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Ma WF, Hodonsky CJ, Turner AW, Wong D, Song Y, Mosquera JV, Ligay AV, Slenders L, Gancayco C, Pan H, Barrientos NB, Mai D, Alencar GF, Owsiany K, Owens GK, Reilly MP, Li M, Pasterkamp G, Mokry M, van der Laan SW, Khomtchouk BB, Miller CL. Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets. Atherosclerosis 2022; 340:12-22. [PMID: 34871816 PMCID: PMC8919504 DOI: 10.1016/j.atherosclerosis.2021.11.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND AND AIMS The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability are not yet available. We sought to develop a scRNA-seq analysis workflow to investigate this environment and uncover potential therapeutic approaches. We designed a user-friendly, reproducible workflow that will be applicable to other disease-specific scRNA-seq datasets. METHODS Here we incorporated automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into a ready-to-deploy workflow. We applied this pipeline to further investigate a previously published human coronary single-cell dataset by Wirka et al. Notably, we developed an interactive web application to enable further exploration and analysis of this and other cardiovascular single-cell datasets. RESULTS We revealed distinct derivations of fibroblast-like cells from smooth muscle cells (SMCs), and showed the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several avenues for future pharmacological development for precision medicine. Further, our interactive web application, PlaqView (www.plaqview.com), allows lay scientists to explore this and other datasets and compare scRNA-seq tools without prior coding knowledge. CONCLUSIONS This publicly available workflow and application will allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems. Our analysis pipeline provides many hypothesis-generating tools to unravel the etiology of coronary artery disease. We also highlight potential mechanisms for several drugs in the atherosclerotic cellular environment. Future releases of PlaqView will feature more scRNA-seq and scATAC-seq atherosclerosis-related datasets to provide a critical resource for the field, and to promote data harmonization and biological interpretation.
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Affiliation(s)
- Wei Feng Ma
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, 22908, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Computer Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA
| | - Alexandra V Ligay
- Master of Science in Biomedical Informatics (MScBMI) Program, University of Chicago, Chicago, IL, 60637, USA
| | - Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Christina Gancayco
- Research Computing, University of Virginia, Charlottesville, VA, 22908, USA
| | - Huize Pan
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA
| | - Nelson B Barrientos
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - David Mai
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Gabriel F Alencar
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA
| | - Katherine Owsiany
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, 22908, USA; Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA
| | - Gary K Owens
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, 22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands; Department of Experimental Cardiology, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584, CX, Utrecht, the Netherlands
| | - Bohdan B Khomtchouk
- Department of Medicine, Section of Computational Biomedicine and Biomedical Data Science, Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL , 60637, USA.
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA , 22908, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA.
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