Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD

Abstract

Background: Whole lung tissue transcriptomic profling studies in chronic obstructive pulmonary disease (COPD) have led to the identifcation of several genes associated with the severity of airfow limitation and/or the presence of emphysema, however, the cell types driving these gene expression signatures remain unidentifed. Methods: To determine cell specifc transcriptomic changes in severe COPD, we conducted single-cell RNA sequencing (scRNA seq) on n=29,961 cells from the peripheral lung parenchymal tissue of nonsmoking subjects without underlying lung disease (n=3) and patients with severe COPD (n=3). The cell type composition and cell specifc gene expression signature was assessed. Gene set enrichment analysis (GSEA) was used to identify the specifc cell types contributing to the previously reported transcriptomic signatures. Results: T-distributed stochastic neighbor embedding and clustering of scRNA seq data revealed a total of 17 distinct populations. Among them, the populations with more diferentially expressed genes in cases vs. controls (log fold change>|0.4| and FDR=0.05) were: monocytes (n=1499); macrophages (n=868) and ciliated epithelial cells (n=590), respectively. Using GSEA, we found that only ciliated and cytotoxic T cells manifested a trend towards enrichment of the previously reported 127 regional emphysema gene signatures (normalized enrichment score [NES]=1.28 and=1.33, FDR=0.085 and=0.092 respectively). Among the signifcantly altered genes present in ciliated epithelial cells of the COPD lungs, QKI and IGFBP5 protein levels were also found to be altered in the COPD lungs. Conclusions: scRNA seq is useful for identifying transcriptional changes and possibly individual protein levels that may contribute to the development of emphysema in a cell-type specifc manner. Keywords: Single cell RNA-seq, COPD, Cigarette smoke