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Zeng Y, Ma Q, Chen J, Kong X, Chen Z, Liu H, Liu L, Qian Y, Wang X, Lu S. Single-cell sequencing: Current applications in various tuberculosis specimen types. Cell Prolif 2024:e13698. [PMID: 38956399 DOI: 10.1111/cpr.13698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (M.tb) and responsible for millions of deaths worldwide each year. It has a complex pathogenesis that primarily affects the lungs but can also impact systemic organs. In recent years, single-cell sequencing technology has been utilized to characterize the composition and proportion of immune cell subpopulations associated with the pathogenesis of TB disease since it has a high resolution that surpasses conventional techniques. This paper reviews the current use of single-cell sequencing technologies in TB research and their application in analysing specimens from various sources of TB, primarily peripheral blood and lung specimens. The focus is on how these technologies can reveal dynamic changes in immune cell subpopulations, genes and proteins during disease progression after M.tb infection. Based on the current findings, single-cell sequencing has significant potential clinical value in the field of TB research. Next, we will focus on the real-world applications of the potential targets identified through single-cell sequencing for diagnostics, therapeutics and the development of effective vaccines.
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Affiliation(s)
- Yuqin Zeng
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Quan Ma
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Jinyun Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xingxing Kong
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Zhanpeng Chen
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Huazhen Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Lanlan Liu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Yan Qian
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Xiaomin Wang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
| | - Shuihua Lu
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China
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Dumonteil E, Tu W, Desale H, Goff K, Marx P, Ortega-Lopez J, Herrera C. Immunoglobulin and T cell receptor repertoire changes induced by a prototype vaccine against Chagas disease in naïve rhesus macaques. J Biomed Sci 2024; 31:58. [PMID: 38824576 PMCID: PMC11143712 DOI: 10.1186/s12929-024-01050-5] [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: 12/16/2023] [Accepted: 05/27/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND A vaccine against Trypanosoma cruzi, the agent of Chagas disease, would be an excellent additional tool for disease control. A recombinant vaccine based on Tc24 and TSA1 parasite antigens was found to be safe and immunogenic in naïve macaques. METHODS We used RNA-sequencing and performed a transcriptomic analysis of PBMC responses to vaccination of naïve macaques after each vaccine dose, to shed light on the immunogenicity of this vaccine and guide the optimization of doses and formulation. We identified differentially expressed genes and pathways and characterized immunoglobulin and T cell receptor repertoires. RESULTS RNA-sequencing analysis indicated a clear transcriptomic response of PBMCs after three vaccine doses, with the up-regulation of several immune cell activation pathways and a broad non-polarized immune profile. Analysis of the IgG repertoire showed that it had a rapid turnover with novel IgGs produced following each vaccine dose, while the TCR repertoire presented several persisting clones that were expanded after each vaccine dose. CONCLUSIONS These data suggest that three vaccine doses may be needed for optimum immunogenicity and support the further evaluation of the protective efficacy of this vaccine.
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Affiliation(s)
- Eric Dumonteil
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA.
| | - Weihong Tu
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
| | - Hans Desale
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
| | - Kelly Goff
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Preston Marx
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Jaime Ortega-Lopez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico, México
| | - Claudia Herrera
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
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Dumonteil E, Tu W, Desale H, Goff K, Marx P, Ortega-Lopez J, Herrera C. Immunoglobin and T cell receptor repertoire changes induced by a prototype vaccine against Chagas disease in naïve rhesus macaques. RESEARCH SQUARE 2023:rs.3.rs-3453582. [PMID: 37961272 PMCID: PMC10635379 DOI: 10.21203/rs.3.rs-3453582/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A vaccine against Trypanosoma cruzi, the agent of Chagas disease, would be an excellent additional tool for disease control. A recombinant vaccine based on Tc24 and TSA1 parasite antigens was found to be safe and immunogenic in naïve macaques. Here we performed a transcriptomic analysis of PBMC responses to vaccination, to shed light on the immunogenicity of this vaccine and guide the optimization of doses and formulation. RNA-sequencing analysis indicated a clear transcriptomic response of PBMCs from macaques after three vaccine doses, with the up-regulation of several immune cell activation pathways and a broad non-polarized immune profile. Analysis of the IgG repertoire showed that it had a rapid turnover with novel IgGs produced following each vaccine dose, while the TCR repertoire presented several persisting clones that were expanded after each vaccine dose. These data suggest that three vaccine doses may be needed for optimum immunogenecity and support the further evaluation of the protective efficacy of this vaccine.
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4
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Ye Y, Shen Y, Wang J, Li D, Zhu Y, Zhao Z, Pan Y, Wang Y, Liu X, Wan J. SIGANEO: Similarity network with GAN enhancement for immunogenic neoepitope prediction. Comput Struct Biotechnol J 2023; 21:5538-5543. [PMID: 38034402 PMCID: PMC10681954 DOI: 10.1016/j.csbj.2023.10.050] [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: 07/19/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Target selection of the personalized cancer neoantigen vaccine, which is highly dependent on computational prediction algorithms, is crucial for its clinical efficacy. Due to the limited number of experimentally validated immunogenic neoepitopes as well as the complexity of neoantigens in eliciting T cell response, the accuracy of neoepitope immunogenicity prediction methods requires persistent efforts for improvement. We present a deep learning framework for neoepitope immunogenicity prediction - SIGANEO by integrating GAN-like network with similarity network to address issues of missing values and limited data concerning neoantigen prediction. This framework exhibits superior performance over competing machine-learning-based neoantigen prediction algorithms over an independent test dataset from TESLA consortium. Particularly for the clinical setting of neoantigen vaccine where only the top 10 and 20 predictions are selected for vaccine production, SIGANEO achieves significantly better accuracy for predicting experimentally validated neoepitopes. Our work demonstrates that deep learning techniques can greatly boost the accuracy of target identification for cancer neoantigen vaccine.
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Affiliation(s)
- Yilin Ye
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Yiming Shen
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Jian Wang
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Dong Li
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Yu Zhu
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Zhao Zhao
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Youdong Pan
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Yi Wang
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Xing Liu
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ji Wan
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
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Pan J, Chang Z, Zhang X, Dong Q, Zhao H, Shi J, Wang G. Research progress of single-cell sequencing in tuberculosis. Front Immunol 2023; 14:1276194. [PMID: 37901241 PMCID: PMC10611525 DOI: 10.3389/fimmu.2023.1276194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Tuberculosis is a major infectious disease caused by Mycobacterium tuberculosis infection. The pathogenesis and immune mechanism of tuberculosis are not clear, and it is urgent to find new drugs, diagnosis, and treatment targets. A useful tool in the quest to reveal the enigmas related to Mycobacterium tuberculosis infection and disease is the single-cell sequencing technique. By clarifying cell heterogeneity, identifying pathogenic cell groups, and finding key gene targets, the map at the single cell level enables people to better understand the cell diversity of complex organisms and the immune state of hosts during infection. Here, we briefly reviewed the development of single-cell sequencing, and emphasized the different applications and limitations of various technologies. Single-cell sequencing has been widely used in the study of the pathogenesis and immune response of tuberculosis. We review these works summarizing the most influential findings. Combined with the multi-molecular level and multi-dimensional analysis, we aim to deeply understand the blank and potential future development of the research on Mycobacterium tuberculosis infection using single-cell sequencing technology.
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Affiliation(s)
| | | | | | | | | | - Jingwei Shi
- Key Laboratory of Pathobiology Ministry of Education, College of Basic Medical Sciences/China-Japan Union Hospital of Jilin University, Jilin University, Changchun, China
| | - Guoqing Wang
- Key Laboratory of Pathobiology Ministry of Education, College of Basic Medical Sciences/China-Japan Union Hospital of Jilin University, Jilin University, Changchun, China
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Qin Y, Wang Q, Shi J. Immune checkpoint modulating T cells and NK cells response to Mycobacterium tuberculosis infection. Microbiol Res 2023; 273:127393. [PMID: 37182283 DOI: 10.1016/j.micres.2023.127393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/07/2023] [Accepted: 04/22/2023] [Indexed: 05/16/2023]
Abstract
Many subversive mechanisms promote the occurrence and development of chronic infectious diseases and cancer, among which the down-regulated expression of immune-activating receptors and the enhanced expression of immune-inhibitory receptors accelerate the occurrence and progression of the disease. Recently, the use of immune checkpoint inhibitors has shown remarkable efficacy in the treatment of tumors in multiple organs. However, the expression of immune checkpoint molecules on natural killer (NK) cells by Mycobacterium tuberculosis (Mtb) infection and its impact on NK cell effector functions have been poorly studied. In this review, we focus on what is currently known about the expression of various immune checkpoints in NK cells following Mtb infection and how it alters NK cell-mediated host cytotoxicity and cytokine secretion. Unraveling the function of NK cells after the infection of host cells by Mtb is crucial for a comprehensive understanding of the innate immune mechanism of NK cells involved in tuberculosis and the evaluation of the efficacy of immunotherapies using immune checkpoint inhibitors to treat tuberculosis. In view of some similarities in the immune characteristics of T cells and NK cells, we reviewed the molecular mechanism of the interaction between T cells and Mtb, which can help us to further understand and explore the specific interaction mechanism between NK cells and Mtb.
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Affiliation(s)
- Yongwei Qin
- Department of Pathogen Biology, Medical College, Nantong University, No. 19 Qixiu Road, Nantong 226001, China.
| | - Qinglan Wang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jiahai Shi
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, No. 20 Xisi Road, Nantong 226001, China
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Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
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Jiang J, Cao Z, Xiao L, Su J, Wang J, Liang J, Yang B, Liu Y, Zhai F, Wang R, Cheng X. Single-cell profiling identifies T cell subsets associated with control of tuberculosis dissemination. Clin Immunol 2023; 248:109266. [PMID: 36796469 DOI: 10.1016/j.clim.2023.109266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
To identify T cell subsets associated with control of tuberculosis, single-cell transcriptome and T cell receptor sequencing were performed on total T cells from patients with tuberculosis and healthy controls. Fourteen distinct subsets of T cells were identified by unbiased UMAP clustering. A GZMK-expressing CD8+ cytotoxic T cell cluster and a SOX4-expressing CD4+ central memory T cell cluster were depleted, while a MKI67-expressing proliferating CD3+ T cell cluster was expanded in patients with tuberculosis compared with healthy controls. The ratio of Granzyme K-expressing CD8+CD161-Ki-67- and CD8+Ki-67+ T cell subsets was significantly reduced and inversely correlated with the extent of TB lesions in patients with TB. In contrast, ratio of Granzyme B-expressing CD8+Ki-67+ and CD4+CD161+Ki-67- T cells and Granzyme A-expressing CD4+CD161+Ki-67- T cells were correlated with the extent of TB lesions. It is concluded that granzyme K-expressing CD8+ T cell subsets might contribute to protection against tuberculosis dissemination.
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Affiliation(s)
- Jing Jiang
- Institute of Research, Beijing Key Laboratory of Organ Transplantation and Immune Regulation, Senior Department of Respiratory and Critical Care Medicine, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Zhihong Cao
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Li Xiao
- Institute of Research, Beijing Key Laboratory of Organ Transplantation and Immune Regulation, Senior Department of Respiratory and Critical Care Medicine, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Jinwen Su
- Division of Critical Care Medicine, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Jinhe Wang
- Second Division of Tuberculosis, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Jianqin Liang
- Second Division of Tuberculosis, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Bingfen Yang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Yanhua Liu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Fei Zhai
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Ruo Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China
| | - Xiaoxing Cheng
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The Eighth Medical Center of PLA General Hospital, Beijing, China.
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He J, Shen J, Luo W, Han Z, Xie F, Pang T, Liao L, Guo Z, Li J, Li Y, Chen H. Research progress on application of single-cell TCR/BCR sequencing technology to the tumor immune microenvironment, autoimmune diseases, and infectious diseases. Front Immunol 2022; 13:969808. [PMID: 36059506 PMCID: PMC9434330 DOI: 10.3389/fimmu.2022.969808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell omics is the profiling of individual cells through sequencing and other technologies including high-throughput analysis for single-cell resolution, cell classification, and identification as well as time series analyses. Unlike multicellular studies, single-cell omics overcomes the problem of cellular heterogeneity. It provides new methods and perspectives for in-depth analyses of the behavior and mechanism of individual cells in the cell population and their relationship with the body, and plays an important role in basic research and precision medicine. Single-cell sequencing technologies mainly include single-cell transcriptome sequencing, single-cell assay for transposase accessible chromatin with high-throughput sequencing, single-cell immune profiling (single-cell T-cell receptor [TCR]/B-cell receptor [BCR] sequencing), and single-cell transcriptomics. Single-cell TCR/BCR sequencing can be used to obtain a large amount of single-cell gene expression and immunomics data at one time, and combined with transcriptome sequencing and TCR/BCR diversity data, can resolve immune cell heterogeneity. This paper summarizes the progress in applying single-cell TCR/BCR sequencing technology to the tumor immune microenvironment, autoimmune diseases, infectious diseases, immunotherapy, and chronic inflammatory diseases, and discusses its shortcomings and prospects for future application.
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Affiliation(s)
- Jinhua He
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
| | - Jian Shen
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
| | - Wenfeng Luo
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
| | - Zeping Han
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
| | - Fangmei Xie
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
| | - Ting Pang
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
| | - Liyin Liao
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
| | - Zhonghui Guo
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
| | - Jianhao Li
- Institute of Cardiovascular Medicine, Central Hospital of Panyu District, Guangzhou, China
- *Correspondence: Hanwei Chen, ; Yuguang Li, ; Jianhao Li,
| | - Yuguang Li
- Administrative Office, He Xian Memorial Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Hanwei Chen, ; Yuguang Li, ; Jianhao Li,
| | - Hanwei Chen
- Central Laboratory, Central Hospital of Panyu District, Guangzhou, China
- Medical Imaging Institute of Panyu, Central Hospital of Panyu District, Guangzhou, China
- *Correspondence: Hanwei Chen, ; Yuguang Li, ; Jianhao Li,
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