Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

Abstract

Pulmonary fibrosis is a form of chronic lung disease characterized by pathologic epithelial remodeling and accumulation of extracellular matrix. In order to comprehensively define the cell types, mechanisms and mediators driving fibrotic remodeling in lungs with pulmonary fibrosis, we performed single-cell RNAsequencing of single-cell suspensions from 10 non-fibrotic control and 20 PF lungs. Analysis of 114,396 cells identified 31 distinct cell types. We report a remarkable shift in epithelial cell phenotypes occurs in the peripheral lung in PF, and identify several previously unrecognized epithelial cell phenotypes including a KRT5 -/KRT17 + , pathologic ECM-producing epithelial cell population that was highly enriched in PF lungs. Multiple fibroblast subtypes were observed to contribute to ECM expansion in a spatially-discrete manner. Together these data provide high-resolution insights into the complexity and plasticity of the distal lung epithelium in human disease, and indicate a diversity of epithelial and mesenchymal cells contribute to pathologic lung fibrosis. One Sentence SummarySingle-cell RNA-sequencing provides new insights into pathologic epithelial and mesenchymal remodeling in the human lung.

Expression ofACE2, the SARS-CoV-2 receptor, andTMPRSS2in prostate epithelial cells

“…Moreover, we found 30 cells that co- Prostate club cells were found to have the greatest proportion of double-positive cells in the human prostate, and these cells bear a strong resemblance to lung club cells [5]. To characterize ACE2 and TMPRSS2 expression in prostate club cells, we compared the expression levels of these genes in lung club cells from one mouse lung [6] and four human lung [7][8][9][10] single-cell datasets ( Supplementary Table 1). We found a higher proportion of cells expressing TMPRSS2 than those expressing ACE2 (Figure 1 Lastly, to test sex differences in expression profiles of ACE2 and TMPRSS2, we compared ACE2 and TMPRSS2 expression differences within the integrated lung epithelial cells dataset stratified by sex [8,10] (Male: N = 12, Female: N = 19, Supplementary Table 1).…”

“…c. Human lung epithelial cells from the Reyfman et al study [8]. d. Human lung epithelial cells from the Habermann study [9]. e. Human lung epithelial cells from Raredon study [10].…”

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

“…3a). These included 6 published datasets [63][64][65][66][67][68] and 16 datasets that are not yet published [69][70][71][72][73] . In the case of unpublished data, we only obtained singlecell expression counts for the three genes, as well as the total UMI counts per cell, cell identity annotations, and the relevant anonymous clinical variables (age and sex, as well as smoking status when ascertained).…”

“…Aggregation of these datasets was enabled by harmonizing the cell type labels of individual datasets within Scanpy 165 (version 1.4.5.1). We harmonized annotations together with data contributors using a preliminary ontology generated on the basis of 5 published datasets [63][64][65][66]174 with 3 levels of annotations (level 1 -lowest resolution; Supplementary Table 2). We further harmonized metadata by collapsing the smoking covariate into "has smoked" and "has never smoked" and by taking mean ages where only age ranges were given.…”

Cell-intrinsic differences between human airway epithelial cells from children and adults

“…A novel CFTR-producing population, the ionocyte (Montoro et al, 2018;Plasschaert et al, 2018), has been described, and we have new insight into cellular differentiation through the resolution of differentiation intermediates; for example, basal luminal progenitor cells (Mori et al, 2015;Rock et al, 2011;Watson et al, 2015), which are defined by an intermediate keratin profile (TP63-/KRT5+/KRT8+/KRT4+/KRT13+) (Braga et al, 2019;García et al, 2019). Efforts in mapping pathologic states have identified mucous ciliated cells (ciliated cells which co-express a number of genes typically associated with goblet cells and are more frequent in asthmatic patients (Braga et al, 2019)), as well as novel pathological epithelial cell subtypes in idiopathic pulmonary fibrosis (Adams et al, 2019;Habermann et al, 2019;Reyfman et al, 2019). In addition, region-specific differences exist in airway epithelial cell phenotype within the bronchial tree such that basal, ciliated and secretory populations in the nasal epithelium differ phenotypically (and maybe functionally) from their counterparts in the large or small airways (Braga et al, 2019;Deprez et al, 2019;Kumar et al, 2011;Travaglini et al, 2019).…”