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Sharma D, Worssam MD, Pedroza AJ, Dalal AR, Alemany H, Kim HJ, Kundu R, Fischbein MP, Cheng P, Wirka R, Quertermous T. Comprehensive Integration of Multiple Single-Cell Transcriptomic Data Sets Defines Distinct Cell Populations and Their Phenotypic Changes in Murine Atherosclerosis. Arterioscler Thromb Vasc Biol 2024; 44:391-408. [PMID: 38152886 DOI: 10.1161/atvbaha.123.320030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND The application of single-cell transcriptomic (single-cell RNA sequencing) analysis to the study of atherosclerosis has provided unique insights into the molecular and genetic mechanisms that mediate disease risk and pathophysiology. However, nonstandardized methodologies and relatively high costs associated with the technique have limited the size and replication of existing data sets and created disparate or contradictory findings that have fostered misunderstanding and controversy. METHODS To address these uncertainties, we have performed a conservative integration of multiple published single-cell RNA sequencing data sets into a single meta-analysis, performed extended analysis of native resident vascular cells, and used in situ hybridization to map the disease anatomic location of the identified cluster cells. To investigate the transdifferentiation of smooth muscle cells to macrophage phenotype, we have developed a classifying algorithm based on the quantification of reporter transgene expression. RESULTS The reporter gene expression tool indicates that within the experimental limits of the examined studies, transdifferentiation of smooth muscle cell to the macrophage lineage is extremely rare. Validated transition smooth muscle cell phenotypes were defined by clustering, and the location of these cells was mapped to lesion anatomy with in situ hybridization. We have also characterized 5 endothelial cell phenotypes and linked these cellular species to different vascular structures and functions. Finally, we have identified a transcriptomically unique cellular phenotype that constitutes the aortic valve. CONCLUSIONS Taken together, these analyses resolve a number of outstanding issues related to differing results reported with vascular disease single-cell RNA sequencing studies, and significantly extend our understanding of the role of resident vascular cells in anatomy and disease.
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Affiliation(s)
- Disha Sharma
- Division of Cardiovascular Medicine (D.S., M.D.W., H.A., H.-J.K., R.K., P.C., T.Q.), Stanford University School of Medicine, CA
| | - Matthew D Worssam
- Division of Cardiovascular Medicine (D.S., M.D.W., H.A., H.-J.K., R.K., P.C., T.Q.), Stanford University School of Medicine, CA
| | - Albert J Pedroza
- Division of Cardiothoracic Surgery (A.J.P., A.R.D., M.P.F.), Stanford University School of Medicine, CA
| | - Alex R Dalal
- Division of Cardiothoracic Surgery (A.J.P., A.R.D., M.P.F.), Stanford University School of Medicine, CA
| | - Haizea Alemany
- Division of Cardiovascular Medicine (D.S., M.D.W., H.A., H.-J.K., R.K., P.C., T.Q.), Stanford University School of Medicine, CA
| | - Hyun-Jung Kim
- Division of Cardiovascular Medicine (D.S., M.D.W., H.A., H.-J.K., R.K., P.C., T.Q.), Stanford University School of Medicine, CA
| | - Ramendra Kundu
- Division of Cardiovascular Medicine (D.S., M.D.W., H.A., H.-J.K., R.K., P.C., T.Q.), Stanford University School of Medicine, CA
| | - Michael P Fischbein
- Division of Cardiothoracic Surgery (A.J.P., A.R.D., M.P.F.), Stanford University School of Medicine, CA
| | - Paul Cheng
- Division of Cardiovascular Medicine (D.S., M.D.W., H.A., H.-J.K., R.K., P.C., T.Q.), Stanford University School of Medicine, CA
| | - Robert Wirka
- Division of Cardiology, McAllister Heart Institute, UNC School of Medicine, Chapel Hill, NC (R.W.)
| | - Thomas Quertermous
- Division of Cardiovascular Medicine (D.S., M.D.W., H.A., H.-J.K., R.K., P.C., T.Q.), Stanford University School of Medicine, CA
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Affiliation(s)
- Jacqueline S Dron
- From the Department of Biochemistry (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Julieta Lazarte
- From the Department of Biochemistry (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Medicine (J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Robert A Hegele
- From the Department of Biochemistry (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Robarts Research Institute (J.S.D., J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Medicine (J.L., R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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