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Xie B, Gao D, Zhou B, Chen S, Wang L. New discoveries in the field of metabolism by applying single-cell and spatial omics. J Pharm Anal 2023; 13:711-725. [PMID: 37577385 PMCID: PMC10422156 DOI: 10.1016/j.jpha.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023] Open
Abstract
Single-cell multi-Omics (SCM-Omics) and spatial multi-Omics (SM-Omics) technologies provide state-of-the-art methods for exploring the composition and function of cell types in tissues/organs. Since its emergence in 2009, single-cell RNA sequencing (scRNA-seq) has yielded many groundbreaking new discoveries. The combination of this method with the emergence and development of SM-Omics techniques has been a pioneering strategy in neuroscience, developmental biology, and cancer research, especially for assessing tumor heterogeneity and T-cell infiltration. In recent years, the application of these methods in the study of metabolic diseases has also increased. The emerging SCM-Omics and SM-Omics approaches allow the molecular and spatial analysis of cells to explore regulatory states and determine cell fate, and thus provide promising tools for unraveling heterogeneous metabolic processes and making them amenable to intervention. Here, we review the evolution of SCM-Omics and SM-Omics technologies, and describe the progress in the application of SCM-Omics and SM-Omics in metabolism-related diseases, including obesity, diabetes, nonalcoholic fatty liver disease (NAFLD) and cardiovascular disease (CVD). We also conclude that the application of SCM-Omics and SM-Omics approaches can help resolve the molecular mechanisms underlying the pathogenesis of metabolic diseases in the body and facilitate therapeutic measures for metabolism-related diseases. This review concludes with an overview of the current status of this emerging field and the outlook for its future.
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Affiliation(s)
- Baocai Xie
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
| | - Dengfeng Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Biqiang Zhou
- Department of Geriatric & Spinal Pain Multi-Department Treatment, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, Guangdong, 518035, China
| | - Shi Chen
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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Shu S, Fu M, Chen X, Zhang N, Zhao R, Chang Y, Cui H, Liu Z, Wang X, Hua X, Li Y, Wang X, Wang X, Feng W, Song J. Cellular Landscapes of Nondiseased Human Cardiac Valves From End-Stage Heart Failure-Explanted Heart. Arterioscler Thromb Vasc Biol 2022; 42:1429-1446. [PMID: 36200446 DOI: 10.1161/atvbaha.122.318314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Exploring the mechanisms of valvular heart disease at the cellular level may be useful to identify new therapeutic targets; however, the comprehensive cellular landscape of nondiseased human cardiac valve leaflets remains unclear. METHODS The cellular landscapes of nondiseased human cardiac valve leaflets (5 aortic valves, 5 pulmonary valves, 5 tricuspid valves, and 3 mitral valves) from end-stage heart failure patients undergoing heart transplantation were explored using single-cell RNA sequencing. Bioinformatics was used to identify the cell types, describe the cell functions, and investigate cellular developmental trajectories and interactions. Differences among the 4 types of cardiac valves at the cellular level were summarized. Pathological staining was performed to validate the key findings of single-cell RNA sequencing. An integrative analysis of our single-cell data and published genome-wide association study-based and bulk RNA sequencing-based data provided insights into the cell-specific contributions to calcific aortic valve diseases. RESULTS Six cell types were identified among 128 412 cells from nondiseased human cardiac valve leaflets. Valvular interstitial cells were the largest population, followed by myeloid cells, lymphocytes, valvular endothelial cells, mast cells, and myofibroblasts. The 4 types of cardiac valve had distinct cellular compositions. The intercellular communication analysis revealed that valvular interstitial cells were at the center of the communication network. The integrative analysis of our single-cell RNA sequencing data revealed key cellular subpopulations involved in the pathogenesis of calcific aortic valve diseases. CONCLUSIONS The cellular landscape differed among the 4 types of nondiseased cardiac valve, which might explain their differences in susceptibility to pathological remodeling and valvular heart disease.
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Affiliation(s)
- Songren Shu
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengxia Fu
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Chen
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ningning Zhang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruojin Zhao
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Chang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Cui
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zirui Liu
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohu Wang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiumeng Hua
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Li
- Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Wang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xianqiang Wang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Feng
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen' China (J.S.)
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