Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations
Heterogeneity in endothelial cell (EC) sub-phenotypes is becoming increasingly appreciated in atherosclerosis progression. Still, studies quantifying EC heterogeneity across whole transcriptomes and epigenomes in both in vitro and in vivo models are lacking. Multiomic profiling concurrently measurin...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2024-04-01
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| Online Access: | https://elifesciences.org/articles/91729 |
| _version_ | 1797221102052704256 |
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| author | Maria L Adelus Jiacheng Ding Binh T Tran Austin C Conklin Anna K Golebiewski Lindsey K Stolze Michael B Whalen Darren A Cusanovich Casey E Romanoski |
| author_facet | Maria L Adelus Jiacheng Ding Binh T Tran Austin C Conklin Anna K Golebiewski Lindsey K Stolze Michael B Whalen Darren A Cusanovich Casey E Romanoski |
| author_sort | Maria L Adelus |
| collection | DOAJ |
| description | Heterogeneity in endothelial cell (EC) sub-phenotypes is becoming increasingly appreciated in atherosclerosis progression. Still, studies quantifying EC heterogeneity across whole transcriptomes and epigenomes in both in vitro and in vivo models are lacking. Multiomic profiling concurrently measuring transcriptomes and accessible chromatin in the same single cells was performed on six distinct primary cultures of human aortic ECs (HAECs) exposed to activating environments characteristic of the atherosclerotic microenvironment in vitro. Meta-analysis of single-cell transcriptomes across 17 human ex vivo arterial specimens was performed and two computational approaches quantitatively evaluated the similarity in molecular profiles between heterogeneous in vitro and ex vivo cell profiles. HAEC cultures were reproducibly populated by four major clusters with distinct pathway enrichment profiles and modest heterogeneous responses: EC1-angiogenic, EC2-proliferative, EC3-activated/mesenchymal-like, and EC4-mesenchymal. Quantitative comparisons between in vitro and ex vivo transcriptomes confirmed EC1 and EC2 as most canonically EC-like, and EC4 as most mesenchymal with minimal effects elicited by siERG and IL1B. Lastly, accessible chromatin regions unique to EC2 and EC4 were most enriched for coronary artery disease (CAD)-associated single-nucleotide polymorphisms from Genome Wide Association Studies (GWAS), suggesting that these cell phenotypes harbor CAD-modulating mechanisms. Primary EC cultures contain markedly heterogeneous cell subtypes defined by their molecular profiles. Surprisingly, the perturbations used here only modestly shifted cells between subpopulations, suggesting relatively stable molecular phenotypes in culture. Identifying consistently heterogeneous EC subpopulations between in vitro and ex vivo models should pave the way for improving in vitro systems while enabling the mechanisms governing heterogeneous cell state decisions. |
| first_indexed | 2024-04-24T13:00:05Z |
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| id | doaj.art-c8175c955d6e480189b526a1dbd02b29 |
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| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-24T13:00:05Z |
| publishDate | 2024-04-01 |
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| series | eLife |
| spelling | doaj.art-c8175c955d6e480189b526a1dbd02b292024-04-05T15:42:06ZengeLife Sciences Publications LtdeLife2050-084X2024-04-011210.7554/eLife.91729Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbationsMaria L Adelus0https://orcid.org/0000-0002-9676-9214Jiacheng Ding1Binh T Tran2Austin C Conklin3Anna K Golebiewski4Lindsey K Stolze5Michael B Whalen6Darren A Cusanovich7https://orcid.org/0000-0001-6889-0095Casey E Romanoski8https://orcid.org/0000-0002-0149-225XThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United States; The Clinical Translational Sciences Graduate Program, The University of Arizona, Tucson, United StatesThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United StatesThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United StatesThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United StatesThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United StatesThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United StatesThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United StatesThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United States; Asthma and Airway Disease Research Center, The University of Arizona, Tucson, United StatesThe Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, United States; The Clinical Translational Sciences Graduate Program, The University of Arizona, Tucson, United States; Asthma and Airway Disease Research Center, The University of Arizona, Tucson, United StatesHeterogeneity in endothelial cell (EC) sub-phenotypes is becoming increasingly appreciated in atherosclerosis progression. Still, studies quantifying EC heterogeneity across whole transcriptomes and epigenomes in both in vitro and in vivo models are lacking. Multiomic profiling concurrently measuring transcriptomes and accessible chromatin in the same single cells was performed on six distinct primary cultures of human aortic ECs (HAECs) exposed to activating environments characteristic of the atherosclerotic microenvironment in vitro. Meta-analysis of single-cell transcriptomes across 17 human ex vivo arterial specimens was performed and two computational approaches quantitatively evaluated the similarity in molecular profiles between heterogeneous in vitro and ex vivo cell profiles. HAEC cultures were reproducibly populated by four major clusters with distinct pathway enrichment profiles and modest heterogeneous responses: EC1-angiogenic, EC2-proliferative, EC3-activated/mesenchymal-like, and EC4-mesenchymal. Quantitative comparisons between in vitro and ex vivo transcriptomes confirmed EC1 and EC2 as most canonically EC-like, and EC4 as most mesenchymal with minimal effects elicited by siERG and IL1B. Lastly, accessible chromatin regions unique to EC2 and EC4 were most enriched for coronary artery disease (CAD)-associated single-nucleotide polymorphisms from Genome Wide Association Studies (GWAS), suggesting that these cell phenotypes harbor CAD-modulating mechanisms. Primary EC cultures contain markedly heterogeneous cell subtypes defined by their molecular profiles. Surprisingly, the perturbations used here only modestly shifted cells between subpopulations, suggesting relatively stable molecular phenotypes in culture. Identifying consistently heterogeneous EC subpopulations between in vitro and ex vivo models should pave the way for improving in vitro systems while enabling the mechanisms governing heterogeneous cell state decisions.https://elifesciences.org/articles/91729endothelial cellsERGinflammationatherosclerosisvascular biologyepigenetics |
| spellingShingle | Maria L Adelus Jiacheng Ding Binh T Tran Austin C Conklin Anna K Golebiewski Lindsey K Stolze Michael B Whalen Darren A Cusanovich Casey E Romanoski Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations eLife endothelial cells ERG inflammation atherosclerosis vascular biology epigenetics |
| title | Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations |
| title_full | Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations |
| title_fullStr | Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations |
| title_full_unstemmed | Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations |
| title_short | Single-cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations |
| title_sort | single cell omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations |
| topic | endothelial cells ERG inflammation atherosclerosis vascular biology epigenetics |
| url | https://elifesciences.org/articles/91729 |
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