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Kiskin FN, Yang Y, Yang H, Zhang JZ. Cracking the code of the cardiovascular enigma: hPSC-derived endothelial cells unveil the secrets of endothelial dysfunction. J Mol Cell Cardiol 2024; 192:65-78. [PMID: 38761989 DOI: 10.1016/j.yjmcc.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Endothelial dysfunction is a central contributor to the development of most cardiovascular diseases and is characterised by the reduced synthesis or bioavailability of the vasodilator nitric oxide together with other abnormalities such as inflammation, senescence, and oxidative stress. The use of patient-specific and genome-edited human pluripotent stem cell-derived endothelial cells (hPSC-ECs) has shed novel insights into the role of endothelial dysfunction in cardiovascular diseases with strong genetic components such as genetic cardiomyopathies and pulmonary arterial hypertension. However, their utility in studying complex multifactorial diseases such as atherosclerosis, metabolic syndrome and heart failure poses notable challenges. In this review, we provide an overview of the different methods used to generate and characterise hPSC-ECs before comprehensively assessing their effectiveness in cardiovascular disease modelling and high-throughput drug screening. Furthermore, we explore current obstacles that will need to be overcome to unleash the full potential of hPSC-ECs in facilitating patient-specific precision medicine. Addressing these challenges holds great promise in advancing our understanding of intricate cardiovascular diseases and in tailoring personalised therapeutic strategies.
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Affiliation(s)
- Fedir N Kiskin
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Yuan Yang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Hao Yang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Joe Z Zhang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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2
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Chandy M, Hill T, Jimenez-Tellez N, Wu JC, Sarles SE, Hensel E, Wang Q, Rahman I, Conklin DJ. Addressing Cardiovascular Toxicity Risk of Electronic Nicotine Delivery Systems in the Twenty-First Century: "What Are the Tools Needed for the Job?" and "Do We Have Them?". Cardiovasc Toxicol 2024; 24:435-471. [PMID: 38555547 DOI: 10.1007/s12012-024-09850-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Cigarette smoking is positively and robustly associated with cardiovascular disease (CVD), including hypertension, atherosclerosis, cardiac arrhythmias, stroke, thromboembolism, myocardial infarctions, and heart failure. However, after more than a decade of ENDS presence in the U.S. marketplace, uncertainty persists regarding the long-term health consequences of ENDS use for CVD. New approach methods (NAMs) in the field of toxicology are being developed to enhance rapid prediction of human health hazards. Recent technical advances can now consider impact of biological factors such as sex and race/ethnicity, permitting application of NAMs findings to health equity and environmental justice issues. This has been the case for hazard assessments of drugs and environmental chemicals in areas such as cardiovascular, respiratory, and developmental toxicity. Despite these advances, a shortage of widely accepted methodologies to predict the impact of ENDS use on human health slows the application of regulatory oversight and the protection of public health. Minimizing the time between the emergence of risk (e.g., ENDS use) and the administration of well-founded regulatory policy requires thoughtful consideration of the currently available sources of data, their applicability to the prediction of health outcomes, and whether these available data streams are enough to support an actionable decision. This challenge forms the basis of this white paper on how best to reveal potential toxicities of ENDS use in the human cardiovascular system-a primary target of conventional tobacco smoking. We identify current approaches used to evaluate the impacts of tobacco on cardiovascular health, in particular emerging techniques that replace, reduce, and refine slower and more costly animal models with NAMs platforms that can be applied to tobacco regulatory science. The limitations of these emerging platforms are addressed, and systems biology approaches to close the knowledge gap between traditional models and NAMs are proposed. It is hoped that these suggestions and their adoption within the greater scientific community will result in fresh data streams that will support and enhance the scientific evaluation and subsequent decision-making of tobacco regulatory agencies worldwide.
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Affiliation(s)
- Mark Chandy
- Robarts Research Institute, Western University, London, N6A 5K8, Canada
| | - Thomas Hill
- Division of Nonclinical Science, Center for Tobacco Products, US Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Nerea Jimenez-Tellez
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - S Emma Sarles
- Biomedical and Chemical Engineering PhD Program, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Edward Hensel
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Qixin Wang
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Daniel J Conklin
- Division of Environmental Medicine, Department of Medicine, Center for Cardiometabolic Science, Christina Lee Brown Envirome Institute, University of Louisville, 580 S. Preston St., Delia Baxter, Rm. 404E, Louisville, KY, 40202, USA.
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3
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Ream MW, Randolph LN, Jiang Y, Chang Y, Bao X, Lian XL. Direct programming of human pluripotent stem cells into endothelial progenitors with SOX17 and FGF2. Stem Cell Reports 2024; 19:579-595. [PMID: 38518781 PMCID: PMC11096437 DOI: 10.1016/j.stemcr.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/24/2024] Open
Abstract
Transcription factors (TFs) are pivotal in guiding stem cell behavior, including their maintenance and differentiation. Using single-cell RNA sequencing, we investigated TFs expressed in endothelial progenitors (EPs) derived from human pluripotent stem cells (hPSCs) and identified upregulated expression of SOXF factors SOX7, SOX17, and SOX18 in the EP population. To test whether overexpression of these factors increases differentiation efficiency, we established inducible hPSC lines for each SOXF factor and found only SOX17 overexpression robustly increased the percentage of cells expressing CD34 and vascular endothelial cadherin (VEC). Conversely, SOX17 knockdown via CRISPR-Cas13d significantly compromised EP differentiation. Intriguingly, we discovered SOX17 overexpression alone was sufficient to generate CD34+VEC+CD31- cells, and, when combined with FGF2 treatment, more than 90% of CD34+VEC+CD31+ EP was produced. These cells are capable of further differentiating into endothelial cells. These findings underscore an undiscovered role of SOX17 in programming hPSCs toward an EP lineage, illuminating pivotal mechanisms in EP differentiation.
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Affiliation(s)
- Michael W Ream
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Lauren N Randolph
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Yuqian Jiang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Yun Chang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaoping Bao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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Carr SM, Owsiany K, Scrivner O, McLaughlin D, Jo H, Brewster LP, Hekman KE. Hyperoxia impairs induced pluripotent stem cell-derived endothelial cells and drives an atherosclerosis-like transcriptional phenotype. JVS Vasc Sci 2024; 5:100193. [PMID: 38770110 PMCID: PMC11103376 DOI: 10.1016/j.jvssci.2024.100193] [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: 10/23/2023] [Accepted: 01/22/2024] [Indexed: 05/22/2024] Open
Abstract
Background Induced pluripotent stem cells (iPSCs) directed to endothelial identity (iPSC-ECs) are emerging as a potent tool for regenerative medicine in vascular disease. However, iPSC-ECs lose expression of key identity markers under standard in vitro conditions, limiting their clinical applications. Methods To model physiological in vivo conditions, we examined the bioenergetics, presence of key cell markers, and proliferative and angiogenic capacity in iPSC-ECs at late and early passage under hyperoxic (21%) and physiological (4%) oxygen concentrations. Results Physoxia resulted in relative preservation of mitochondrial bioenergetic activity, as well as CD144 expression in late passage iPSC-ECs, but not proliferative capacity or tube formation. Single cell RNA sequencing (scRNA-seq) revealed that late passage hyperoxic iPSC-ECs develop an endothelial-to-mesenchymal phenotype. Comparing scRNA-seq data from iPSC-ECs and from atherosclerotic ECs revealed overlap of their transcriptional phenotypes. Conclusions Taken together, our studies demonstrate that physiological 4% oxygen culture conditions were sufficient to improve mitochondrial function in high passage cells, but alone was insufficient to preserve angiogenic capacity. Furthermore, late passage cells under typical conditions take on an endothelial-to-mesenchymal phenotype with similarities to ECs found in atherosclerosis.
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Affiliation(s)
- Sean M. Carr
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
- Atlanta VA Healthcare System, Surgical and Research Services, Decatur, Georgia
| | - Katherine Owsiany
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
- Atlanta VA Healthcare System, Surgical and Research Services, Decatur, Georgia
| | - Ottis Scrivner
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
- Atlanta VA Healthcare System, Surgical and Research Services, Decatur, Georgia
| | - Dylan McLaughlin
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
- Atlanta VA Healthcare System, Surgical and Research Services, Decatur, Georgia
| | - Hanjoong Jo
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Luke P. Brewster
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
- Atlanta VA Healthcare System, Surgical and Research Services, Decatur, Georgia
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Katherine E. Hekman
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
- Atlanta VA Healthcare System, Surgical and Research Services, Decatur, Georgia
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Wu X, Ni Y, Li W, Yang B, Yang X, Zhu Z, Zhang J, Wu X, Shen Q, Liao Z, Yuan L, Chen Y, Du Q, Wang C, Liu P, Miao Y, Li N, Zhang S, Liao M, Hua J. Rapid conversion of porcine pluripotent stem cells into macrophages with chemically defined conditions. J Biol Chem 2024; 300:105556. [PMID: 38097188 PMCID: PMC10825052 DOI: 10.1016/j.jbc.2023.105556] [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: 08/11/2023] [Revised: 11/19/2023] [Accepted: 11/30/2023] [Indexed: 01/11/2024] Open
Abstract
A renewable source of porcine macrophages derived from pluripotent stem cells (PSCs) would be a valuable alternative to primary porcine alveolar macrophages (PAMs) in the research of host-pathogen interaction mechanisms. We developed an efficient and rapid protocol, within 11 days, to derive macrophages from porcine PSCs (pPSCs). The pPSC-derived macrophages (pPSCdMs) exhibited molecular and functional characteristics of primary macrophages. The pPSCdMs showed macrophage-specific surface protein expression and macrophage-specific transcription factors, similar to PAMs. The pPSCdMs also exhibited the functional characteristics of macrophages, such as endocytosis, phagocytosis, porcine respiratory and reproductive syndrome virus infection and the response to lipopolysaccharide stimulation. Furthermore, we performed transcriptome sequencing of the whole differentiation process to track the fate transitions of porcine PSCs involved in the signaling pathway. The activation of transforming growth factor beta signaling was required for the formation of mesoderm and the inhibition of the transforming growth factor beta signaling pathway at the hematopoietic endothelium stage could enhance the fate transformation of hematopoiesis. In summary, we developed an efficient and rapid protocol to generate pPSCdMs that showed aspects of functional maturity comparable with PAMs. pPSCdMs could provide a broad prospect for the platforms of host-pathogen interaction mechanisms.
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Affiliation(s)
- Xiaolong Wu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Ni
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenhao Li
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bin Yang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinchun Yang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhenshuo Zhu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Juqing Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojie Wu
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiaoyan Shen
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zheng Liao
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Liming Yuan
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yunlong Chen
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qian Du
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengbao Wang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Pentao Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yiliang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Na Li
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shiqiang Zhang
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China.
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jinlian Hua
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, China.
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Chen W, Li C, Chen Y, Bin J, Chen Y. Cardiac cellular diversity and functionality in cardiac repair by single-cell transcriptomics. Front Cardiovasc Med 2023; 10:1237208. [PMID: 37920179 PMCID: PMC10619858 DOI: 10.3389/fcvm.2023.1237208] [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: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
Cardiac repair after myocardial infarction (MI) is orchestrated by multiple intrinsic mechanisms in the heart. Identifying cardiac cell heterogeneity and its effect on processes that mediate the ischemic myocardium repair may be key to developing novel therapeutics for preventing heart failure. With the rapid advancement of single-cell transcriptomics, recent studies have uncovered novel cardiac cell populations, dynamics of cell type composition, and molecular signatures of MI-associated cells at the single-cell level. In this review, we summarized the main findings during cardiac repair by applying single-cell transcriptomics, including endogenous myocardial regeneration, myocardial fibrosis, angiogenesis, and the immune microenvironment. Finally, we also discussed the integrative analysis of spatial multi-omics transcriptomics and single-cell transcriptomics. This review provided a basis for future studies to further advance the mechanism and development of therapeutic approaches for cardiac repair.
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Affiliation(s)
- Wei Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
| | - Chuling Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
| | - Yijin Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
| | - Jianping Bin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
| | - Yanmei Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangzhou, China
- Department of Cardiology, Ganzhou People’s Hospital, Ganzhou, China
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Bailin SS, Kropski JA, Gangula RD, Hannah L, Simmons JD, Mashayekhi M, Ye F, Fan R, Mallal S, Warren CM, Kalams SA, Gabriel CL, Wanjalla CN, Koethe JR. Changes in subcutaneous white adipose tissue cellular composition and molecular programs underlie glucose intolerance in persons with HIV. Front Immunol 2023; 14:1152003. [PMID: 37711619 PMCID: PMC10499182 DOI: 10.3389/fimmu.2023.1152003] [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: 01/27/2023] [Accepted: 08/07/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Subcutaneous adipose tissue (SAT) is a critical regulator of systemic metabolic homeostasis. Persons with HIV (PWH) have an increased risk of metabolic diseases and significant alterations in the SAT immune environment compared with the general population. Methods We generated a comprehensive single-cell multi-omic SAT atlas to characterize cellular compositional and transcriptional changes in 59 PWH across a spectrum of metabolic health. Results Glucose intolerance was associated with increased lipid-associated macrophages, CD4+ and CD8+ T effector memory cells, and decreased perivascular macrophages. We observed a coordinated intercellular regulatory program which enriched for genes related to inflammation and lipid-processing across multiple cell types as glucose intolerance increased. Increased CD4+ effector memory tissue-resident cells most strongly associated with altered expression of adipocyte genes critical for lipid metabolism and cellular regulation. Intercellular communication analysis demonstrated enhanced pro-inflammatory and pro-fibrotic signaling between immune cells and stromal cells in PWH with glucose intolerance compared with non-diabetic PWH. Lastly, while cell type-specific gene expression among PWH with diabetes was globally similar to HIV-negative individuals with diabetes, we observed substantially divergent intercellular communication pathways. Discussion These findings suggest a central role of tissue-resident immune cells in regulating SAT inflammation among PWH with metabolic disease, and underscore unique mechanisms that may converge to promote metabolic disease.
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Affiliation(s)
- Samuel S. Bailin
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jonathan A. Kropski
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, United States
- Deparment of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
| | - Rama D. Gangula
- Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, United States
| | - LaToya Hannah
- Department of Medicine, Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joshua D. Simmons
- Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mona Mashayekhi
- Department of Medicine, Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Fei Ye
- Department of Biostatics, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Run Fan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Simon Mallal
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
- Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Insitute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
- Vanderbilt Technologies for Advanced Genomics, Vanderbilt University Medical Center, Nashville, TN, United States
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Christian M. Warren
- Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Spyros A. Kalams
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
- Tennessee Center for AIDS Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Curtis L. Gabriel
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Nashville, TN, United States
| | - Celestine N. Wanjalla
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - John R. Koethe
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, United States
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
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Liu C, Yang F, Su X, Zhang Z, Xing Y. ScRNA-seq and spatial transcriptomics: exploring the occurrence and treatment of coronary-related diseases starting from development. Front Cardiovasc Med 2023; 10:1064949. [PMID: 37416923 PMCID: PMC10319627 DOI: 10.3389/fcvm.2023.1064949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 05/22/2023] [Indexed: 07/08/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a new technology that can be used to explore molecular changes in complex cell clusters at the single-cell level. Single-cell spatial transcriptomic technology complements the cell-space location information lost during single-cell sequencing. Coronary artery disease is an important cardiovascular disease with high mortality rates. Many studies have explored the physiological development and pathological changes in coronary arteries from the perspective of single cells using single-cell spatial transcriptomic technology. This article reviews the molecular mechanisms underlying coronary artery development and diseases as revealed by scRNA-seq combined with spatial transcriptomic technology. Based on these mechanisms, we discuss the possible new treatments for coronary diseases.
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9
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Koslow M, Mondaca-Ruff D, Xu X. Transcriptome studies of inherited dilated cardiomyopathies. Mamm Genome 2023; 34:312-322. [PMID: 36749382 PMCID: PMC10426000 DOI: 10.1007/s00335-023-09978-z] [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: 07/25/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
Abstract
Dilated cardiomyopathy (DCM) is a group of heart muscle diseases that often lead to heart failure, with more than 50 causative genes have being linked to DCM. The heterogenous nature of the inherited DCMs suggest the need of precision medicine. Consistent with this emerging concept, transcriptome studies in human patients with DCM indicated distinct molecular signature for DCMs of different genetic etiology. To facilitate this line of research, we reviewed the status of transcriptome studies of inherited DCMs by focusing on three predominant DCM causative genes, TTN, LMNA, and BAG3. Besides studies in human patients, we summarized transcriptomic analysis of these inherited DCMs in a variety of model systems ranging from iPSCs to rodents and zebrafish. We concluded that the RNA-seq technology is a powerful genomic tool that has already led to the discovery of new modifying genes, signaling pathways, and related therapeutic avenues. We also pointed out that both temporal (different pathological stages) and spatial (different cell types) information need to be considered for future transcriptome studies. While an important bottle neck is the low throughput in experimentally testing differentially expressed genes, new technologies in efficient animal models such as zebrafish starts to be developed. It is anticipated that the RNA-seq technology will continue to uncover both unique and common pathological events, aiding the development of precision medicine for inherited DCMs.
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Affiliation(s)
- Matthew Koslow
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David Mondaca-Ruff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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10
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Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Transfer learning enables predictions in network biology. Nature 2023; 618:616-624. [PMID: 37258680 PMCID: PMC10949956 DOI: 10.1038/s41586-023-06139-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Mapping gene networks requires large amounts of transcriptomic data to learn the connections between genes, which impedes discoveries in settings with limited data, including rare diseases and diseases affecting clinically inaccessible tissues. Recently, transfer learning has revolutionized fields such as natural language understanding1,2 and computer vision3 by leveraging deep learning models pretrained on large-scale general datasets that can then be fine-tuned towards a vast array of downstream tasks with limited task-specific data. Here, we developed a context-aware, attention-based deep learning model, Geneformer, pretrained on a large-scale corpus of about 30 million single-cell transcriptomes to enable context-specific predictions in settings with limited data in network biology. During pretraining, Geneformer gained a fundamental understanding of network dynamics, encoding network hierarchy in the attention weights of the model in a completely self-supervised manner. Fine-tuning towards a diverse panel of downstream tasks relevant to chromatin and network dynamics using limited task-specific data demonstrated that Geneformer consistently boosted predictive accuracy. Applied to disease modelling with limited patient data, Geneformer identified candidate therapeutic targets for cardiomyopathy. Overall, Geneformer represents a pretrained deep learning model from which fine-tuning towards a broad range of downstream applications can be pursued to accelerate discovery of key network regulators and candidate therapeutic targets.
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Affiliation(s)
- Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School Genetics Training Program, Boston, USA.
| | - Ling Xiao
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Chopra
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zeina R Al Sayed
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Hill
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Helene Mantineo
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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11
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Miranda AMA, Janbandhu V, Maatz H, Kanemaru K, Cranley J, Teichmann SA, Hübner N, Schneider MD, Harvey RP, Noseda M. Single-cell transcriptomics for the assessment of cardiac disease. Nat Rev Cardiol 2023; 20:289-308. [PMID: 36539452 DOI: 10.1038/s41569-022-00805-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
Cardiovascular disease is the leading cause of death globally. An advanced understanding of cardiovascular disease mechanisms is required to improve therapeutic strategies and patient risk stratification. State-of-the-art, large-scale, single-cell and single-nucleus transcriptomics facilitate the exploration of the cardiac cellular landscape at an unprecedented level, beyond its descriptive features, and can further our understanding of the mechanisms of disease and guide functional studies. In this Review, we provide an overview of the technical challenges in the experimental design of single-cell and single-nucleus transcriptomics studies, as well as a discussion of the type of inferences that can be made from the data derived from these studies. Furthermore, we describe novel findings derived from transcriptomics studies for each major cardiac cell type in both health and disease, and from development to adulthood. This Review also provides a guide to interpreting the exhaustive list of newly identified cardiac cell types and states, and highlights the consensus and discordances in annotation, indicating an urgent need for standardization. We describe advanced applications such as integration of single-cell data with spatial transcriptomics to map genes and cells on tissue and define cellular microenvironments that regulate homeostasis and disease progression. Finally, we discuss current and future translational and clinical implications of novel transcriptomics approaches, and provide an outlook of how these technologies will change the way we diagnose and treat heart disease.
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Affiliation(s)
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Henrike Maatz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Kazumasa Kanemaru
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - James Cranley
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sarah A Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Deptartment of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
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12
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Lv J, Meng S, Gu Q, Zheng R, Gao X, Kim JD, Chen M, Xia B, Zuo Y, Zhu S, Zhao D, Li Y, Wang G, Wang X, Meng Q, Cao Q, Cooke JP, Fang L, Chen K, Zhang L. Epigenetic landscape reveals MECOM as an endothelial lineage regulator. Nat Commun 2023; 14:2390. [PMID: 37185814 PMCID: PMC10130150 DOI: 10.1038/s41467-023-38002-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
A comprehensive understanding of endothelial cell lineage specification will advance cardiovascular regenerative medicine. Recent studies found that unique epigenetic signatures preferentially regulate cell identity genes. We thus systematically investigate the epigenetic landscape of endothelial cell lineage and identify MECOM to be the leading candidate as an endothelial cell lineage regulator. Single-cell RNA-Seq analysis verifies that MECOM-positive cells are exclusively enriched in the cell cluster of bona fide endothelial cells derived from induced pluripotent stem cells. Our experiments demonstrate that MECOM depletion impairs human endothelial cell differentiation, functions, and Zebrafish angiogenesis. Through integrative analysis of Hi-C, DNase-Seq, ChIP-Seq, and RNA-Seq data, we find MECOM binds enhancers that form chromatin loops to regulate endothelial cell identity genes. Further, we identify and verify the VEGF signaling pathway to be a key target of MECOM. Our work provides important insights into epigenetic regulation of cell identity and uncovered MECOM as an endothelial cell lineage regulator.
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Affiliation(s)
- Jie Lv
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Shu Meng
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Qilin Gu
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Rongbin Zheng
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xinlei Gao
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jun-Dae Kim
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Min Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bo Xia
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Yihan Zuo
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sen Zhu
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Dongyu Zhao
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Yanqiang Li
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Guangyu Wang
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xin Wang
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Qingshu Meng
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Qi Cao
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John P Cooke
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
| | - Longhou Fang
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
| | - Kaifu Chen
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Lili Zhang
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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13
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Yu D, Zhang S, Liu Z, Xu L, Chen L, Xie L. Single-Cell RNA Sequencing Analysis of Gene Regulatory Network Changes in the Development of Lung Adenocarcinoma. Biomolecules 2023; 13:671. [PMID: 37189418 PMCID: PMC10135828 DOI: 10.3390/biom13040671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/31/2023] [Accepted: 04/09/2023] [Indexed: 05/17/2023] Open
Abstract
Lung cancer is a highly heterogeneous disease. Cancer cells and other cells within the tumor microenvironment interact to determine disease progression, as well as response to or escape from treatment. Understanding the regulatory relationship between cancer cells and their tumor microenvironment in lung adenocarcinoma is of great significance for exploring the heterogeneity of the tumor microenvironment and its role in the genesis and development of lung adenocarcinoma. This work uses public single-cell transcriptome data (distant normal, nLung; early LUAD, tLung; advanced LUAD, tL/B), to draft a cell map of lung adenocarcinoma from onset to progression, and provide a cell-cell communication view of lung adenocarcinoma in the different disease stages. Based on the analysis of cell populations, it was found that the proportion of macrophages was significantly reduced in the development of lung adenocarcinoma, and patients with lower proportions of macrophages exhibited poor prognosis. We therefore constructed a process to screen an intercellular gene regulatory network that reduces any error generated by single cell communication analysis and increases the credibility of selected cell communication signals. Based on the key regulatory signals in the macrophage-tumor cell regulatory network, we performed a pseudotime analysis of the macrophages and found that signal molecules (TIMP1, VEGFA, SPP1) are highly expressed in immunosuppression-associated macrophages. These molecules were also validated using an independent dataset and were significantly associated with poor prognosis. Our study provides an effective method for screening the key regulatory signals in the tumor microenvironment and the selected signal molecules may serve as a reference to guide the development of diagnostic biomarkers for risk stratification and therapeutic targets for lung adenocarcinoma.
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Affiliation(s)
- Dongshuo Yu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Siwen Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
| | - Zhenhao Liu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
| | - Linfeng Xu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics (Chinese National Human Genome Center at Shanghai), Institute of Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200037, China; (S.Z.); (Z.L.); (L.X.)
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14
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Ameen M, Sundaram L, Shen M, Banerjee A, Kundu S, Nair S, Shcherbina A, Gu M, Wilson KD, Varadarajan A, Vadgama N, Balsubramani A, Wu JC, Engreitz JM, Farh K, Karakikes I, Wang KC, Quertermous T, Greenleaf WJ, Kundaje A. Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease. Cell 2022; 185:4937-4953.e23. [PMID: 36563664 PMCID: PMC10122433 DOI: 10.1016/j.cell.2022.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 09/13/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
To define the multi-cellular epigenomic and transcriptional landscape of cardiac cellular development, we generated single-cell chromatin accessibility maps of human fetal heart tissues. We identified eight major differentiation trajectories involving primary cardiac cell types, each associated with dynamic transcription factor (TF) activity signatures. We contrasted regulatory landscapes of iPSC-derived cardiac cell types and their in vivo counterparts, which enabled optimization of in vitro differentiation of epicardial cells. Further, we interpreted sequence based deep learning models of cell-type-resolved chromatin accessibility profiles to decipher underlying TF motif lexicons. De novo mutations predicted to affect chromatin accessibility in arterial endothelium were enriched in congenital heart disease (CHD) cases vs. controls. In vitro studies in iPSCs validated the functional impact of identified variation on the predicted developmental cell types. This work thus defines the cell-type-resolved cis-regulatory sequence determinants of heart development and identifies disruption of cell type-specific regulatory elements in CHD.
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Affiliation(s)
- Mohamed Ameen
- Department of Cancer Biology, Stanford University, Stanford, CA, USA; Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Laksshman Sundaram
- Department of Computer Science, Stanford University, Stanford, CA, USA; Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Mengcheng Shen
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | - Abhimanyu Banerjee
- Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA; Department of Physics, Stanford University, Stanford, CA, USA
| | - Soumya Kundu
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Biomedical Informatics, Stanford University, Stanford, CA, USA
| | - Mingxia Gu
- Center for Stem Cell and Organoid Medicine, CuSTOM, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Avyay Varadarajan
- Department of Computer Science, California Institute of Technology, Pasadena, CA, USA
| | - Nirmal Vadgama
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | | | - Joseph C Wu
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | | | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, Foster City, CA, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA; Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA.
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
| | - Thomas Quertermous
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Applied Physics, Stanford University, Stanford, CA, USA.
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA.
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15
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Cao X, Mircea M, Yakala GK, van den Hil FE, Brescia M, Mei H, Mummery CL, Semrau S, Orlova VV. ETV2 Upregulation Marks the Specification of Early Cardiomyocytes and Endothelial Cells During Co-differentiation. Stem Cells 2022; 41:140-152. [PMID: 36512477 PMCID: PMC9982073 DOI: 10.1093/stmcls/sxac086] [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: 05/21/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022]
Abstract
The ability to differentiate human-induced pluripotent stem cells (hiPSCs) efficiently into defined cardiac lineages, such as cardiomyocytes and cardiac endothelial cells, is crucial to study human heart development and model cardiovascular diseases in vitro. The mechanisms underlying the specification of these cell types during human development are not well understood which limits fine-tuning and broader application of cardiac model systems. Here, we used the expression of ETV2, a master regulator of hematoendothelial specification in mice, to identify functionally distinct subpopulations during the co-differentiation of endothelial cells and cardiomyocytes from hiPSCs. Targeted analysis of single-cell RNA-sequencing data revealed differential ETV2 dynamics in the 2 lineages. A newly created fluorescent reporter line allowed us to identify early lineage-predisposed states and show that a transient ETV2-high-state initiates the specification of endothelial cells. We further demonstrated, unexpectedly, that functional cardiomyocytes can originate from progenitors expressing ETV2 at a low level. Our study thus sheds light on the in vitro differentiation dynamics of 2 important cardiac lineages.
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Affiliation(s)
- Xu Cao
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maria Mircea
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Gopala Krishna Yakala
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Francijna E van den Hil
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcella Brescia
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Christine L Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Valeria V Orlova
- Corresponding author: Stefan Semrau, Ph.D., Leiden Institute of Physics, Leiden University, 2333 RA, Leiden, The Netherlands. ; or, Valeria V. Orlova, Ph.D., Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, 2333ZC Leiden, The Netherlands.
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16
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Patient-specific and gene-corrected induced pluripotent stem cell-derived endothelial cells elucidate single-cell phenotype of pulmonary veno-occlusive disease. Stem Cell Reports 2022; 17:2674-2689. [PMID: 36400028 PMCID: PMC9768576 DOI: 10.1016/j.stemcr.2022.10.014] [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: 04/15/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 11/19/2022] Open
Abstract
Pulmonary veno-occlusive disease (PVOD) is a rare form of pulmonary hypertension characterized by the preferential remodeling of the pulmonary venules. Hereditary PVOD is caused by biallelic variants of the EIF2AK4 gene. Three PVOD patients who carried the compound heterozygous variants of EIF2AK4 and two healthy controls were recruited and induced pluripotent stem cells (iPSCs) were generated from human peripheral blood mononuclear cells (PBMCs). The EIF2AK4 c.2965C>T variant (PVOD#1), c.3460A>T variant (PVOD#2), and c.4832_4833insAAAG variant (PVOD#3) were corrected by CRISPR-Cas9 in PVOD-iPSCs to generate isogenic controls and gene-corrected-iPSCs (GC-iPSCs). PVOD-iPSC-endothelial cells (ECs) exhibited a decrease in GCN2 protein and mRNA expression when compared with control and GC-ECs. PVOD-ECs exhibited an abnormal EC phenotype featured by excessive proliferation and angiogenesis. The abnormal phenotype of PVOD-ECs was normalized by protein kinase B inhibitors AZD5363 and MK2206. These findings help elucidate the underlying molecular mechanism of PVOD in humans and to identify promising therapeutic drugs for treating the disease.
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17
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Mansfield C, Zhao MT, Basu M. Translational potential of hiPSCs in predictive modeling of heart development and disease. Birth Defects Res 2022; 114:926-947. [PMID: 35261209 PMCID: PMC9458775 DOI: 10.1002/bdr2.1999] [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: 02/01/2022] [Accepted: 02/21/2022] [Indexed: 11/11/2022]
Abstract
Congenital heart disease (CHD) represents a major class of birth defects worldwide and is associated with cardiac malformations that often require surgical intervention immediately after birth. Despite the intense efforts from multicentric genome/exome sequencing studies that have identified several genetic variants, the etiology of CHD remains diverse and often unknown. Genetically modified animal models with candidate gene deficiencies continue to provide novel molecular insights that are responsible for fetal cardiac development. However, the past decade has seen remarkable advances in the field of human induced pluripotent stem cell (hiPSC)-based disease modeling approaches to better understand the development of CHD and discover novel preventative therapies. The iPSCs are derived from reprogramming of differentiated somatic cells to an embryonic-like pluripotent state via overexpression of key transcription factors. In this review, we describe how differentiation of hiPSCs to specialized cardiac cellular identities facilitates our understanding of the development and pathogenesis of CHD subtypes. We summarize the molecular and functional characterization of hiPSC-derived differentiated cells in support of normal cardiogenesis, those that go awry in CHD and other heart diseases. We illustrate how stem cell-based disease modeling enables scientists to dissect the molecular mechanisms of cell-cell interactions underlying CHD. We highlight the current state of hiPSC-based studies that are in the verge of translating into clinical trials. We also address limitations including hiPSC-model reproducibility and scalability and differentiation methods leading to cellular heterogeneity. Last, we provide future perspective on exploiting the potential of hiPSC technology as a predictive model for patient-specific CHD, screening pharmaceuticals, and provide a source for cell-based personalized medicine. In combination with existing clinical and animal model studies, data obtained from hiPSCs will yield further understanding of oligogenic, gene-environment interaction, pathophysiology, and management for CHD and other genetic cardiac disorders.
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Affiliation(s)
- Corrin Mansfield
- Center for Cardiovascular Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Ming-Tao Zhao
- Center for Cardiovascular Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Madhumita Basu
- Center for Cardiovascular Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
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18
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Sen T, Thummer RP. CRISPR and iPSCs: Recent Developments and Future Perspectives in Neurodegenerative Disease Modelling, Research, and Therapeutics. Neurotox Res 2022; 40:1597-1623. [PMID: 36044181 PMCID: PMC9428373 DOI: 10.1007/s12640-022-00564-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/17/2022] [Accepted: 08/19/2022] [Indexed: 11/15/2022]
Abstract
Neurodegenerative diseases are prominent causes of pain, suffering, and death worldwide. Traditional approaches modelling neurodegenerative diseases are deficient, and therefore, improved strategies that effectively recapitulate the pathophysiological conditions of neurodegenerative diseases are the need of the hour. The generation of human-induced pluripotent stem cells (iPSCs) has transformed our ability to model neurodegenerative diseases in vitro and provide an unlimited source of cells (including desired neuronal cell types) for cell replacement therapy. Recently, CRISPR/Cas9-based genome editing has also been gaining popularity because of the flexibility they provide to generate and ablate disease phenotypes. In addition, the recent advancements in CRISPR/Cas9 technology enables researchers to seamlessly target and introduce precise modifications in the genomic DNA of different human cell lines, including iPSCs. CRISPR-iPSC-based disease modelling, therefore, allows scientists to recapitulate the pathological aspects of most neurodegenerative processes and investigate the role of pathological gene variants in healthy non-patient cell lines. This review outlines how iPSCs, CRISPR/Cas9, and CRISPR-iPSC-based approaches accelerate research on neurodegenerative diseases and take us closer to a cure for neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Amyotrophic Lateral Sclerosis, and so forth.
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Affiliation(s)
- Tirthankar Sen
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati - 781039, Assam, India.
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19
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Brittain EL, Thenappan T, Huston JH, Agrawal V, Lai YC, Dixon D, Ryan JJ, Lewis EF, Redfield MM, Shah SJ, Maron BA. Elucidating the Clinical Implications and Pathophysiology of Pulmonary Hypertension in Heart Failure With Preserved Ejection Fraction: A Call to Action: A Science Advisory From the American Heart Association. Circulation 2022; 146:e73-e88. [PMID: 35862198 PMCID: PMC9901193 DOI: 10.1161/cir.0000000000001079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This science advisory focuses on the need to better understand the epidemiology, pathophysiology, and treatment of pulmonary hypertension in patients with heart failure with preserved ejection fraction. This clinical phenotype is important because it is common, is strongly associated with adverse outcomes, and lacks evidence-based therapies. Our goal is to clarify key knowledge gaps in pulmonary hypertension attributable to heart failure with preserved ejection fraction and to suggest specific, actionable scientific directions for addressing such gaps. Areas in need of additional investigation include refined disease definitions and interpretation of hemodynamics, as well as greater insights into noncardiac contributors to pulmonary hypertension risk, optimized animal models, and further molecular studies in patients with combined precapillary and postcapillary pulmonary hypertension. We highlight translational approaches that may provide important biological insight into pathophysiology and reveal new therapeutic targets. Last, we discuss the current and future landscape of potential therapies for patients with heart failure with preserved ejection fraction and pulmonary vascular dysfunction, including considerations of precision medicine, novel trial design, and device-based therapies, among other considerations. This science advisory provides a synthesis of important knowledge gaps, culminating in a collection of specific research priorities that we argue warrant investment from the scientific community.
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20
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Hu Y, Zhang Y, Liu Y, Gao Y, San T, Li X, Song S, Yan B, Zhao Z. Advances in application of single-cell RNA sequencing in cardiovascular research. Front Cardiovasc Med 2022; 9:905151. [PMID: 35958408 PMCID: PMC9360414 DOI: 10.3389/fcvm.2022.905151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) provides high-resolution information on transcriptomic changes at the single-cell level, which is of great significance for distinguishing cell subtypes, identifying stem cell differentiation processes, and identifying targets for disease treatment. In recent years, emerging single-cell RNA sequencing technologies have been used to make breakthroughs regarding decoding developmental trajectories, phenotypic transitions, and cellular interactions in the cardiovascular system, providing new insights into cardiovascular disease. This paper reviews the technical processes of single-cell RNA sequencing and the latest progress based on single-cell RNA sequencing in the field of cardiovascular system research, compares single-cell RNA sequencing with other single-cell technologies, and summarizes the extended applications and advantages and disadvantages of single-cell RNA sequencing. Finally, the prospects for applying single-cell RNA sequencing in the field of cardiovascular research are discussed.
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Affiliation(s)
- Yue Hu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Ying Zhang
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Yutong Liu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Yan Gao
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Tiantian San
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Xiaoying Li
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- Department of Emergency, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Sensen Song
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Binglong Yan
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Zhuo Zhao
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- *Correspondence: Zhuo Zhao
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21
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PDGFD switches on stem cell endothelial commitment. Angiogenesis 2022; 25:517-533. [PMID: 35859222 PMCID: PMC9519648 DOI: 10.1007/s10456-022-09847-4] [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: 02/06/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022]
Abstract
The critical factors regulating stem cell endothelial commitment and renewal remain not well understood. Here, using loss- and gain-of-function assays together with bioinformatic analysis and multiple model systems, we show that PDGFD is an essential factor that switches on endothelial commitment of embryonic stem cells (ESCs). PDGFD genetic deletion or knockdown inhibits ESC differentiation into EC lineage and increases ESC self-renewal, and PDGFD overexpression activates ESC differentiation towards ECs. RNA sequencing reveals a critical requirement of PDGFD for the expression of vascular-differentiation related genes in ESCs. Importantly, PDGFD genetic deletion or knockdown increases ESC self-renewal and decreases blood vessel densities in both embryonic and neonatal mice and in teratomas. Mechanistically, we reveal that PDGFD fulfills this function via the MAPK/ERK pathway. Our findings provide new insight of PDGFD as a novel regulator of ESC fate determination, and suggest therapeutic implications of modulating PDGFD activity in stem cell therapy.
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22
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Zhu J, Yan M, Yan H, Xu L, Jiang Z, Liao G, Zhou Y, Liu W, Liang X, Li X, Xiao Y, Zhang Y. Single-Cell Transcriptomic Analysis Reveals the Crosstalk Propensity Between the Tumor Intermediate State and the CD8+ T Exhausted State to be Associated with Clinical Benefits in Melanoma. Front Immunol 2022; 13:766852. [PMID: 35903095 PMCID: PMC9314667 DOI: 10.3389/fimmu.2022.766852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 06/20/2022] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous crosstalk between tumor cells and CD8+ T cells leads to substantial variation in clinical benefits from immunotherapy in melanoma. Due to spatial distribution and functional state heterogeneity, it is still unknown whether there is a crosstalk propensity between tumor cells and CD8+ T cells in melanoma, and how this crosstalk propensity affects the clinical outcome of patients. Using public single-cell transcriptome data, extensive heterogeneous functional states and ligand–receptor interactions of tumor cells and CD8+ T cells were revealed in melanoma. Furthermore, based on the association between cell–cell communication intensity and cell state activity in a single cell, we identified a crosstalk propensity between the tumor intermediate state and the CD8+ T exhausted state. This crosstalk propensity was further verified by pseudo-spatial proximity, spatial co-location, and the intra/intercellular signal transduction network. At the sample level, the tumor intermediate state and the CD8+ T exhausted state synergistically indicated better prognosis and both reduced in immunotherapy-resistant samples. The risk groups defined based on these two cell states could comprehensively reflect tumor genomic mutations and anti-tumor immunity information. The low-risk group had a higher BRAF mutation fraction as well as stronger antitumor immune response. Our findings highlighted the crosstalk propensity between the tumor intermediate state and the CD8+ T exhausted state, which may serve as a reference to guide the development of diagnostic biomarkers for risk stratification and therapeutic targets for new therapeutic strategies.
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Affiliation(s)
- Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Liang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
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23
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Ang LT, Nguyen AT, Liu KJ, Chen A, Xiong X, Curtis M, Martin RM, Raftry BC, Ng CY, Vogel U, Lander A, Lesch BJ, Fowler JL, Holman AR, Chai T, Vijayakumar S, Suchy FP, Nishimura T, Bhadury J, Porteus MH, Nakauchi H, Cheung C, George SC, Red-Horse K, Prescott JB, Loh KM. Generating human artery and vein cells from pluripotent stem cells highlights the arterial tropism of Nipah and Hendra viruses. Cell 2022; 185:2523-2541.e30. [PMID: 35738284 DOI: 10.1016/j.cell.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/26/2022] [Accepted: 05/26/2022] [Indexed: 02/07/2023]
Abstract
Stem cell research endeavors to generate specific subtypes of classically defined "cell types." Here, we generate >90% pure human artery or vein endothelial cells from pluripotent stem cells within 3-4 days. We specified artery cells by inhibiting vein-specifying signals and vice versa. These cells modeled viral infection of human vasculature by Nipah and Hendra viruses, which are extraordinarily deadly (∼57%-59% fatality rate) and require biosafety-level-4 containment. Generating pure populations of artery and vein cells highlighted that Nipah and Hendra viruses preferentially infected arteries; arteries expressed higher levels of their viral-entry receptor. Virally infected artery cells fused into syncytia containing up to 23 nuclei, which rapidly died. Despite infecting arteries and occupying ∼6%-17% of their transcriptome, Nipah and Hendra largely eluded innate immune detection, minimally eliciting interferon signaling. We thus efficiently generate artery and vein cells, introduce stem-cell-based toolkits for biosafety-level-4 virology, and explore the arterial tropism and cellular effects of Nipah and Hendra viruses.
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Affiliation(s)
- Lay Teng Ang
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Alana T Nguyen
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Kevin J Liu
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela Chen
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Xiaochen Xiong
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Matthew Curtis
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | - Renata M Martin
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Brian C Raftry
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Chun Yi Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Uwe Vogel
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Angelika Lander
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Benjamin J Lesch
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Jonas L Fowler
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Alyssa R Holman
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Timothy Chai
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Siva Vijayakumar
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Fabian P Suchy
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Toshinobu Nishimura
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joydeep Bhadury
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Steven C George
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | - Kristy Red-Horse
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Prescott
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany.
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA.
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24
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Nguyen T, Wei Y, Nakada Y, Zhou Y, Zhang J. Cardiomyocyte Cell-Cycle Regulation in Neonatal Large Mammals: Single Nucleus RNA-Sequencing Data Analysis via an Artificial-Intelligence–Based Pipeline. Front Bioeng Biotechnol 2022; 10:914450. [PMID: 35860330 PMCID: PMC9289371 DOI: 10.3389/fbioe.2022.914450] [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: 04/06/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
Adult mammalian cardiomyocytes have very limited capacity to proliferate and repair the myocardial infarction. However, when apical resection (AR) was performed in pig hearts on postnatal day (P) 1 (ARP1) and acute myocardial infarction (MI) was induced on P28 (MIP28), the animals recovered with no evidence of myocardial scarring or decline in contractile performance. Furthermore, the repair process appeared to be driven by cardiomyocyte proliferation, but the regulatory molecules that govern the ARP1-induced enhancement of myocardial recovery remain unclear. Single-nucleus RNA sequencing (snRNA-seq) data collected from fetal pig hearts and the hearts of pigs that underwent ARP1, MIP28, both ARP1 and MI, or neither myocardial injury were evaluated via autoencoder, cluster analysis, sparse learning, and semisupervised learning. Ten clusters of cardiomyocytes (CM1–CM10) were identified across all experimental groups and time points. CM1 was only observed in ARP1 hearts on P28 and was enriched for the expression of T-box transcription factors 5 and 20 (TBX5 and TBX20, respectively), Erb-B2 receptor tyrosine kinase 4 (ERBB4), and G Protein-Coupled Receptor Kinase 5 (GRK5), as well as genes associated with the proliferation and growth of cardiac muscle. CM1 cardiomyocytes also highly expressed genes for glycolysis while lowly expressed genes for adrenergic signaling, which suggested that CM1 were immature cardiomyocytes. Thus, we have identified a cluster of cardiomyocytes, CM1, in neonatal pig hearts that appeared to be generated in response to AR injury on P1 and may have been primed for activation of CM cell-cycle activation and proliferation by the upregulation of TBX5, TBX20, ERBB4, and GRK5.
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Affiliation(s)
- Thanh Nguyen
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yuhua Wei
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yuji Nakada
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yang Zhou
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jianyi Zhang
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
- Cardiovascular Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Jianyi Zhang,
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25
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Mullen M, Wen Tan WL, Rhee JW, Wu JC. Modeling Susceptibility to Cardiotoxicity in Cancer Therapy Using Human iPSC-Derived Cardiac Cells and Systems Biology. Heart Fail Clin 2022; 18:335-347. [PMID: 35718410 DOI: 10.1016/j.hfc.2022.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of human-induced pluripotent stem cell-derived cardiac cell types has created a new paradigm in assessing drug-induced cardiotoxicity. Advances in genomics and epigenomics have also implicated several genomic loci and biological pathways that may contribute to susceptibility to cancer therapies. In this review, we first provide a brief overview of the cardiotoxicity associated with chemotherapy. We then provide a detailed summary of systems biology approaches being applied to elucidate potential molecular mechanisms involved in cardiotoxicity. Finally, we discuss combining systems biology approaches with iPSC technology to help discover molecular mechanisms associated with cardiotoxicity.
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Affiliation(s)
- McKay Mullen
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA
| | - Wilson Lek Wen Tan
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA
| | - June-Wha Rhee
- Department of Medicine, City of Hope Comprehensive Cancer Center, 1500 E Duarte Rd, Duarte, CA 91010, USA.
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University; Department of Radiology, Stanford University, 265 Campus Drive G1120B, Stanford, CA 94304, USA.
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26
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Mizrak D, Feng H, Yang B. Dissecting the Heterogeneity of Human Thoracic Aortic Aneurysms Using Single-Cell Transcriptomics. Arterioscler Thromb Vasc Biol 2022; 42:919-930. [PMID: 35708028 PMCID: PMC9339526 DOI: 10.1161/atvbaha.122.317484] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Thoracic aortic aneurysm is a life-threatening condition caused by weakening of the thoracic aorta wall, often developing silently until dissection or rupture occurs. Despite substantial efforts in the past decade, there have been no significant therapeutic advances to prevent or clinically manage diverse forms of thoracic aortic aneurysm and dissection with the only effective treatment being surgical repair. There is an urgent need to understand intra- and inter-aneurysmal heterogeneity underlying thoracic aortic aneurysm and dissection pathogenesis. The human aortic wall consists of many cell types and exhibits significant regional heterogeneity. High-throughput single-cell RNA sequencing has emerged as the principal tool to reveal the complexity in human tissues and clinical specimens. Recent single-cell RNA sequencing studies of different aortic cell populations both in vivo and in vitro began to dissect this complexity and have provided valuable information. In this review, we summarize these findings and discuss the potential applications of single-cell transcriptomics and related high-content technologies in human thoracic aortic aneurysm and dissection research, as well as the challenges associated with it.
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Affiliation(s)
- Dogukan Mizrak
- Department of Cardiac Surgery, University of Michigan, Ann Arbor (D.M., H.F., B.Y.)
| | - Hao Feng
- Department of Cardiac Surgery, University of Michigan, Ann Arbor (D.M., H.F., B.Y.).,Xiangya School of Medicine, Central South University, Changsha, China (H.F.)
| | - Bo Yang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor (D.M., H.F., B.Y.)
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27
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Wei TT, Chandy M, Nishiga M, Zhang A, Kumar KK, Thomas D, Manhas A, Rhee S, Justesen JM, Chen IY, Wo HT, Khanamiri S, Yang JY, Seidl FJ, Burns NZ, Liu C, Sayed N, Shie JJ, Yeh CF, Yang KC, Lau E, Lynch KL, Rivas M, Kobilka BK, Wu JC. Cannabinoid receptor 1 antagonist genistein attenuates marijuana-induced vascular inflammation. Cell 2022; 185:1676-1693.e23. [PMID: 35489334 PMCID: PMC9400797 DOI: 10.1016/j.cell.2022.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 02/01/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022]
Abstract
Epidemiological studies reveal that marijuana increases the risk of cardiovascular disease (CVD); however, little is known about the mechanism. Δ9-tetrahydrocannabinol (Δ9-THC), the psychoactive component of marijuana, binds to cannabinoid receptor 1 (CB1/CNR1) in the vasculature and is implicated in CVD. A UK Biobank analysis found that cannabis was an risk factor for CVD. We found that marijuana smoking activated inflammatory cytokines implicated in CVD. In silico virtual screening identified genistein, a soybean isoflavone, as a putative CB1 antagonist. Human-induced pluripotent stem cell-derived endothelial cells were used to model Δ9-THC-induced inflammation and oxidative stress via NF-κB signaling. Knockdown of the CB1 receptor with siRNA, CRISPR interference, and genistein attenuated the effects of Δ9-THC. In mice, genistein blocked Δ9-THC-induced endothelial dysfunction in wire myograph, reduced atherosclerotic plaque, and had minimal penetration of the central nervous system. Genistein is a CB1 antagonist that attenuates Δ9-THC-induced atherosclerosis.
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Affiliation(s)
- Tzu-Tang Wei
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA; Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program in Chemical Biology and Molecular Biophysics (TIGP-CBMB), Academia Sinica, Taipei, Taiwan
| | - Mark Chandy
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA; Greenstone Biosciences, Palo Alto, CA 94304, USA
| | - Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Angela Zhang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Kaavya Krishna Kumar
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dilip Thomas
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Amit Manhas
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Siyeon Rhee
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA; Greenstone Biosciences, Palo Alto, CA 94304, USA
| | - Johanne Marie Justesen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ian Y Chen
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Hung-Ta Wo
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA; Division of Cardiology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Saereh Khanamiri
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Johnson Y Yang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | | | - Noah Z Burns
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Chun Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
| | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chih-Fan Yeh
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Kai-Chien Yang
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Edward Lau
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Manuel Rivas
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA; Greenstone Biosciences, Palo Alto, CA 94304, USA.
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28
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Deciphering Cardiac Biology and Disease by Single-Cell Transcriptomic Profiling. Biomolecules 2022; 12:biom12040566. [PMID: 35454155 PMCID: PMC9032111 DOI: 10.3390/biom12040566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022] Open
Abstract
By detecting minute molecular changes in hundreds to millions of single cells, single-cell RNA sequencing allows for the comprehensive characterization of the diversity and dynamics of cells in the heart. Our understanding of the heart has been transformed through the recognition of cellular heterogeneity, the construction of regulatory networks, the building of lineage trajectories, and the mapping of intercellular crosstalk. In this review, we introduce cardiac progenitors and their transcriptional regulation during embryonic development, highlight cellular heterogeneity and cell subtype functions in cardiac health and disease, and discuss insights gained from the study of pluripotent stem-cell-derived cardiomyocytes.
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Robinson EL, Baker AH, Brittan M, McCracken I, Condorelli G, Emanueli C, Srivastava PK, Gaetano C, Thum T, Vanhaverbeke M, Angione C, Heymans S, Devaux Y, Pedrazzini T, Martelli F. Dissecting the transcriptome in cardiovascular disease. Cardiovasc Res 2022; 118:1004-1019. [PMID: 33757121 PMCID: PMC8930073 DOI: 10.1093/cvr/cvab117] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
The human transcriptome comprises a complex network of coding and non-coding RNAs implicated in a myriad of biological functions. Non-coding RNAs exhibit highly organized spatial and temporal expression patterns and are emerging as critical regulators of differentiation, homeostasis, and pathological states, including in the cardiovascular system. This review defines the current knowledge gaps, unmet methodological needs, and describes the challenges in dissecting and understanding the role and regulation of the non-coding transcriptome in cardiovascular disease. These challenges include poor annotation of the non-coding genome, determination of the cellular distribution of transcripts, assessment of the role of RNA processing and identification of cell-type specific changes in cardiovascular physiology and disease. We highlight similarities and differences in the hurdles associated with the analysis of the non-coding and protein-coding transcriptomes. In addition, we discuss how the lack of consensus and absence of standardized methods affect reproducibility of data. These shortcomings should be defeated in order to make significant scientific progress and foster the development of clinically applicable non-coding RNA-based therapeutic strategies to lessen the burden of cardiovascular disease.
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Affiliation(s)
- Emma L Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
- The Division of Cardiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mairi Brittan
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ian McCracken
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - G Condorelli
- Humanitas Research Hospital, Humanitas University, Via Manzoni 113, Rozzano, MI 20089, Italy
| | - C Emanueli
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - P K Srivastava
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - C Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, Pavia 27100, Italy
| | - T Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Carl-Neuberg-Straße 1 30625 Hannover, Germany
| | - M Vanhaverbeke
- UZ Gasthuisberg Campus, KU Leuven, Herestraat 49 3000 Leuven, Belgium
| | - C Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, TS4 3BX, UK
| | - S Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
| | - Y Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - T Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland
| | - F Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Piazza Edmondo Malan, 2, 20097 San Donato, Milan, Italy
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Gil CH, Chakraborty D, Vieira CP, Prasain N, Calzi SL, Fortmann SD, Hu P, Banno K, Jamal M, Huang C, Sielski MS, Lin Y, Huang X, Dupont MD, Floyd JL, Prasad R, Longhini ALF, McGill TJ, Chung HM, Murphy MP, Kotton DN, Boulton ME, Yoder MC, Grant MB. Specific mesoderm subset derived from human pluripotent stem cells ameliorates microvascular pathology in type 2 diabetic mice. SCIENCE ADVANCES 2022; 8:eabm5559. [PMID: 35245116 PMCID: PMC8896785 DOI: 10.1126/sciadv.abm5559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) were differentiated into a specific mesoderm subset characterized by KDR+CD56+APLNR+ (KNA+) expression. KNA+ cells had high clonal proliferative potential and specification into endothelial colony-forming cell (ECFCs) phenotype. KNA+ cells differentiated into perfused blood vessels when implanted subcutaneously into the flank of nonobese diabetic/severe combined immunodeficient mice and when injected into the vitreous of type 2 diabetic mice (db/db mice). Transcriptomic analysis showed that differentiation of hiPSCs derived from diabetics into KNA+ cells was sufficient to change baseline differences in gene expression caused by the diabetic status and reprogram diabetic cells to a pattern similar to KNA+ cells derived from nondiabetic hiPSCs. Proteomic array studies performed on retinas of db/db mice injected with either control or diabetic donor-derived KNA+ cells showed correction of aberrant signaling in db/db retinas toward normal healthy retina. These data provide "proof of principle" that KNA+ cells restore perfusion and correct vascular dysfunction in db/db mice.
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Affiliation(s)
- Chang-Hyun Gil
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dibyendu Chakraborty
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Cristiano P. Vieira
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Nutan Prasain
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Astellas Institute for Regenerative Medicine (AIRM), Westborough, MA 01581, USA
| | - Sergio Li Calzi
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Seth D. Fortmann
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
- Medical Scientist Training Program (MSTP), School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ping Hu
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Kimihiko Banno
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Mohamed Jamal
- Center for Regenerative Medicine, Pulmonary Center, and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Endodontics, Hamdan Bin Mohammed College of Dental Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 00000, UAE
| | - Chao Huang
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Micheli S. Sielski
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Yang Lin
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xinxin Huang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Zhongshan-Xuhui Hospital and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 310104, China
| | - Mariana D. Dupont
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Jason L. Floyd
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Ana Leda F. Longhini
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY 10065, USA
| | - Trevor J. McGill
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Hyung-Min Chung
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Michael P. Murphy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Pulmonary Center, and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Michael E. Boulton
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
| | - Mervin C. Yoder
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Maria B. Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA
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Guo FH, Guan YN, Guo JJ, Zhang LJ, Qiu JJ, Ji Y, Chen AF, Jing Q. Single-Cell Transcriptome Analysis Reveals Embryonic Endothelial Heterogeneity at Spatiotemporal Level and Multifunctions of MicroRNA-126 in Mice. Arterioscler Thromb Vasc Biol 2022; 42:326-342. [PMID: 35021856 PMCID: PMC8860216 DOI: 10.1161/atvbaha.121.317093] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Supplemental Digital Content is available in the text. Endothelial cells (ECs) play a critical role in angiogenesis and vascular remodeling. The heterogeneity of ECs has been reported at adult stages, yet it has not been fully investigated. This study aims to assess the transcriptional heterogeneity of developmental ECs at spatiotemporal level and to reveal the changes of embryonic ECs clustering when endothelium-enriched microRNA-126 (miR-126) was specifically knocked out.
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Affiliation(s)
- Fang-Hao Guo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Innovation Center for Intervention of Chronic Disease and Promotion of Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China (F.-H.G., Y.-N.G., J.-J.G., J.J.Q., Q.J.)
| | - Ya-Na Guan
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Innovation Center for Intervention of Chronic Disease and Promotion of Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China (F.-H.G., Y.-N.G., J.-J.G., J.J.Q., Q.J.)
| | - Jun-Jun Guo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Innovation Center for Intervention of Chronic Disease and Promotion of Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China (F.-H.G., Y.-N.G., J.-J.G., J.J.Q., Q.J.)
| | - Lu-Jun Zhang
- Department of Cardiology, Changhai Hospital, Shanghai, China (L.-J.Z.)
| | - Jing-Jing Qiu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Innovation Center for Intervention of Chronic Disease and Promotion of Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China (F.-H.G., Y.-N.G., J.-J.G., J.J.Q., Q.J.)
| | - Yong Ji
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Jiangsu, China (Y.J.)
| | - Alex F Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, China (A.F.C.)
| | - Qing Jing
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Innovation Center for Intervention of Chronic Disease and Promotion of Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China (F.-H.G., Y.-N.G., J.-J.G., J.J.Q., Q.J.)
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Son JS, Park CY, Lee G, Park JY, Kim HJ, Kim G, Chi KY, Woo DH, Han C, Kim SK, Park HJ, Kim DW, Kim JH. Therapeutic correction of hemophilia A using 2D endothelial cells and multicellular 3D organoids derived from CRISPR/Cas9-engineered patient iPSCs. Biomaterials 2022; 283:121429. [DOI: 10.1016/j.biomaterials.2022.121429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 01/26/2022] [Accepted: 02/17/2022] [Indexed: 01/19/2023]
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Qiu M, Zong JB, He QW, Liu YX, Wan Y, Li M, Zhou YF, Wu JH, Hu B. Cell Heterogeneity Uncovered by Single-Cell RNA Sequencing Offers Potential Therapeutic Targets for Ischemic Stroke. Aging Dis 2022; 13:1436-1454. [PMID: 36186129 PMCID: PMC9466965 DOI: 10.14336/ad.2022.0212] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/12/2022] [Indexed: 11/06/2022] Open
Abstract
Ischemic stroke is a detrimental neurological disease characterized by an irreversible infarct core surrounded by an ischemic penumbra, a salvageable region of brain tissue. Unique roles of distinct brain cell subpopulations within the neurovascular unit and peripheral immune cells during ischemic stroke remain elusive due to the heterogeneity of cells in the brain. Single-cell RNA sequencing (scRNA-seq) allows for an unbiased determination of cellular heterogeneity at high-resolution and identification of cell markers, thereby unveiling the principal brain clusters within the cell-type-specific gene expression patterns as well as cell-specific subclusters and their functions in different pathways underlying ischemic stroke. In this review, we have summarized the changes in differentiation trajectories of distinct cell types and highlighted the specific pathways and genes in brain cells that are impacted by stroke. This review is expected to inspire new research and provide directions for investigating the potential pathological mechanisms and novel treatment strategies for ischemic stroke at the level of a single cell.
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Affiliation(s)
| | | | | | | | | | | | | | - Jie-hong Wu
- Correspondence should be addressed to: Dr. Bo Hu () and Dr. Jie-hong Wu (), Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Hu
- Correspondence should be addressed to: Dr. Bo Hu () and Dr. Jie-hong Wu (), Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Mathur T, Tronolone JJ, Jain A. Comparative Analysis of Blood-Derived Endothelial Cells for Designing Next-Generation Personalized Organ-on-Chips. J Am Heart Assoc 2021; 10:e022795. [PMID: 34743553 PMCID: PMC8751908 DOI: 10.1161/jaha.121.022795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Organ‐on‐chip technology has accelerated in vitro preclinical research of the vascular system, and a key strength of this platform is its promise to impact personalized medicine by providing a primary human cell–culture environment where endothelial cells are directly biopsied from individual tissue or differentiated through stem cell biotechniques. However, these methods are difficult to adopt in laboratories, and often result in impurity and heterogeneity of cells. This limits the power of organ‐chips in making accurate physiological predictions. In this study, we report the use of blood‐derived endothelial cells as alternatives to primary and induced pluripotent stem cell–derived endothelial cells. Methods and Results Here, the genotype, phenotype, and organ‐chip functional characteristics of blood‐derived outgrowth endothelial cells were compared against commercially available and most used primary endothelial cells and induced pluripotent stem cell–derived endothelial cells. The methods include RNA‐sequencing, as well as criterion standard assays of cell marker expression, growth kinetics, migration potential, and vasculogenesis. Finally, thromboinflammatory responses under shear using vessel‐chips engineered with blood‐derived endothelial cells were assessed. Blood‐derived endothelial cells exhibit the criterion standard hallmarks of typical endothelial cells. There are differences in gene expression profiles between different sources of endothelial cells, but blood‐derived cells are relatively closer to primary cells than induced pluripotent stem cell–derived. Furthermore, blood‐derived endothelial cells are much easier to obtain from individuals and yet, they serve as an equally effective cell source for functional studies and organ‐chips compared with primary cells or induced pluripotent stem cell–derived cells. Conclusions Blood‐derived endothelial cells may be used in preclinical research for developing more robust and personalized next‐generation disease models using organ‐on‐chips.
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Affiliation(s)
- Tanmay Mathur
- Department of Biomedical Engineering, College of Engineering Texas A&M University College Station TX
| | - James J Tronolone
- Department of Biomedical Engineering, College of Engineering Texas A&M University College Station TX
| | - Abhishek Jain
- Department of Biomedical Engineering, College of Engineering Texas A&M University College Station TX.,Department of Medical Physiology College of MedicineTexas A&M Health Science Center Bryan TX.,Department of Cardiovascular Sciences Houston Methodist Research Institute Houston TX
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Human Induced Pluripotent Stem Cell-Derived Vascular Cells: Recent Progress and Future Directions. J Cardiovasc Dev Dis 2021; 8:jcdd8110148. [PMID: 34821701 PMCID: PMC8622843 DOI: 10.3390/jcdd8110148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) hold great promise for cardiovascular regeneration following ischemic injury. Considerable effort has been made toward the development and optimization of methods to differentiate hiPSCs into vascular cells, such as endothelial and smooth muscle cells (ECs and SMCs). In particular, hiPSC-derived ECs have shown robust potential for promoting neovascularization in animal models of cardiovascular diseases, potentially achieving significant and sustained therapeutic benefits. However, the use of hiPSC-derived SMCs that possess high therapeutic relevance is a relatively new area of investigation, still in the earlier investigational stages. In this review, we first discuss different methodologies to derive vascular cells from hiPSCs with a particular emphasis on the role of key developmental signals. Furthermore, we propose a standardized framework for assessing and defining the EC and SMC identity that might be suitable for inducing tissue repair and regeneration. We then highlight the regenerative effects of hiPSC-derived vascular cells on animal models of myocardial infarction and hindlimb ischemia. Finally, we address several obstacles that need to be overcome to fully implement the use of hiPSC-derived vascular cells for clinical application.
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Han JK, Shin Y, Kim HS. Direct Conversion of Cell Fate and Induced Endothelial Cells. Circ J 2021; 86:1925-1933. [PMID: 34732599 DOI: 10.1253/circj.cj-21-0703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Advances in nuclear reprogramming technology have enabled the dedifferentiation and transdifferentiation of mammalian cells. Forced induction of the key transcription factors constituting a transcriptional network can convert cells back to their pluripotent status or directly to another cell fate without inducing pluripotency. To date, direct conversion to several cell types, including cardiomyocytes, various types of neurons, and pancreatic β-cells, has been reported. We previously demonstrated direct lineage reprogramming of adult fibroblasts into induced endothelial cells (iECs) in mice and humans. In contrast to induced pluripotent stem cells, for which there is consensus on the criteria defining pluripotency, such criteria have not yet been established in the field of direct conversion. We thus suggest that careful assessment of the status of converted cells using genetic and epigenetic profiling, various functional assays, and the use of multiple readouts is essential to determine successful conversion. As direct conversion does not go through pluripotent status, this technique can be utilized for therapeutic purposes without the risk of tumorigenesis. Further, direct conversion can be induced in vivo by gene delivery to the target tissue or organ in situ. Thus, direct conversion technology can be developed into cell therapy or gene therapy for regenerative purposes. Here, we review the potential and future directions of direct cell fate conversion and iECs.
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Affiliation(s)
- Jung-Kyu Han
- Department of Internal Medicine, and Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital
| | - Youngchul Shin
- Department of Internal Medicine, and Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital
| | - Hyo-Soo Kim
- Department of Internal Medicine, and Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital
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Parrello D, Vlasenok M, Kranz L, Nechaev S. Targeting the Transcriptome Through Globally Acting Components. Front Genet 2021; 12:749850. [PMID: 34603400 PMCID: PMC8481634 DOI: 10.3389/fgene.2021.749850] [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: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.
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Affiliation(s)
- Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Maria Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lincoln Kranz
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
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Kohela A, van Kampen SJ, Moens T, Wehrens M, Molenaar B, Boogerd CJ, Monshouwer-Kloots J, Perini I, Goumans MJ, Smits AM, van Tintelen JP, van Rooij E. Epicardial differentiation drives fibro-fatty remodeling in arrhythmogenic cardiomyopathy. Sci Transl Med 2021; 13:eabf2750. [PMID: 34550725 DOI: 10.1126/scitranslmed.abf2750] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Arrhythmogenic cardiomyopathy (ACM) is an inherited disorder often caused by pathogenic variants in desmosomal genes and characterized by progressive fibrotic and fat tissue accumulation in the heart. The cellular origin and responsible molecular mechanisms of fibro-fatty deposits have been a matter of debate, due to limitations in animal models recapitulating this phenotype. Here, we used human-induced pluripotent stem cell (hiPSC)–derived cardiac cultures, single-cell RNA sequencing (scRNA-seq), and explanted human ACM hearts to study the epicardial contribution to fibro-fatty remodeling in ACM. hiPSC-epicardial cells generated from patients with ACM showed spontaneous fibro-fatty cellular differentiation that was absent in isogenic controls. This was further corroborated upon siRNA-mediated targeting of desmosomal genes in hiPSC-epicardial cells generated from healthy donors. scRNA-seq analysis identified the transcription factor TFAP2A (activating enhancer-binding protein 2 alpha) as a key trigger promoting this process. Gain- and loss-of-function studies on hiPSC-epicardial cells and primary adult epicardial-derived cells demonstrated that TFAP2A mediated epicardial differentiation through enhancing epithelial-to-mesenchymal transition (EMT). Furthermore, examination of explanted hearts from patients with ACM revealed epicardial activation and expression of TFAP2A in the subepicardial mesenchyme. These data suggest that TFAP2A-mediated epicardial EMT underlies fibro-fatty remodeling in ACM, a process amenable to therapeutic intervention.
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Affiliation(s)
- Arwa Kohela
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands
| | - Sebastiaan J van Kampen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands
| | - Tara Moens
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands
| | - Martijn Wehrens
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands
| | - Bas Molenaar
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands
| | - Cornelis J Boogerd
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands
| | - Jantine Monshouwer-Kloots
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands
| | - Ilaria Perini
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands
| | - Marie José Goumans
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, Netherlands
| | - Anke M Smits
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, Netherlands
| | - J Peter van Tintelen
- Department of Genetics, University Medical Centre Utrecht, 3584 CX Utrecht, Netherlands
| | - Eva van Rooij
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), 3584 CT Utrecht, Netherlands.,Department of Cardiology, University Medical Centre Utrecht, 3584 CX Utrecht, Netherlands
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39
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Ewald ML, Chen YH, Lee AP, Hughes CCW. The vascular niche in next generation microphysiological systems. LAB ON A CHIP 2021; 21:3244-3262. [PMID: 34396383 PMCID: PMC8635227 DOI: 10.1039/d1lc00530h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In recent years, microphysiological system (MPS, also known as, organ-on-a-chip or tissue chip) platforms have emerged with great promise to improve the predictive capacity of preclinical modeling thereby reducing the high attrition rates when drugs move into trials. While their designs can vary quite significantly, in general MPS are bioengineered in vitro microenvironments that recapitulate key functional units of human organs, and that have broad applications in human physiology, pathophysiology, and clinical pharmacology. A critical next step in the evolution of MPS devices is the widespread incorporation of functional vasculature within tissues. The vasculature itself is a major organ that carries nutrients, immune cells, signaling molecules and therapeutics to all other organs. It also plays critical roles in inducing and maintaining tissue identity through expression of angiocrine factors, and in providing tissue-specific milieus (i.e., the vascular niche) that can support the survival and function of stem cells. Thus, organs are patterned, maintained and supported by the vasculature, which in turn receives signals that drive tissue specific gene expression. In this review, we will discuss published vascularized MPS platforms and present considerations for next-generation devices looking to incorporate this critical constituent. Finally, we will highlight the organ-patterning processes governed by the vasculature, and how the incorporation of a vascular niche within MPS platforms will establish a unique opportunity to study stem cell development.
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Affiliation(s)
- Makena L Ewald
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA.
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40
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Shen J, Xu Y, Zhang S, Lyu S, Huo Y, Zhu Y, Tang K, Mou J, Li X, Hoyle DL, Wang M, Wang J, Li X, Wang ZZ, Cheng T. Single-cell transcriptome of early hematopoiesis guides arterial endothelial-enhanced functional T cell generation from human PSCs. SCIENCE ADVANCES 2021; 7:eabi9787. [PMID: 34516916 PMCID: PMC8442917 DOI: 10.1126/sciadv.abi9787] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/14/2021] [Indexed: 05/10/2023]
Abstract
Hematopoietic differentiation of human pluripotent stem cells (hPSCs) requires orchestration of dynamic cell and gene regulatory networks but often generates blood cells that lack natural function. Here, we performed extensive single-cell transcriptomic analyses to map fate choices and gene expression patterns during hematopoietic differentiation of hPSCs and showed that oxidative metabolism was dysregulated during in vitro directed differentiation. Applying hypoxic conditions at the stage of endothelial-to-hematopoietic transition in vitro effectively promoted the development of arterial specification programs that governed the generation of hematopoietic progenitor cells (HPCs) with functional T cell potential. Following engineered expression of the anti-CD19 chimeric antigen receptor, the T cells generated from arterial endothelium-primed HPCs inhibited tumor growth both in vitro and in vivo. Collectively, our study provides benchmark datasets as a resource to further understand the origins of human hematopoiesis and represents an advance in guiding in vitro generation of functional T cells for clinical applications.
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Affiliation(s)
- Jun Shen
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yingxi Xu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Key Laboratory of Blood Disease Cell Therapy, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shuo Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shuzhen Lyu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yingying Huo
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yaoyao Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Department of Laboratory, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Kejing Tang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Key Laboratory of Blood Disease Cell Therapy, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Junli Mou
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Key Laboratory of Blood Disease Cell Therapy, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Xinjie Li
- School of Medicine, Sun Yat-sen University, Guangzhou 510006, China
| | - Dixie L. Hoyle
- Division of Hematology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Min Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Key Laboratory of Blood Disease Cell Therapy, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Tianjin 300020, China
| | - Xin Li
- School of Medicine, Sun Yat-sen University, Guangzhou 510006, China
| | - Zack Z. Wang
- Division of Hematology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China
- Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
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41
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Cell-based therapies for vascular regeneration: Past, present and future. Pharmacol Ther 2021; 231:107976. [PMID: 34480961 DOI: 10.1016/j.pharmthera.2021.107976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/01/2021] [Accepted: 08/05/2021] [Indexed: 12/27/2022]
Abstract
Tissue vascularization remains one of the outstanding challenges in regenerative medicine. Beyond its role in circulating oxygen and nutrients, the vasculature is critical for organ development, function and homeostasis. Importantly, effective vascular regeneration is key in generating large 3D tissues for regenerative medicine applications to enable the survival of cells post-transplantation, organ growth, and integration into the host system. Therefore, the absence of clinically applicable means of (re)generating vessels is one of the main obstacles in cell replacement therapy. In this review, we highlight cell-based vascularization strategies which demonstrate clinical potential, discuss their strengths and limitations and highlight the main obstacles hindering cell-based therapeutic vascularization.
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42
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Mesenchymal stromal cells in the bone marrow niche consist of multi-populations with distinct transcriptional and epigenetic properties. Sci Rep 2021; 11:15811. [PMID: 34349154 PMCID: PMC8338933 DOI: 10.1038/s41598-021-94186-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/30/2021] [Indexed: 12/29/2022] Open
Abstract
Although multiple studies have investigated the mesenchymal stem and progenitor cells (MSCs) that give rise to mature bone marrow, high heterogeneity in their morphologies and properties causes difficulties in molecular separation of their distinct populations. In this study, by taking advantage of the resolution of the single cell transcriptome, we analyzed Sca-1 and PDGFR-α fraction in the mouse bone marrow tissue. The single cell transcriptome enabled us to further classify the population into seven populations according to their gene expression profiles. We then separately obtained the seven populations based on candidate marker genes, and specified their gene expression properties and epigenetic landscape by ATAC-seq. Our findings will enable to elucidate the stem cell niche signal in the bone marrow microenvironment, reconstitute bone marrow in vitro, and shed light on the potentially important role of identified subpopulation in various clinical applications to the treatment of bone- and bone marrow-related diseases.
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43
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Grancharova T, Gerbin KA, Rosenberg AB, Roco CM, Arakaki JE, DeLizo CM, Dinh SQ, Donovan-Maiye RM, Hirano M, Nelson AM, Tang J, Theriot JA, Yan C, Menon V, Palecek SP, Seelig G, Gunawardane RN. A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes. Sci Rep 2021; 11:15845. [PMID: 34349150 PMCID: PMC8338992 DOI: 10.1038/s41598-021-94732-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
We performed a comprehensive analysis of the transcriptional changes occurring during human induced pluripotent stem cell (hiPSC) differentiation to cardiomyocytes. Using single cell RNA-seq, we sequenced > 20,000 single cells from 55 independent samples representing two differentiation protocols and multiple hiPSC lines. Samples included experimental replicates ranging from undifferentiated hiPSCs to mixed populations of cells at D90 post-differentiation. Differentiated cell populations clustered by time point, with differential expression analysis revealing markers of cardiomyocyte differentiation and maturation changing from D12 to D90. We next performed a complementary cluster-independent sparse regression analysis to identify and rank genes that best assigned cells to differentiation time points. The two highest ranked genes between D12 and D24 (MYH7 and MYH6) resulted in an accuracy of 0.84, and the three highest ranked genes between D24 and D90 (A2M, H19, IGF2) resulted in an accuracy of 0.94, revealing that low dimensional gene features can identify differentiation or maturation stages in differentiating cardiomyocytes. Expression levels of select genes were validated using RNA FISH. Finally, we interrogated differences in cardiac gene expression resulting from two differentiation protocols, experimental replicates, and three hiPSC lines in the WTC-11 background to identify sources of variation across these experimental variables.
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Affiliation(s)
| | | | - Alexander B Rosenberg
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,, Parse Biosciences, Seattle, WA, USA
| | - Charles M Roco
- , Parse Biosciences, Seattle, WA, USA.,Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Matthew Hirano
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA
| | | | - Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Julie A Theriot
- Allen Institute for Cell Science, Seattle, WA, USA.,Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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44
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Cornelissen A, Guo L, Fernandez R, Kelly MC, Janifer C, Kuntz S, Sakamoto A, Jinnouchi H, Sato Y, Paek KH, Kolodgie FD, Romero ME, Surve D, Virmani R, Finn AV. Endothelial Recovery in Bare Metal Stents and Drug-Eluting Stents on a Single-Cell Level. Arterioscler Thromb Vasc Biol 2021; 41:2277-2292. [PMID: 34162228 DOI: 10.1161/atvbaha.121.316472] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Anne Cornelissen
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.).,Department of Cardiology, University Hospital RWTH Aachen, Germany (A.C.)
| | - Liang Guo
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Raquel Fernandez
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Michael C Kelly
- Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD (M.C.K.)
| | - Christine Janifer
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Salome Kuntz
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Atsushi Sakamoto
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Hiroyuki Jinnouchi
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Yu Sato
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Ka Hyun Paek
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Frank D Kolodgie
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Maria E Romero
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Dipti Surve
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Renu Virmani
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.)
| | - Aloke V Finn
- CVPath Institute, Gaithersburg, MD (A.C., L.G., R.F., C.J., S.K., A.S., H.J., Y.S., K.H.P., F.D.K., M.E.R., D.S., R.V., A.V.F.).,University of Maryland, School of Medicine, Baltimore (A.V.F.)
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45
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Sayed N, Liu C, Ameen M, Himmati F, Zhang JZ, Khanamiri S, Moonen JR, Wnorowski A, Cheng L, Rhee JW, Gaddam S, Wang KC, Sallam K, Boyd JH, Woo YJ, Rabinovitch M, Wu JC. Clinical trial in a dish using iPSCs shows lovastatin improves endothelial dysfunction and cellular cross-talk in LMNA cardiomyopathy. Sci Transl Med 2021; 12:12/554/eaax9276. [PMID: 32727917 DOI: 10.1126/scitranslmed.aax9276] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 02/13/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022]
Abstract
Mutations in LMNA, the gene that encodes lamin A and C, causes LMNA-related dilated cardiomyopathy (DCM) or cardiolaminopathy. LMNA is expressed in endothelial cells (ECs); however, little is known about the EC-specific phenotype of LMNA-related DCM. Here, we studied a family affected by DCM due to a frameshift variant in LMNA Human induced pluripotent stem cell (iPSC)-derived ECs were generated from patients with LMNA-related DCM and phenotypically characterized. Patients with LMNA-related DCM exhibited clinical endothelial dysfunction, and their iPSC-ECs showed decreased functionality as seen by impaired angiogenesis and nitric oxide (NO) production. Moreover, genome-edited isogenic iPSC lines recapitulated the EC disease phenotype in which LMNA-corrected iPSC-ECs showed restoration of EC function. Simultaneous profiling of chromatin accessibility and gene expression dynamics by combining assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) as well as loss-of-function studies identified Krüppel-like factor 2 (KLF2) as a potential transcription factor responsible for the EC dysfunction. Gain-of-function studies showed that treatment of LMNA iPSC-ECs with KLF2 agonists, including lovastatin, rescued the EC dysfunction. Patients with LMNA-related DCM treated with lovastatin showed improvements in clinical endothelial dysfunction as indicated by increased reactive hyperemia index. Furthermore, iPSC-derived cardiomyocytes (iPSC-CMs) from patients exhibiting the DCM phenotype showed improvement in CM function when cocultured with iPSC-ECs and lovastatin. These results suggest that impaired cross-talk between ECs and CMs can contribute to the pathogenesis of LMNA-related DCM, and statin may be an effective therapy for vascular dysfunction in patients with cardiolaminopathy.
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Affiliation(s)
- Nazish Sayed
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chun Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mohamed Ameen
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Farhan Himmati
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joe Z Zhang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Saereh Khanamiri
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jan-Renier Moonen
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexa Wnorowski
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Linling Cheng
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - June-Wha Rhee
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sadhana Gaddam
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin C Wang
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karim Sallam
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jack H Boyd
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Y Joseph Woo
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marlene Rabinovitch
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
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46
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Liu C, Medina P, Thomas D, Chen IY, Sallam K, Sayed D, Sayed N. A protocol for transdifferentiation of human cardiac fibroblasts into endothelial cells via activation of innate immunity. STAR Protoc 2021; 2:100556. [PMID: 34151292 PMCID: PMC8190482 DOI: 10.1016/j.xpro.2021.100556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Endothelial cells (ECs) have emerged as key pathogenic players in cardiac disease due to their proximity with cardiomyocytes. Induced pluripotent stem cells (iPSCs) have been employed to generate ECs. However, it may be more clinically relevant to transdifferentiate fibroblasts into ECs directly without introducing pluripotent or virally driven transcription factors. Here, we present a protocol that describes the direct conversion of human cardiac fibroblasts into ECs by leveraging the innate immune system. Our protocol produces bona fide human ECs with 95%-98% purity by first passage. For complete details on the use and execution of this protocol, please refer to Liu et al. (2020) and Sayed et al. (2015).
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Affiliation(s)
- Chun Liu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Pedro Medina
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Dilip Thomas
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ian Y. Chen
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Karim Sallam
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Danish Sayed
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Department of Surgery, Division of Vascular Surgery, Stanford University, Stanford, CA 94305, USA
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47
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Alsaigh T, Di Bartolo BA, Mulangala J, Figtree GA, Leeper NJ. Bench-to-Bedside in Vascular Medicine: Optimizing the Translational Pipeline for Patients With Peripheral Artery Disease. Circ Res 2021; 128:1927-1943. [PMID: 34110900 PMCID: PMC8208504 DOI: 10.1161/circresaha.121.318265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peripheral arterial disease is a growing worldwide problem with a wide spectrum of clinical severity and is projected to consume >$21 billion per year in the United States alone. While vascular researchers have brought several therapies to the clinic in recent years, few of these approaches have leveraged advances in high-throughput discovery screens, novel translational models, or innovative trial designs. In the following review, we discuss recent advances in unbiased genomics and broader omics technology platforms, along with preclinical vascular models designed to enhance our understanding of disease pathobiology and prioritize targets for additional investigation. Furthermore, we summarize novel approaches to clinical studies in subjects with claudication and ischemic ulceration, with an emphasis on streamlining and accelerating bench-to-bedside translation. By providing a framework designed to enhance each aspect of future clinical development programs, we hope to enrich the pipeline of therapies that may prevent loss of life and limb for those with peripheral arterial disease.
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Affiliation(s)
- Tom Alsaigh
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Belinda A. Di Bartolo
- Cardiothoracic and Vascular Health, Kolling Institute and Department of Cardiology, Royal North Shore Hospital, Northern Sydney Local Health District, Australia
| | | | - Gemma A. Figtree
- Cardiothoracic and Vascular Health, Kolling Institute and Department of Cardiology, Royal North Shore Hospital, Northern Sydney Local Health District, Australia
| | - Nicholas J. Leeper
- Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, California, United States of America
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48
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Nguyen J, Lin YY, Gerecht S. The next generation of endothelial differentiation: Tissue-specific ECs. Cell Stem Cell 2021; 28:1188-1204. [PMID: 34081899 DOI: 10.1016/j.stem.2021.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Endothelial cells (ECs) sense and respond to fluid flow and regulate immune cell trafficking in all organs. Despite sharing the same mesodermal origin, ECs exhibit heterogeneous tissue-specific characteristics. Human pluripotent stem cells (hPSCs) can potentially be harnessed to capture this heterogeneity and further elucidate endothelium behavior to satisfy the need for increased accuracy and breadth of disease models and therapeutics. Here, we review current strategies for hPSC differentiation to blood vascular ECs and their maturation into continuous, fenestrated, and sinusoidal tissues. We then discuss the contribution of hPSC-derived ECs to recent advances in organoid development and organ-on-chip approaches.
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Affiliation(s)
- Jane Nguyen
- Department of Chemical and Biomolecular Engineering, The Institute for NanoBioTechnology, Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ying-Yu Lin
- Department of Chemical and Biomolecular Engineering, The Institute for NanoBioTechnology, Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sharon Gerecht
- Department of Chemical and Biomolecular Engineering, The Institute for NanoBioTechnology, Physical Sciences-Oncology Center, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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49
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Peng Y, Chu S, Yang Y, Zhang Z, Pang Z, Chen N. Neuroinflammatory In Vitro Cell Culture Models and the Potential Applications for Neurological Disorders. Front Pharmacol 2021; 12:671734. [PMID: 33967814 PMCID: PMC8103160 DOI: 10.3389/fphar.2021.671734] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Abstract
Cell cultures are used in pharmaceutical, medical and biological sciences. Due to the ethical and cost limitations of in vivo models, the replaceable cell model that is more closely related to the characteristics of organisms, which has broad prospects and can be used for high-throughput drug screening is urgent. Neuronal and glial cell models have been widely used in the researches of neurological disorders. And the current researches on neuroinflammation contributes to blood-brain barrier (BBB) damage. In this review, we describe the features of healthy and inflamed BBB and summarize the main immortalized cell lines of the central nervous system (PC12, SH-SY5Y, BV2, HA, and HBMEC et al.) and their use in the anti-inflammatory potential of neurological disorders. Especially, different co-culture models of neuroinflammatory, in association with immune cells in both 2D and 3D models are discussed in this review. In summary, 2D co-culture is easily practicable and economical but cannot fully reproduce the microenvironment in vivo. While 3D models called organs-on-chips or biochips are the most recent and very promising approach, which made possible by bioengineering and biotechnological improvements and more accurately mimic the BBB microenvironment.
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Affiliation(s)
- Ye Peng
- School of Pharmacy, Minzu University of China, Beijing, China.,State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica and Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shifeng Chu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica and Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yantao Yang
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Zhao Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica and Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zongran Pang
- School of Pharmacy, Minzu University of China, Beijing, China
| | - Naihong Chen
- School of Pharmacy, Minzu University of China, Beijing, China.,State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica and Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
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50
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Han JK, Shin Y, Sohn MH, Choi SB, Shin D, You Y, Shin JY, Seo JS, Kim HS. Direct conversion of adult human fibroblasts into functional endothelial cells using defined factors. Biomaterials 2021; 272:120781. [PMID: 33848809 DOI: 10.1016/j.biomaterials.2021.120781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 12/02/2020] [Accepted: 03/20/2021] [Indexed: 02/06/2023]
Abstract
We aimed to directly convert adult human dermal fibroblasts (aHDFs) into functional endothelial cells (ECs). Lentiviral vectors encoding endothelial transcription factors (TFs) were constructed. We examined whether five TFs (FOXO1, ER71, KLF2, TAL1, and LMO2) used for the generation of mouse induced ECs (iECs) could convert the aHDFs into human iECs. Twenty-eight days after transduction with lentiviral constructs, 32.1 ± 5.1% cells expressed vascular endothelial (VE)-cadherin. Factor screening revealed that only three factors (3F: ER71, KLF2, and TAL1) were necessary to induce VE-cadherin (+) cells (49.4 ± 3.5%). However, whole transcriptome sequencing showed that VE-cadherin (+) cells were not completely reprogrammed. Mature iECs double-positive for VE-cadherin/Pecam1 (DP cells) with a cobblestone appearance were obtained at a frequency of only 5.1 ± 0.6%. Using whole transcriptome analysis, the potential factors that could block the conversion were screened. Among candidates TWIST1-knockdown enhanced efficiency of conversion. Rosiglitazone, an inhibitor of epithelial-mesenchymal transition (EMT), also improved the conversion efficiency. Moreover, a 2nd second-stage conversion process, in which VE-cadherin (+) cells were incubated for additional two weeks, further enhanced the efficiency. The final protocol for 6 weeks yielded a conversion rate of 19.6 ± 3.0% iECs, defined by DP cells depicting the nature of mature ECs in various analyses. Further analyses revealed that the genetic and epigenetic profiles of iECs resembled those of functional ECs. Collectively, aHDFs can be converted into functional ECs through the transduction of ER71, KLF2, and TAL1, combined with two EMT inhibitors (siTWIST1 and rosiglitazone), followed by 2nd stage conversion.
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Affiliation(s)
- Jung-Kyu Han
- Division of Cardiology, Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Youngchul Shin
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital, Seoul, South Korea; Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Min-Hwan Sohn
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea; Gong-Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, South Korea; Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea; Macrogen Inc., Seoul, South Korea
| | - Saet-Byeol Choi
- Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Dasom Shin
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital, Seoul, South Korea; Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Youngrang You
- Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital, Seoul, South Korea; Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Jong-Yeon Shin
- Gong-Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, South Korea; Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea; Macrogen Inc., Seoul, South Korea
| | - Jeong-Sun Seo
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea; Gong-Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, South Korea; Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea; Macrogen Inc., Seoul, South Korea; Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Hyo-Soo Kim
- Division of Cardiology, Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea.
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