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Khan SU, Huang Y, Ali H, Ali I, Ahmad S, Khan SU, Hussain T, Ullah M, Lu K. Single-cell RNA Sequencing (scRNA-seq): Advances and Challenges for Cardiovascular Diseases (CVDs). Curr Probl Cardiol 2024; 49:102202. [PMID: 37967800 DOI: 10.1016/j.cpcardiol.2023.102202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 11/17/2023]
Abstract
Implementing Single-cell RNA sequencing (scRNA-seq) has significantly enhanced our comprehension of cardiovascular diseases (CVDs), providing new opportunities to strengthen the prevention of CVDs progression. Cardiovascular diseases continue to be the primary cause of death worldwide. Improving treatment strategies and patient risk assessment requires a deeper understanding of the fundamental mechanisms underlying these disorders. The advanced and widespread use of Single-cell RNA sequencing enables a comprehensive investigation of the complex cellular makeup of the heart, surpassing essential descriptive aspects. This enhances our understanding of disease causes and directs functional research. The significant advancement in understanding cellular phenotypes has enhanced the study of fundamental cardiovascular science. scRNA-seq enables the identification of discrete cellular subgroups, unveiling previously unknown cell types in the heart and vascular systems that may have relevance to different disease pathologies. Moreover, scRNA-seq has revealed significant heterogeneity in phenotypes among distinct cell subtypes. Finally, we will examine current and upcoming scRNA-seq studies about various aspects of the cardiovascular system, assessing their potential impact on our understanding of the cardiovascular system and offering insight into how these technologies may revolutionise the diagnosis and treatment of cardiac conditions.
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Affiliation(s)
- Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China; Women Medical and Dental College, Khyber Medical University, Peshawar, KPK, 22020, Pakistan
| | - Yuqing Huang
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China; Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Hamid Ali
- Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad-44000
| | - Ijaz Ali
- Centre for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Hawally 32093, Kuwait
| | - Saleem Ahmad
- Cardiovascular Center of Excellence, Louisiana State University Health Sciences Center, New Orleans 70112 LA, USA
| | - Safir Ullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Talib Hussain
- Women Dental College Abbottabad, KPK, 22020, Pakistan
| | - Muneeb Ullah
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, KPK, Pakistan
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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2
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Hou P, Fang J, Liu Z, Shi Y, Agostini M, Bernassola F, Bove P, Candi E, Rovella V, Sica G, Sun Q, Wang Y, Scimeca M, Federici M, Mauriello A, Melino G. Macrophage polarization and metabolism in atherosclerosis. Cell Death Dis 2023; 14:691. [PMID: 37863894 PMCID: PMC10589261 DOI: 10.1038/s41419-023-06206-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/22/2023]
Abstract
Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of fatty deposits in the inner walls of vessels. These plaques restrict blood flow and lead to complications such as heart attack or stroke. The development of atherosclerosis is influenced by a variety of factors, including age, genetics, lifestyle, and underlying health conditions such as high blood pressure or diabetes. Atherosclerotic plaques in stable form are characterized by slow growth, which leads to luminal stenosis, with low embolic potential or in unstable form, which contributes to high risk for thrombotic and embolic complications with rapid clinical onset. In this complex scenario of atherosclerosis, macrophages participate in the whole process, including the initiation, growth and eventually rupture and wound healing stages of artery plaque formation. Macrophages in plaques exhibit high heterogeneity and plasticity, which affect the evolving plaque microenvironment, e.g., leading to excessive lipid accumulation, cytokine hyperactivation, hypoxia, apoptosis and necroptosis. The metabolic and functional transitions of plaque macrophages in response to plaque microenvironmental factors not only influence ongoing and imminent inflammatory responses within the lesions but also directly dictate atherosclerotic progression or regression. In this review, we discuss the origin of macrophages within plaques, their phenotypic diversity, metabolic shifts, and fate and the roles they play in the dynamic progression of atherosclerosis. It also describes how macrophages interact with other plaque cells, particularly T cells. Ultimately, targeting pathways involved in macrophage polarization may lead to innovative and promising approaches for precision medicine. Further insights into the landscape and biological features of macrophages within atherosclerotic plaques may offer valuable information for optimizing future clinical treatment for atherosclerosis by targeting macrophages.
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Affiliation(s)
- Pengbo Hou
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
- The First Affiliated Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou, China
| | - Jiankai Fang
- The First Affiliated Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou, China
| | - Zhanhong Liu
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
- The First Affiliated Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou, China
| | - Yufang Shi
- The First Affiliated Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou, China
| | - Massimiliano Agostini
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Pierluigi Bove
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Valentina Rovella
- Department of System Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giuseppe Sica
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Qiang Sun
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
- The First Affiliated Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou, China
| | - Ying Wang
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
- The First Affiliated Hospital of Soochow University, Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College of Soochow University, Suzhou, China
| | - Manuel Scimeca
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Massimo Federici
- Department of System Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Alessandro Mauriello
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy.
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy.
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3
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Makinde HKM, Dunn JLM, Gadhvi G, Carns M, Aren K, Chung AH, Muhammad LN, Song J, Cuda CM, Dominguez S, Pandolfino JE, Dematte D’Amico JE, Budinger GS, Assassi S, Frech TM, Khanna D, Shaeffer A, Perlman H, Hinchcliff M, Winter DR. Three Distinct Transcriptional Profiles of Monocytes Associate with Disease Activity in Scleroderma Patients. Arthritis Rheumatol 2023; 75:595-608. [PMID: 36281773 PMCID: PMC10165944 DOI: 10.1002/art.42380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Patients with diffuse cutaneous systemic sclerosis (dcSSc) display a complex clinical phenotype. Transcriptional profiling of whole blood or tissue from patients are affected by changes in cellular composition that drive gene expression and an inability to detect minority cell populations. We undertook this study to focus on the 2 main subtypes of circulating monocytes, classical monocytes (CMs) and nonclassical monocytes (NCMs) as a biomarker of SSc disease severity. METHODS SSc patients were recruited from the Prospective Registry for Early Systemic Sclerosis. Clinical data were collected, as well as peripheral blood for isolation of CMs and NCMs. Age-, sex-, and race-matched healthy volunteers were recruited as controls. Bulk macrophages were isolated from the skin in a separate cohort. All samples were assayed by RNA sequencing (RNA-seq). RESULTS We used an unbiased approach to cluster patients into 3 groups (groups A-C) based on the transcriptional signatures of CMs relative to controls. Each group maintained their characteristic transcriptional signature in NCMs. Genes up-regulated in group C demonstrated the highest expression compared to the other groups in SSc skin macrophages, relative to controls. Patients from groups B and C exhibited worse lung function than group A, although there was no difference in SSc skin disease at baseline, relative to controls. We validated our approach by applying our group classifications to published bulk monocyte RNA-seq data from SSc patients, and we found that patients without skin disease were most likely to be classified as group A. CONCLUSION We are the first to show that transcriptional signatures of CMs and NCMs can be used to unbiasedly stratify SSc patients and correlate with disease activity outcome measures.
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Affiliation(s)
- Hadijat-Kubura M. Makinde
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Julia L. M. Dunn
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
- Cincinnati Children’s Hospital Medical Center, Division of Allergy & Immunology. Cincinnati, OH 45229 (current affiliation)
| | - Gaurav Gadhvi
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Mary Carns
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Kathleen Aren
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Anh H. Chung
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Lutfiyya N. Muhammad
- Northwestern University, Feinberg School of Medicine Department of Preventive Medicine. Chicago, IL 60611
| | - Jing Song
- Northwestern University, Feinberg School of Medicine Department of Preventive Medicine. Chicago, IL 60611
| | - Carla M. Cuda
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Salina Dominguez
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - John E. Pandolfino
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Gastroenterology and Hepatology. Chicago, IL 60611
| | - Jane E. Dematte D’Amico
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Division of Pulmonary and Critical Care. Chicago, IL 60611
| | - G. Scott Budinger
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Division of Pulmonary and Critical Care. Chicago, IL 60611
| | - Shervin Assassi
- Prospective Registry of Early Systemic Sclerosis (PRESS) consortium. Shervin Assassi MD MS- University of Texas Health Sciences Center at Houston (TX), Elana Bernstein MD MS- Columbia University (NY), Robyn Domsic MD MS - University of Pittsburgh (PA), Tracy Frech MD MS - University of Utah (UT), Jessica Gordon - Hospital for Special Surgery (NY), Faye Hant - Medical University of South Carolina (SC), Monique Hinchcliff – Yale School of Medicine (CT), Dinesh Khanna MD MS - University of Michigan (MI), Ami Shah - Johns Hopkins University (MD), Victoria Shanmugam - George Washington University (DC)
- University of Texas Health Science Center at Houston, Division of Rheumatology, Houston, Texas 77030
| | - Tracy M. Frech
- Prospective Registry of Early Systemic Sclerosis (PRESS) consortium. Shervin Assassi MD MS- University of Texas Health Sciences Center at Houston (TX), Elana Bernstein MD MS- Columbia University (NY), Robyn Domsic MD MS - University of Pittsburgh (PA), Tracy Frech MD MS - University of Utah (UT), Jessica Gordon - Hospital for Special Surgery (NY), Faye Hant - Medical University of South Carolina (SC), Monique Hinchcliff – Yale School of Medicine (CT), Dinesh Khanna MD MS - University of Michigan (MI), Ami Shah - Johns Hopkins University (MD), Victoria Shanmugam - George Washington University (DC)
- Vanderbilt University, Department of Medicine, Division of Rheumatology and Immunology. Nashville, TN 37232
| | - Dinesh Khanna
- Prospective Registry of Early Systemic Sclerosis (PRESS) consortium. Shervin Assassi MD MS- University of Texas Health Sciences Center at Houston (TX), Elana Bernstein MD MS- Columbia University (NY), Robyn Domsic MD MS - University of Pittsburgh (PA), Tracy Frech MD MS - University of Utah (UT), Jessica Gordon - Hospital for Special Surgery (NY), Faye Hant - Medical University of South Carolina (SC), Monique Hinchcliff – Yale School of Medicine (CT), Dinesh Khanna MD MS - University of Michigan (MI), Ami Shah - Johns Hopkins University (MD), Victoria Shanmugam - George Washington University (DC)
- University of Michigan, Department of Medicine, Division of Rheumatology. Ann Arbor, MI 48109
| | - Alex Shaeffer
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Harris Perlman
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
| | - Monique Hinchcliff
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
- Prospective Registry of Early Systemic Sclerosis (PRESS) consortium. Shervin Assassi MD MS- University of Texas Health Sciences Center at Houston (TX), Elana Bernstein MD MS- Columbia University (NY), Robyn Domsic MD MS - University of Pittsburgh (PA), Tracy Frech MD MS - University of Utah (UT), Jessica Gordon - Hospital for Special Surgery (NY), Faye Hant - Medical University of South Carolina (SC), Monique Hinchcliff – Yale School of Medicine (CT), Dinesh Khanna MD MS - University of Michigan (MI), Ami Shah - Johns Hopkins University (MD), Victoria Shanmugam - George Washington University (DC)
- Yale University, School of Medicine, Section of Rheumatology, Allergy & Immunology. New Haven, CT 06520
| | - Deborah R. Winter
- Northwestern University, Feinberg School of Medicine Department of Medicine, Division of Rheumatology. Chicago, IL 60611
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4
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Yu L, Zhang Y, Liu C, Wu X, Wang S, Sui W, Zhang Y, Zhang C, Zhang M. Heterogeneity of macrophages in atherosclerosis revealed by single-cell RNA sequencing. FASEB J 2023; 37:e22810. [PMID: 36786718 DOI: 10.1096/fj.202201932rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/15/2023]
Abstract
Technology at the single-cell level has advanced dramatically in characterizing molecular heterogeneity. These technologies have enabled cell subtype diversity to be seen in all tissues, including atherosclerotic plaques. Critical in atherosclerosis pathogenesis and progression are macrophages. Previous studies have only determined macrophage phenotypes within the plaque, mainly by bulk analysis. However, recent progress in single-cell technologies now enables the comprehensive mapping of macrophage subsets and phenotypes present in plaques. In this review, we have updated and discussed the definition and classification of macrophage subsets in mice and humans using single-cell RNA sequencing. We summarized the different classification methods and perspectives: traditional classification with an updated scoring system, inflammatory macrophages, foamy macrophages, and atherosclerotic-resident macrophages. In addition, some special types of macrophages were identified by specific markers, including IFN-inducible and cavity macrophages. Furthermore, we discussed macrophage subset-specific markers and their functions. In the future, these novel insights into the characteristics and phenotypes of these macrophage subsets within atherosclerotic plaques can provide additional therapeutic targets for cardiovascular diseases.
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Affiliation(s)
- Liwen Yu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yujie Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Changhao Liu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiao Wu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shasha Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenhai Sui
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Cheng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Meng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
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5
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Ke Y, Jian-yuan H, Ping Z, Yue W, Na X, Jian Y, Kai-xuan L, Yi-fan S, Han-bin L, Rong L. The progressive application of single-cell RNA sequencing technology in cardiovascular diseases. Biomed Pharmacother 2022; 154:113604. [DOI: 10.1016/j.biopha.2022.113604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/02/2022] Open
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6
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Abstract
PURPOSE OF REVIEW Myeloid cells - granulocytes, monocytes, macrophages and dendritic cells (DCs) - are innate immune cells that play key roles in pathogen defense and inflammation, as well as in tissue homeostasis and repair. Over the past 5 years, in part due to more widespread use of single cell omics technologies, it has become evident that these cell types are significantly more heterogeneous than was previously appreciated. In this review, we consider recent studies that have demonstrated heterogeneity among neutrophils, monocytes, macrophages and DCs in mice and humans. We also discuss studies that have revealed the sources of their heterogeneity. RECENT FINDINGS Recent studies have confirmed that ontogeny is a key determinant of diversity, with specific subsets of myeloid cells arising from distinct progenitors. However, diverse microenvironmental cues also strongly influence myeloid fate and function. Accumulating evidence therefore suggests that a combination of these mechanisms underlies myeloid cell diversity. SUMMARY Consideration of the heterogeneity of myeloid cells is critical for understanding their diverse activities, such as the role of macrophages in tissue damage versus repair, or tumor growth versus elimination. Insights into these mechanisms are informing the design of novel therapeutic approaches.
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Affiliation(s)
- Alberto Yáñez
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Cristina Bono
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Helen S. Goodridge
- Board of Governors Regenerative Medicine Institute and Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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7
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Shi W, Ye J, Shi Z, Pan C, Zhang Q, Lin Y, Luo Y, Su W, Zheng Y, Liu Y. Chromatin accessibility analysis reveals regulatory dynamics and therapeutic relevance of Vogt-Koyanagi-Harada disease. Commun Biol 2022; 5:506. [PMID: 35618758 PMCID: PMC9135711 DOI: 10.1038/s42003-022-03430-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/29/2022] [Indexed: 12/19/2022] Open
Abstract
The barrier to curing Vogt-Koyanagi-Harada disease (VKH) is thought to reside in a lack of understanding in the roles and regulations of peripheral inflammatory immune cells. Here we perform a single-cell multi-omic study of 166,149 cells in peripheral blood mononuclear cells from patients with VKH, profile the chromatin accessibility and gene expression in the same blood samples, and uncover prominent cellular heterogeneity. Immune cells in VKH blood are highly activated and pro-inflammatory. Notably, we describe an enrichment of transcription targets for nuclear factor kappa B in conventional dendritic cells (cDCs) that governed inflammation. Integrative analysis of transcriptomic and chromatin maps shows that the RELA in cDCs is related to disease complications and poor prognosis. Ligand-receptor interaction pairs also identify cDC as an important predictor that regulated multiple immune subsets. Our results reveal epigenetic and transcriptional dynamics in auto-inflammation, especially the cDC subtype that might lead to therapeutic strategies in VKH.
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Affiliation(s)
- Wen Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100085, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jinguo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhuoxing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Caineng Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Qikai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yuheng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yuanting Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China. .,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100085, China. .,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China.
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100085, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
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8
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Brian BF, Sauer ML, Greene JT, Senevirathne SE, Lindstedt AJ, Funk OL, Ruis BL, Ramirez LA, Auger JL, Swanson WL, Nunez MG, Moriarity BS, Lowell CA, Binstadt BA, Freedman TS. A dominant function of LynB kinase in preventing autoimmunity. SCIENCE ADVANCES 2022; 8:eabj5227. [PMID: 35452291 PMCID: PMC9032976 DOI: 10.1126/sciadv.abj5227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Here, we report that the LynB splice variant of the Src-family kinase Lyn exerts a dominant immunosuppressive function in vivo, whereas the LynA isoform is uniquely required to restrain autoimmunity in female mice. We used CRISPR-Cas9 gene editing to constrain lyn splicing and expression, generating single-isoform LynA knockout (LynAKO) or LynBKO mice. Autoimmune disease in total LynKO mice is characterized by production of antinuclear antibodies, glomerulonephritis, impaired B cell development, and overabundance of activated B cells and proinflammatory myeloid cells. Expression of LynA or LynB alone uncoupled the developmental phenotype from the autoimmune disease: B cell transitional populations were restored, but myeloid cells and differentiated B cells were dysregulated. These changes were isoform-specific, sexually dimorphic, and distinct from the complete LynKO. Despite the apparent differences in disease etiology and penetrance, loss of either LynA or LynB had the potential to induce severe autoimmune disease with parallels to human systemic lupus erythematosus (SLE).
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Affiliation(s)
- Ben F. Brian
- Graduate Program in Molecular Pharmacology and Therapeutics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Monica L. Sauer
- Graduate Program in Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joseph T. Greene
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - S. Erandika Senevirathne
- Graduate Program in Molecular Pharmacology and Therapeutics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anders J. Lindstedt
- Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, Minneapolis, MN 55455, USA
- Medical Scientist Training Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Olivia L. Funk
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian L. Ruis
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Luis A. Ramirez
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jennifer L. Auger
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Whitney L. Swanson
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Myra G. Nunez
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Branden S. Moriarity
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Clifford A. Lowell
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bryce A. Binstadt
- Department of Pediatrics, Division of Rheumatology, Allergy and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tanya S. Freedman
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Autoimmune Diseases Research, University of Minnesota, Minneapolis, MN 55455, USA
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9
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Barvalia M, Harder KW. An End-to-End Workflow for Interrogating Tumor-Infiltrating Myeloid Cells Using Mass Cytometry. Methods Mol Biol 2022; 2508:147-168. [PMID: 35737239 DOI: 10.1007/978-1-0716-2376-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Myeloid cells are a highly heterogeneous group of innate immune cells which include a diverse collection of cell types and cell states. Distinct subsets can impact tumor progression differently, with conventional type 1 DCs important in protective anti-tumor immune responses, while immunosuppressive tumor-associated macrophages and myeloid-derived suppressive cells (MDSCs) play tumor-promoting roles. Deep phenotyping of myeloid cells using single-cell technologies such as mass cytometry provides the unprecedented opportunity to comprehensively characterize the underlying heterogeneity of myeloid cells. Here we provide a detailed end-to-end workflow including both experimental and computational protocols enabling deep phenotyping of tumor-infiltrating myeloid cells using mass cytometry. A protocol that facilitates interrogation of phosphoproteins in circulating and tumor-infiltrating myeloid cells has been provided together with detailed scripts for Phenograph analysis of tumor-infiltrating myeloid cells.
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Affiliation(s)
- Maunish Barvalia
- Life Science Institute, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Kenneth W Harder
- Life Science Institute, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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10
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Talker SC, Barut GT, Lischer HE, Rufener R, von Münchow L, Bruggmann R, Summerfield A. Monocyte biology conserved across species: Functional insights from cattle. Front Immunol 2022; 13:889175. [PMID: 35967310 PMCID: PMC9373011 DOI: 10.3389/fimmu.2022.889175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Similar to human monocytes, bovine monocytes can be split into CD14highCD16- classical, CD14highCD16high intermediate and CD14-/dimCD16high nonclassical monocytes (cM, intM, and ncM, respectively). Here, we present an in-depth analysis of their steady-state bulk- and single-cell transcriptomes, highlighting both pronounced functional specializations and transcriptomic relatedness. Bulk gene transcription indicates pro-inflammatory and antibacterial roles of cM, while ncM and intM appear to be specialized in regulatory/anti-inflammatory functions and tissue repair, as well as antiviral responses and T-cell immunomodulation. Notably, intM stood out by high expression of several genes associated with antigen presentation. Anti-inflammatory and antiviral functions of ncM are further supported by dominant oxidative phosphorylation and selective strong responses to TLR7/8 ligands, respectively. Moreover, single-cell RNA-seq revealed previously unappreciated heterogeneity within cM and proposes intM as a transient differentiation intermediate between cM and ncM.
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Affiliation(s)
- Stephanie C. Talker
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- *Correspondence: Stephanie C. Talker,
| | - G. Tuba Barut
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Heidi E.L. Lischer
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Reto Rufener
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Artur Summerfield
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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11
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Vinci R, Pedicino D, Bonanni A, D'Aiello A, Severino A, Pisano E, Ponzo M, Canonico F, Ciampi P, Russo G, Di Sario M, Montone RA, Trani C, Conte C, Grimaldi MC, Cribari F, Massetti M, Crea F, Liuzzo G. A Novel Monocyte Subset as a Unique Signature of Atherosclerotic Plaque Rupture. Front Cell Dev Biol 2021; 9:753223. [PMID: 34712669 PMCID: PMC8545820 DOI: 10.3389/fcell.2021.753223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/03/2021] [Indexed: 12/28/2022] Open
Abstract
The evaluation of monocyte subset distribution among acute coronary syndrome (ACS) patients according to culprit coronary plaque morphology has never been explored. We evaluated whether there were significant differences in frequency of circulating monocyte subsets isolated from ACS patients according to optical coherence tomography (OCT) investigation of plaque erosion and rupture. We enrolled 74 patients with non-ST-elevation ACS (NSTE-ACS), 21 of them underwent OCT investigation of the culprit coronary plaque and local macrophage infiltration (MØI) assessment. As control, we enrolled 30 chronic coronary syndrome (CCS) patients. We assessed the frequency of monocyte subsets in the whole study population, in reliance on their CD14 and CD16 expression (classical, CM: CD14++CD16–; intermediates, IM: CD14++CD16+; non-classical, NCM: CD14+CD16++). Then, we tested the effect of lipopolysaccharide (LPS) (a CD14 ligand) on peripheral blood mononuclear cells (PBMCs) of NSTE-ACS patients, quantifying the inflammatory cytokine levels in cell-culture supernatants. Our data proved that monocyte subsets isolated from NSTE-ACS patients represent a peculiar biological signature of the pathophysiological mechanism lying beneath atherosclerotic plaque with a ruptured fibrous cap (RFC) as compared with plaque erosion. Moreover, the magnitude of LPS-mediated effects on IL-1β, IL-6, and IL-10 cytokine release in cell-culture supernatants appeared to be greater in NSTE-ACS patients with RFC. Finally, we described a fourth monocyte population never explored before in this clinical setting (pre-classical monocytes, PCM: CD14+CD16–) that was prevalent in NSTE-ACS patients as compared with CCS and, especially, in patients with RFC and culprit plaque with MØI.
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Affiliation(s)
- Ramona Vinci
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Daniela Pedicino
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy.,Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alice Bonanni
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Alessia D'Aiello
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Anna Severino
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Eugenia Pisano
- Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Myriana Ponzo
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Francesco Canonico
- Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Pellegrino Ciampi
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Giulio Russo
- Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Marianna Di Sario
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Rocco Antonio Montone
- Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Carlo Trani
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy.,Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Cristina Conte
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Maria Chiara Grimaldi
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Francesco Cribari
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy
| | - Massimo Massetti
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy.,Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Filippo Crea
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy.,Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giovanna Liuzzo
- Department of Cardiovascular and Pneumological Sciences, Catholic University of the Sacred Heart, Rome, Italy.,Department of Cardiovascular Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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12
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Kan H, Zhang K, Mao A, Geng L, Gao M, Feng L, You Q, Ma X. Single-cell transcriptome analysis reveals cellular heterogeneity in the ascending aortas of normal and high-fat diet-fed mice. Exp Mol Med 2021; 53:1379-1389. [PMID: 34548614 PMCID: PMC8492660 DOI: 10.1038/s12276-021-00671-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 01/26/2023] Open
Abstract
The aorta contains numerous cell types that contribute to vascular inflammation and thus the progression of aortic diseases. However, the heterogeneity and cellular composition of the ascending aorta in the setting of a high-fat diet (HFD) have not been fully assessed. We performed single-cell RNA sequencing on ascending aortas from mice fed a normal diet and mice fed a HFD. Unsupervised cluster analysis of the transcriptional profiles from 24,001 aortic cells identified 27 clusters representing 10 cell types: endothelial cells (ECs), fibroblasts, vascular smooth muscle cells (SMCs), immune cells (B cells, T cells, macrophages, and dendritic cells), mesothelial cells, pericytes, and neural cells. After HFD intake, subpopulations of endothelial cells with lipid transport and angiogenesis capacity and extensive expression of contractile genes were defined. In the HFD group, three major SMC subpopulations showed increased expression of extracellular matrix-degradation genes, and a synthetic SMC subcluster was proportionally increased. This increase was accompanied by upregulation of proinflammatory genes. Under HFD conditions, aortic-resident macrophage numbers were increased, and blood-derived macrophages showed the strongest expression of proinflammatory cytokines. Our study elucidates the nature and range of the cellular composition of the ascending aorta and increases understanding of the development and progression of aortic inflammatory disease.
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Affiliation(s)
- Hao Kan
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Ka Zhang
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Aiqin Mao
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Li Geng
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Mengru Gao
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Lei Feng
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Qingjun You
- Department of Thoracic Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Xin Ma
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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13
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Fu M, Song J. Single-Cell Transcriptomics Reveals the Cellular Heterogeneity of Cardiovascular Diseases. Front Cardiovasc Med 2021; 8:643519. [PMID: 34179129 PMCID: PMC8225933 DOI: 10.3389/fcvm.2021.643519] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/13/2021] [Indexed: 12/23/2022] Open
Abstract
"A world in a wild flower, and a bodhi in a leaf," small cells contain huge secrets. The vasculature is composed of many multifunctional cell subpopulations, each of which is involved in the occurrence and development of cardiovascular diseases. Single-cell transcriptomics captures the full picture of genes expressed within individual cells, identifies rare or de novo cell subpopulations, analyzes single-cell trajectory and stem cell or progenitor cell lineage conversion, and compares healthy tissue and disease-related tissue at single-cell resolution. Single-cell transcriptomics has had a profound effect on the field of cardiovascular research over the past decade, as evidenced by the construction of cardiovascular cell landscape, as well as the clarification of cardiovascular diseases and the mechanism of stem cell or progenitor cell differentiation. The classification and proportion of cell subpopulations in vasculature vary with species, location, genotype, and disease, exhibiting unique gene expression characteristics in organ development, disease progression, and regression. Specific gene markers are expected to be the diagnostic criteria, therapeutic targets, or prognostic indicators of diseases. Therefore, treatment of vascular disease still has lots of potentials to develop. Herein, we summarize the cell clusters and gene expression patterns in normal vasculature and atherosclerosis, aortic aneurysm, and pulmonary hypertension to reveal vascular heterogeneity and new regulatory factors of cardiovascular disease in the use of single-cell transcriptomics and discuss its current limitations and promising clinical potential.
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Affiliation(s)
- Mengxia Fu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- The Cardiomyopathy Research Group at Fuwai Hospital, Beijing, China
| | - 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, China
- The Cardiomyopathy Research Group at Fuwai Hospital, Beijing, China
- Department of Cardiovascular Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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14
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Andueza A, Kumar S, Kim J, Kang DW, Mumme HL, Perez JI, Villa-Roel N, Jo H. Endothelial Reprogramming by Disturbed Flow Revealed by Single-Cell RNA and Chromatin Accessibility Study. Cell Rep 2020; 33:108491. [PMID: 33326796 PMCID: PMC7801938 DOI: 10.1016/j.celrep.2020.108491] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/26/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
Disturbed flow (d-flow) induces atherosclerosis by regulating gene expression in endothelial cells (ECs). For further mechanistic understanding, we carried out a single-cell RNA sequencing (scRNA-seq) and scATAC-seq study using endothelial-enriched single cells from the left- and right carotid artery exposed to d-flow (LCA) and stable-flow (s-flow in RCA) using the mouse partial carotid ligation (PCL) model. We find eight EC clusters along with immune cells, fibroblasts, and smooth muscle cells. Analyses of marker genes, pathways, and pseudotime reveal that ECs are highly heterogeneous and plastic. D-flow induces a dramatic transition of ECs from atheroprotective phenotypes to pro-inflammatory cells, mesenchymal (EndMT) cells, hematopoietic stem cells, endothelial stem/progenitor cells, and an unexpected immune cell-like (EndICLT) phenotypes. While confirming KLF4/KLF2 as an s-flow-sensitive transcription factor binding site, we also find those sensitive to d-flow (RELA, AP1, STAT1, and TEAD1). D-flow reprograms ECs from atheroprotective to proatherogenic phenotypes, including EndMT and potentially EndICLT.
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Affiliation(s)
- Aitor Andueza
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Juyoung Kim
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Dong-Won Kang
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Hope L Mumme
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Julian I Perez
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Nicolas Villa-Roel
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Emory University, Atlanta, GA, USA.
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15
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Kott KA, Vernon ST, Hansen T, de Dreu M, Das SK, Powell J, Fazekas de St Groth B, Di Bartolo BA, McGuire HM, Figtree GA. Single-Cell Immune Profiling in Coronary Artery Disease: The Role of State-of-the-Art Immunophenotyping With Mass Cytometry in the Diagnosis of Atherosclerosis. J Am Heart Assoc 2020; 9:e017759. [PMID: 33251927 PMCID: PMC7955359 DOI: 10.1161/jaha.120.017759] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coronary artery disease remains the leading cause of death globally and is a major burden to every health system in the world. There have been significant improvements in risk modification, treatments, and mortality; however, our ability to detect asymptomatic disease for early intervention remains limited. Recent discoveries regarding the inflammatory nature of atherosclerosis have prompted investigation into new methods of diagnosis and treatment of coronary artery disease. This article reviews some of the highlights of the important developments in cardioimmunology and summarizes the clinical evidence linking the immune system and atherosclerosis. It provides an overview of the major serological biomarkers that have been associated with atherosclerosis, noting the limitations of these markers attributable to low specificity, and then contrasts these serological markers with the circulating immune cell subtypes that have been found to be altered in coronary artery disease. This review then outlines the technique of mass cytometry and its ability to provide high-dimensional single-cell data and explores how this high-resolution quantification of specific immune cell subpopulations may assist in the diagnosis of early atherosclerosis in combination with other complimentary techniques such as single-cell RNA sequencing. We propose that this improved specificity has the potential to transform the detection of coronary artery disease in its early phases, facilitating targeted preventative approaches in the precision medicine era.
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Affiliation(s)
- Katharine A Kott
- Cardiothoracic and Vascular Health Kolling Institute of Medical Research Sydney Australia.,Department of Cardiology Royal North Shore Hospital Northern Sydney Local Health District Sydney Australia.,School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia
| | - Stephen T Vernon
- Cardiothoracic and Vascular Health Kolling Institute of Medical Research Sydney Australia.,Department of Cardiology Royal North Shore Hospital Northern Sydney Local Health District Sydney Australia.,School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia
| | - Thomas Hansen
- Cardiothoracic and Vascular Health Kolling Institute of Medical Research Sydney Australia.,School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia
| | - Macha de Dreu
- School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia.,Ramaciotti Facility for Human Systems Biology Charles Perkins Centre University of Sydney Sydney Australia
| | - Souvik K Das
- Department of Cardiology Royal North Shore Hospital Northern Sydney Local Health District Sydney Australia
| | - Joseph Powell
- Garvan-Weizmann Centre for Cellular Genomics Garvan Institute Sydney Australia.,UNSW Cellular Genomics Futures Institute University of New South Wales Sydney Australia
| | - Barbara Fazekas de St Groth
- School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia.,Ramaciotti Facility for Human Systems Biology Charles Perkins Centre University of Sydney Sydney Australia.,Charles Perkins Centre University of Sydney Sydney Australia
| | - Belinda A Di Bartolo
- Cardiothoracic and Vascular Health Kolling Institute of Medical Research Sydney Australia
| | - Helen M McGuire
- School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia.,Ramaciotti Facility for Human Systems Biology Charles Perkins Centre University of Sydney Sydney Australia.,Charles Perkins Centre University of Sydney Sydney Australia
| | - Gemma A Figtree
- Cardiothoracic and Vascular Health Kolling Institute of Medical Research Sydney Australia.,Department of Cardiology Royal North Shore Hospital Northern Sydney Local Health District Sydney Australia.,School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia.,Charles Perkins Centre University of Sydney Sydney Australia
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16
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Affiliation(s)
- Rajat M Gupta
- From the Division of Cardiovascular Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Vivian S Lee-Kim
- From the Division of Cardiovascular Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Peter Libby
- From the Division of Cardiovascular Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
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17
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Xiang Y, Liang B, Zhang X, Zheng F. Lower HDL-C levels are associated with higher expressions of CD16 on monocyte subsets in coronary atherosclerosis. Int J Med Sci 2020; 17:2171-2179. [PMID: 32922178 PMCID: PMC7484662 DOI: 10.7150/ijms.47998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/29/2020] [Indexed: 01/17/2023] Open
Abstract
Background: Increased expressions of CD16 on classical monocytes precede their transition to intermediate monocytes. Thus far, the influence of lipids on the expression of CD14 and CD16 on monocyte subsets in coronary atherosclerosis (CA) remains unclear. The aim of this study was to investigate the underlying association between blood lipids and the expression of CD14 and CD16 on monocyte subsets. Methods: This study enrolled 112 healthy controls and 110 CA patients. Monocyte subsets [CD14++CD16- (classical), CD14++CD16+ (intermediate) and CD14+CD16++ (non-classical)] were analyzed by flow cytometry. Median fluorescent intensity (MFI) was used to evaluate the expression levels of CD14 and CD16 on monocyte subsets. Results: Compared with the control group, the expression of CD16 was significantly increased on all three monocyte subsets in the patient group. Correlation analysis revealed that serum HDL-C was inversely associated with the expression of CD16 on intermediate monocytes after Bonferroni correction in the control group. In addition, a significant decrease in classical monocytes and an increase in intermediate monocytes were detected in patients. In linear regression analysis, intermediate monocytes showed an inverse association with serum HDL-C in the control group. Although CD14 was correlated with serum TC and HDL-C, there was no statistical difference in CD14 expression between the two groups. Conclusion: Low serum HDL-C may induce upregulation of CD16 on classical monocytes, which may in turn lead to the increase of intermediate monocytes in coronary atherosclerosis patients.
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Affiliation(s)
- Yang Xiang
- Center for Gene Diagnosis, and Clinical Lab, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan 430071, China
| | - Bin Liang
- Center for Gene Diagnosis, and Clinical Lab, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan 430071, China
| | - Xiaokang Zhang
- Center for Gene Diagnosis, and Clinical Lab, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan 430071, China
| | - Fang Zheng
- Center for Gene Diagnosis, and Clinical Lab, Zhongnan Hospital of Wuhan University, Donghu Road 169, Wuhan 430071, China
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