Tissue Type(s): Lung Fibrosis

Contributed by: Jonathan A. Kropski, Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, Department of Veterans Affairs Medical Center, Nashville, TN, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN

Manuscript: 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 (https://www.biorxiv.org/content/10.1101/2020.04.19.049254v1)

Description: This study allows one to visualize and query genes as well as explore cell types, technical batches, and cell metrics associated with the manuscript. If published, this version of the data set is focused on the manuscript and is a subset of what may be made available by the original manuscript.

Original Publication: Habermann, Arun C., et al. "Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis." bioRxiv (2019): 753806.

Full dataset: The raw and processed 10X genomics data can be found on GEO using the accession number: GSE135893, and the relevant processed data is shared here in the downloads tab.

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 RNA-sequencing 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.