Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis

Abstract

Pulmonary fibrosis is a devastating disorder that results in the progressive replacement of normal lung tissue with fibrotic scar. Available therapies slow disease progression, but most patients go on to die or require lung transplantation. Single-cell RNA-seq is a powerful tool that can reveal cellular identity via analysis of the transcriptome, but its ability to provide biologically or clinically meaningful insights in a disease context is largely unexplored.Accordingly, we performed single-cell RNA-seq on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and one bronchoscopic cryobiospy sample.Integrated single-cell transcriptomic analysis of donors and patients with pulmonary fibrosis identified the emergence of distinct populations of epithelial cells and macrophages that were common to all patients with lung fibrosis. Analysis of transcripts in the Wnt pathway suggested that within the same cell type, Wnt secretion and response are restricted to distinct nonoverlapping cells, which was confirmed using in situ RNA hybridization. Single-cell RNA-seq revealed heterogeneity within alveolar macrophages from individual patients, which was confirmed by immunohistochemistry. These results support the feasibility of discovery-based approaches applying next generation sequencing technologies to clinically obtained samples with a goal of developing personalized therapies.

Transcriptomics and single‐cell RNA‐sequencing

“…), suggesting that the complexity of alveolar macrophage taxonomy has been underappreciated (unpublished data). Whilst these observations are preliminary, they are in line with similar reports by groups employing scRNA‐seq to describe macrophage taxonomy and differences in the alveolar macrophage phenotype in fibrosis . These early studies underpin the utility and importance of interrogating macrophage phenotypes in human lung disease using BAL, and provide a window to the practical application of scRNA‐seq.…”

“…Whilst these observations are preliminary, they are in line with similar reports by groups employing scRNA-seq to describe macrophage taxonomy and differences in the alveolar macrophage phenotype in fibrosis. 27,34 These early studies underpin the utility and importance of interrogating macrophage phenotypes in human lung disease using BAL, and provide a window to the practical application of scRNAseq. The analysis of a BAL differential cell count has recently been noted by expert consensus to be an important component of the diagnostic workup for patients with interstitial lung disease, 35 and as the data provided by scRNA-seq is many orders of magnitude more precise and informative than a simple count of the proportion of lymphocytes in a BAL sample, scRNA-seq of BAL cells may provide even greater scope to improve the accuracy of diagnostic algorithms.…”

Integrated single cell analysis of human lung fibrosis resolves cellular origins of predictive protein signatures in body fluids

“…This includes recent international efforts towards building a human Lung Cell Atlas in health and disease 9 . A first draft of the cellular composition of mouse and human lung has been established [10][11][12][13][14] , and several recent single cell profiling studies reported cellular and molecular changes associated with pulmonary fibrosis [15][16][17][18] . However, this nascent draft of a human Lung Cell Atlas currently lacks extension into the complexity of the proteome layer.…”

“…To improve statistical power, to ensure generalization across cohorts and to achieve a more balanced ratio of diseased and healthy patients, our Munich single-cell RNA-seq data set was combined with the filtered count matrices from the Chicago cohort (Reyfman et al 17 ) and the Nashville cohort (Habermann et al 15 ). Before combining these, the count matrices from Chicago and Nashville were processed separately.…”

Association between Sleep Disturbances and Cardiovascular Diseases: Results from NHANES

“…Sleep is a crucial function of health, coordinated by the brain; consisting of interplays between rapid eye movement and non-rapid eye movement sleep (NREM) [1]. For decades, sleep has been regarded as an essential lifestyle behavior that can impact cardiovascular disease (CVD) and mortality [2].…”