Integrated Single Cell Atlas of Endothelial Cells of the Human Lung

Abstract

Background: Despite its importance in health and disease, the cellular diversity of the lung endothelium has not been systematically characterized in humans. Here we provide a reference atlas of human lung endothelial cells (ECs), to facilitate a better understanding of the phenotypic diversity and composition of cells comprising the lung endothelium, both in health and disease. Methods: We reprocessed control single cell RNA sequencing (scRNAseq) data from five datasets of whole lungs that were used for the analysis of pan-endothelial markers, we later included a sixth dataset of sorted control EC for the vascular subpopulation analysis. EC populations were characterized through iterative clustering with subsequent differential expression analysis. Marker genes were validated by immunohistochemistry and in situ hybridization. Signaling network between different lung cell types was studied using connectomic analysis. For cross species analysis we applied the same methods to scRNAseq data obtained from mouse lungs. Results: The six lung scRNAseq datasets were reanalyzed and annotated to identify over 15,000 vascular EC cells from 73 individuals. Differential expression analysis of EC revealed signatures corresponding to endothelial lineage, including pan-endothelial, pan-vascular and subpopulation-specific marker gene sets. Beyond the broad cellular categories of lymphatic, capillary, arterial and venous ECs we found previously indistinguishable subpopulations; among venous EC we identified two previously indistinguishable populations, pulmonary-venous ECs (COL15A1neg) localized to the lung parenchyma and systemic-venous ECs (COL15A1pos) localized to the airways and the visceral pleura; among capillary EC we confirmed their subclassification into recently discovered aerocytes characterized by EDNRB, SOSTDC1 and TBX2 and general capillary EC. We confirmed that all six endothelial cell types, including the systemic-venous EC and aerocytes are present in mice and identified endothelial marker genes conserved in humans and mice. Ligand-Receptor connectome analysis revealed important homeostatic crosstalk of EC with other lung resident cell types. Our manuscript is accompanied by an online data mining tool (www.LungEndothelialCellAtlas.com). Conclusion: Our integrated analysis provides the comprehensive and well-crafted reference atlas of lung endothelial cells in the normal lung and confirms and describes in detail previously unrecognized endothelial populations across a large number of humans and mice.

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

“…4d, 4e). The remaining four subpopulations were identified using imputation and comparison to other lung and endothelial cell atlases 35, 36 (Supplemental Fig. 4f).…”

“…ECA - endothelial cell atlas markers Schupp et al . 36 , HCLA - human cell lung atlas markers Gillich et al . 108 g. Batch correction within lineage.…”

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

“…We identified seven endothelial subsets (Extended Data Fig. 2m, 4b) 18,19 : arterial; venous and lymphatic; capillary aerocytes; capillary EC-1; and capillary EC-2 and a mixed subset (Methods), and three stromal subsets: fibroblasts; proliferative fibroblasts; and myofibroblasts 19 (Extended Data Fig. 2n, Supplementary Information Table 3).…”

Single-cell Chromatin Accessibility and Lipid Profiling Reveals a Metabolic Shift in Adipocytes Induced by Bariatric Surgery

“…This cluster represented adipocyte progenitor cells (APCs) based on accessibility at known APC markers Fbn1, Timp2, Mfap5, Anxa3 (Cho et al, 2019). The next cluster (End), identified as endothelial cells, had signatures of angiogenesis and tight junction enrichments and known marker genes Cldn5, S1pr1, Pecam1, Ptprb, Kdr (Schupp et al, 2020). Two clusters of immune cells (Mac, Tcell) had distinct gene accessibility.…”