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Chen L, Li H, Liu X, Zhang N, Wang K, Shi A, Gao H, Akdis D, Saguner AM, Xu X, Osto E, Van de Veen W, Li G, Bayés-Genís A, Duru F, Song J, Li X, Hu S. PBX/Knotted 1 homeobox-2 (PKNOX2) is a novel regulator of myocardial fibrosis. Signal Transduct Target Ther 2024; 9:94. [PMID: 38644381 PMCID: PMC11033280 DOI: 10.1038/s41392-024-01804-5] [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: 03/14/2023] [Revised: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 04/23/2024] Open
Abstract
Much effort has been made to uncover the cellular heterogeneities of human hearts by single-nucleus RNA sequencing. However, the cardiac transcriptional regulation networks have not been systematically described because of the limitations in detecting transcription factors. In this study, we optimized a pipeline for isolating nuclei and conducting single-nucleus RNA sequencing targeted to detect a higher number of cell signal genes and an optimal number of transcription factors. With this unbiased protocol, we characterized the cellular composition of healthy human hearts and investigated the transcriptional regulation networks involved in determining the cellular identities and functions of the main cardiac cell subtypes. Particularly in fibroblasts, a novel regulator, PKNOX2, was identified as being associated with physiological fibroblast activation in healthy hearts. To validate the roles of these transcription factors in maintaining homeostasis, we used single-nucleus RNA-sequencing analysis of transplanted failing hearts focusing on fibroblast remodelling. The trajectory analysis suggested that PKNOX2 was abnormally decreased from fibroblast activation to pathological myofibroblast formation. Both gain- and loss-of-function in vitro experiments demonstrated the inhibitory role of PKNOX2 in pathological fibrosis remodelling. Moreover, fibroblast-specific overexpression and knockout of PKNOX2 in a heart failure mouse model induced by transverse aortic constriction surgery significantly improved and aggravated myocardial fibrosis, respectively. In summary, this study established a high-quality pipeline for single-nucleus RNA-sequencing analysis of heart muscle. With this optimized protocol, we described the transcriptional regulation networks of the main cardiac cell subtypes and identified PKNOX2 as a novel regulator in suppressing fibrosis and a potential therapeutic target for future translational studies.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Haotong Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Xiaorui Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Ningning Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Kui Wang
- School of Statistics and Data Science, Nankai University, Tianjin, China
| | - Anteng Shi
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Hang Gao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Deniz Akdis
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Ardan M Saguner
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Xinjie Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Elena Osto
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute for Clinical Chemistry, University Hospital Zurich and University of Zürich, Zurich, Switzerland
| | - Willem Van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Guangyu Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Antoni Bayés-Genís
- Heart Institute, Hospital Universitari Germans Trias i Pujol, Badalona, CIBERCV, Spain
| | - Firat Duru
- Department of Cardiology, University Heart Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
| | - Xiangjie Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China.
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Jung Y, Kim J, Jang H, Kim G, Kwon YW. Strategy of Patient-Specific Therapeutics in Cardiovascular Disease Through Single-Cell RNA Sequencing. Korean Circ J 2022; 53:1-16. [PMID: 36627736 PMCID: PMC9834554 DOI: 10.4070/kcj.2022.0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Recently, single cell RNA sequencing (scRNA-seq) technology has enabled the discovery of novel or rare subtypes of cells and their characteristics. This technique has advanced unprecedented biomedical research by enabling the profiling and analysis of the transcriptomes of single cells at high resolution and throughput. Thus, scRNA-seq has contributed to recent advances in cardiovascular research by the generation of cell atlases of heart and blood vessels and the elucidation of mechanisms involved in cardiovascular development and diseases. This review summarizes the overall workflow of the scRNA-seq technique itself and key findings in the cardiovascular development and diseases based on the previous studies. In particular, we focused on how the single-cell sequencing technology can be utilized in clinical field and precision medicine to treat specific diseases.
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Affiliation(s)
- Yunseo Jung
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes & Cancer, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Juyeong Kim
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Howon Jang
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Gwanhyeon Kim
- Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
| | - Yoo-Wook Kwon
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes & Cancer, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea.,Department of Medicine, Seoul National University College of Medicine, Seoul National University, Seoul, Korea
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Hu Y, Zhang Y, Liu Y, Gao Y, San T, Li X, Song S, Yan B, Zhao Z. Advances in application of single-cell RNA sequencing in cardiovascular research. Front Cardiovasc Med 2022; 9:905151. [PMID: 35958408 PMCID: PMC9360414 DOI: 10.3389/fcvm.2022.905151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) provides high-resolution information on transcriptomic changes at the single-cell level, which is of great significance for distinguishing cell subtypes, identifying stem cell differentiation processes, and identifying targets for disease treatment. In recent years, emerging single-cell RNA sequencing technologies have been used to make breakthroughs regarding decoding developmental trajectories, phenotypic transitions, and cellular interactions in the cardiovascular system, providing new insights into cardiovascular disease. This paper reviews the technical processes of single-cell RNA sequencing and the latest progress based on single-cell RNA sequencing in the field of cardiovascular system research, compares single-cell RNA sequencing with other single-cell technologies, and summarizes the extended applications and advantages and disadvantages of single-cell RNA sequencing. Finally, the prospects for applying single-cell RNA sequencing in the field of cardiovascular research are discussed.
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Affiliation(s)
- Yue Hu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Ying Zhang
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Yutong Liu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Yan Gao
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Tiantian San
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Xiaoying Li
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- Department of Emergency, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Sensen Song
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Binglong Yan
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Zhuo Zhao
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- *Correspondence: Zhuo Zhao
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