). Taking advantage of RNA-Seq providing quantitative mRNA levels, that data demonstrates that while the SAE shares its transcriptome with many cell types, it has unique characteristics that are enriched in this cell population. Coverage of RNA-Seq expression was also compared to the HG-U133 Plus 2.0 microarray expression of 27 previously published healthy nonsmoker samples presented here.

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Expression data from surface airway epithelial basal cells, ciliated cells, and club cells.

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