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Circulation. 2019 Jul 9;140(2):147-163. doi: 10.1161/CIRCULATIONAHA.118.038362. Epub 2019 May 31.

Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations.

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Broad Institute of MIT and Harvard University, Cambridge, MA (A.S.K., S.K.V., L.N., A.S., P.T.E., A.R., S.K., R.M.G.).
Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge (A.S.K., E.R.E.).
Center for Genomic Medicine (S.K.V., S.K., R.M.G.), Massachusetts General Hospital, Boston.
Division of Cardiovascular Medicine, Department of Medicine (E.R.E., R.M.G.), Brigham and Women's Hospital, Boston MA.
Cardiology Division, Department of Medicine (P.T.E., S.K.), Massachusetts General Hospital, Boston.
Division of Genetics (R.M.G.), Brigham and Women's Hospital, Boston MA.



The cells that form the arterial wall contribute to multiple vascular diseases. The extent of cellular heterogeneity within these populations has not been fully characterized. Recent advances in single-cell RNA-sequencing make it possible to identify and characterize cellular subpopulations.


We validate a method for generating a droplet-based single-cell atlas of gene expression in a normal blood vessel. Enzymatic dissociation of 4 whole mouse aortas was followed by single-cell sequencing of >10‚ÄČ000 cells.


Clustering analysis of gene expression from aortic cells identified 10 populations of cells representing each of the main arterial cell types: fibroblasts, vascular smooth muscle cells, endothelial cells (ECs), and immune cells, including monocytes, macrophages, and lymphocytes. The most significant cellular heterogeneity was seen in the 3 distinct EC populations. Gene set enrichment analysis of these EC subpopulations identified a lymphatic EC cluster and 2 other populations more specialized in lipoprotein handling, angiogenesis, and extracellular matrix production. These subpopulations persist and exhibit similar changes in gene expression in response to a Western diet. Immunofluorescence for Vcam1 and Cd36 demonstrates regional heterogeneity in EC populations throughout the aorta.


We present a comprehensive single-cell atlas of all cells in the aorta. By integrating expression from >1900 genes per cell, we are better able to characterize cellular heterogeneity compared with conventional approaches. Gene expression signatures identify cell subpopulations with vascular disease-relevant functions.


aortic diseases; biology; endothelial cells; sequence analysis, RNA; transcriptome

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