Despite substantial progress in the understanding of pulmonary fibrosis (PF) in laboratory animals, researchers have a limited perspective of the cellular and molecular processes that determine the characteristics of lungs with the condition.
Dr. Ivan Rosas at Baylor College of Medicine, Dr. Naftali Kaminski from Yale School of Medicine and colleagues have taken a major step toward a deeper appreciation of pulmonary fibrosis and other chronic pulmonary diseases such as chronic obstructive pulmonary disease (COPD).
“This is a technological accomplishment and is a new perspective on the two diseases, but it is also the starting point for analysis that will lead to a better understanding of the disease and the development of therapy,” said Rosas, the co-lead researcher and co-senior author of the study and chief of pulmonary, critical care and sleep medicine in the Department of Medicine at Baylor.
They developed the largest single-cell data set of a chronic lung disease by sequencing the RNA of more than 300,000 cells from lungs affected with these conditions. The results, published in the journal Science Advances, offer an online cell atlas that allows the public to explore the individual cells in lungs with the diseases.
(A) Overview of experimental design. (i) Disease lung explants and unused donor lungs collected. (ii) Lungs dissociated to single-cell suspension. (iii) Droplet-based scRNA-seq library preparation (iv) sequencing. (v) Exploratory analysis. (vi) Spatial localization with IHC. (B) Uniform Manifold Approximation and Projection (UMAP) representation of 312,928 cells from 32 IPF, 18 COPD, and 28 control donor lungs; each dot represents a single cell, and cells are labeled as one of 38 discrete cell varieties. AT, alveolar type; cDC, classical dendritic cell; pDC, plasmacytoid dendritic cell; M, macrophage; NK, natural killer; ILC, innate lymphoid cell; PNEC, pulmonary neuroendocrine cell; SMC, smooth muscle cell; VE, vascular endothelial. (C) Heat map of marker genes for all 38 identified cell types, categorized into four broad cell categories. Each cell type is represented by the top five genes ranked by false discovery rate (FDR) adjusted P value of a Wilcoxon rank sum test between the average expression per subject value for each cell type against the other average subject expression of the other cell types in their respective grouping. Each column represents the average expression value for one subject, hierarchically grouped by disease status and cell type. Gene expression values are unity normalized from 0 to 1 across rows within each categorical cell type group.
Rosas explains that the cell atlas was achieved by separating all of the individual the cells within the lung and then measuring RNA expression of all the cells in each individual cell. Although this method has been done for other diseases, this is the largest single-cell gene expression dataset that has been completed in a chronic lung disease.
“When we analyzed the data we were surprised by how dramatically different were cells obtained from patients with PF from all other lungs – we actually found cells that were not described before, and this may have significant implications on diagnosis and management for the disease,” said Kaminski, the co-senior author on the study and chief of pulmonary, critical care and sleep medicine at Yale.
“This data is now publicly available so it’s going to broadly impact science and these diseases,” Rosas said. “People can now download the data set and conduct their own independent analysis and research.”
“Because physicians need a further understanding of chronic lung diseases like PF, Rosas explains that having a large and accessible data set of PF or COPD cells is an essential tool to begin developing therapies to target the disease.”
Rosas led the study during his time at Harvard Medical School in Boston. The continuation of studies on IPF will continue in laboratories at Baylor College of Medicine.
“Chronic lung diseases are one of the leading causes of morbidity and death in diagnosed patients, but this innovative technology is the starting point for more pointed research in terms of the pathogenesis and the mechanisms of the disease and also the potential therapy that could be derived from the information,” Rosas said.
The research is funded by the NIH National Heart, Lung, and Blood Institute and a $1 million gift from the venture philanthropy group Three Lakes Partners, whose mission is to accelerate progress in IPF research.