1
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Maynard A, Soretić M, Treutlein B. Single-cell genomic profiling to study regeneration. Curr Opin Genet Dev 2024; 87:102231. [PMID: 39053027 DOI: 10.1016/j.gde.2024.102231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/27/2024]
Abstract
Regenerative capacities and strategies vary dramatically across animals, as well as between cell types, organs, and with age. In recent years, high-throughput single-cell transcriptomics and other single-cell profiling technologies have been applied to many animal models to gain an understanding of the cellular and molecular mechanisms underlying regeneration. Here, we review recent single-cell studies of regeneration in diverse contexts and summarize key concepts that have emerged. The immense regenerative capacity of some invertebrates, exemplified by planarians, is driven mainly by the differentiation of abundant adult pluripotent stem cells, whereas in many other cases, regeneration involves the reactivation of embryonic or developmental gene-regulatory networks in differentiated cell types. However, regeneration also differs from development in many ways, including the use of regeneration-specific cell types and gene regulatory networks.
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Affiliation(s)
- Ashley Maynard
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Mateja Soretić
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Barbara Treutlein
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland.
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2
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Aztekin C. Mechanisms of regeneration: to what extent do they recapitulate development? Development 2024; 151:dev202541. [PMID: 39045847 DOI: 10.1242/dev.202541] [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] [Indexed: 07/25/2024]
Abstract
One of the enduring debates in regeneration biology is the degree to which regeneration mirrors development. Recent technical advances, such as single-cell transcriptomics and the broad applicability of CRISPR systems, coupled with new model organisms in research, have led to the exploration of this longstanding concept from a broader perspective. In this Review, I outline the historical parallels between development and regeneration before focusing on recent research that highlights how dissecting the divergence between these processes can uncover previously unreported biological mechanisms. Finally, I discuss how these advances position regeneration as a more dynamic and variable process with expanded possibilities for morphogenesis compared with development. Collectively, these insights into mechanisms that orchestrate morphogenesis may reshape our understanding of the evolution of regeneration, reveal hidden biology activated by injury, and offer non-developmental strategies for restoring lost or damaged organs and tissues.
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Affiliation(s)
- Can Aztekin
- School of Life Sciences, Swiss Federal Institute of Technology Lausanne, EPFL, 1015 Lausanne, Switzerland
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3
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Wong D, Martinez J, Quijada P. Exploring the Function of Epicardial Cells Beyond the Surface. Circ Res 2024; 135:353-371. [PMID: 38963865 PMCID: PMC11225799 DOI: 10.1161/circresaha.124.321567] [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: 07/06/2024]
Abstract
The epicardium, previously viewed as a passive outer layer around the heart, is now recognized as an essential component in development, regeneration, and repair. In this review, we explore the cellular and molecular makeup of the epicardium, highlighting its roles in heart regeneration and repair in zebrafish and salamanders, as well as its activation in young and adult postnatal mammals. We also examine the latest technologies used to study the function of epicardial cells for therapeutic interventions. Analysis of highly regenerative animal models shows that the epicardium is essential in regulating cardiomyocyte proliferation, transient fibrosis, and neovascularization. However, despite the epicardium's unique cellular programs to resolve cardiac damage, it remains unclear how to replicate these processes in nonregenerative mammalian organisms. During myocardial infarction, epicardial cells secrete signaling factors that modulate fibrotic, vascular, and inflammatory remodeling, which differentially enhance or inhibit cardiac repair. Recent transcriptomic studies have validated the cellular and molecular heterogeneity of the epicardium across various species and developmental stages, shedding further light on its function under pathological conditions. These studies have also provided insights into the function of regulatory epicardial-derived signaling molecules in various diseases, which could lead to new therapies and advances in reparative cardiovascular medicine. Moreover, insights gained from investigating epicardial cell function have initiated the development of novel techniques, including using human pluripotent stem cells and cardiac organoids to model reparative processes within the cardiovascular system. This growing understanding of epicardial function holds the potential for developing innovative therapeutic strategies aimed at addressing developmental heart disorders, enhancing regenerative therapies, and mitigating cardiovascular disease progression.
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Affiliation(s)
- David Wong
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90029
- Molecular, Cellular and Integrative Physiology Graduate Program, University of California, Los Angeles, CA 90029
| | - Julie Martinez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90029
- Molecular, Cellular and Integrative Physiology Graduate Program, University of California, Los Angeles, CA 90029
| | - Pearl Quijada
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90029
- Eli and Edythe Broad Stem Research Center, University of California, Los Angeles, CA 90029
- Molecular Biology Institute, University of California, Los Angeles, CA 90029
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4
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Abu Nahia K, Sulej A, Migdał M, Ochocka N, Ho R, Kamińska B, Zagorski M, Winata CL. scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation. iScience 2024; 27:110083. [PMID: 38872974 PMCID: PMC11170199 DOI: 10.1016/j.isci.2024.110083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/26/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.
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Affiliation(s)
- Karim Abu Nahia
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdał
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Natalia Ochocka
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Richard Ho
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
- The Njord Centre, Department of Physics, University of Oslo, Oslo, Norway
| | - Bożena Kamińska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcin Zagorski
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
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5
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Shin K, Rodriguez-Parks A, Kim C, Silaban IM, Xia Y, Sun J, Dong C, Keles S, Wang J, Cao J, Kang J. Harnessing the regenerative potential of interleukin11 to enhance heart repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577788. [PMID: 38352555 PMCID: PMC10862709 DOI: 10.1101/2024.01.29.577788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Balancing between regenerative processes and fibrosis is crucial for heart repair, yet strategies regulating this balance remain a barrier to developing therapies. While Interleukin11 (IL11) is known as a fibrotic factor, its contribution to heart regeneration is poorly understood. We uncovered that il11a, an Il11 homolog in zebrafish, can trigger robust regenerative programs in zebrafish hearts, including cardiomyocytes proliferation and coronary expansion, even in the absence of injury. However, prolonged il11a induction in uninjured hearts causes persistent fibroblast emergence, resulting in fibrosis. While deciphering the regenerative and fibrotic effects of il11a, we found that il11-dependent fibrosis, but not regeneration, is mediated through ERK activity, suggesting to potentially uncouple il11a dual effects on regeneration and fibrosis. To harness the il11a's regenerative ability, we devised a combinatorial treatment through il11a induction with ERK inhibition. This approach enhances cardiomyocyte proliferation with mitigated fibrosis, achieving a balance between regenerative processes and fibrosis. Thus, we unveil the mechanistic insights into regenerative il11 roles, offering therapeutic avenues to foster cardiac repair without exacerbating fibrosis.
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Affiliation(s)
- Kwangdeok Shin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Anjelica Rodriguez-Parks
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Chanul Kim
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Isabella M Silaban
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Yu Xia
- Cardiovascular Research Institute, Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jisheng Sun
- Cardiology Division, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Chenyang Dong
- Departments of Statistics and of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Sunduz Keles
- Departments of Statistics and of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Jinhu Wang
- Cardiology Division, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
- UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
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6
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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. SCIENCE ADVANCES 2024; 10:eadn6603. [PMID: 38838146 PMCID: PMC11152119 DOI: 10.1126/sciadv.adn6603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Standard zebrafish transgenesis involves random transgene integration with resource-intensive screening. While phiC31 integrase-based attP/attB recombination has streamlined transgenesis in mice and Drosophila, validated attP-based landing sites for universal applications are lacking in zebrafish. Here, we developed phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET) as transgenesis approach, with two attP landing sites pIGLET14a and pIGLET24b from well-validated Tol2 transgenes. Both sites facilitate diverse transgenesis applications including reporters and Cre/loxP transgenes. The pIGLET14a and pIGLET24b landing sites consistently yield 25 to 50% germline transmission, substantially reducing the resources needed for transgenic line generation. Transgenesis into these sites enables reproducible expression patterns in F0 zebrafish embryos for enhancer discovery and testing of gene regulatory variants. Together, our new landing sites streamline targeted, reproducible zebrafish transgenesis as a robust platform for various applications while minimizing the workload for generating transgenic lines.
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Affiliation(s)
| | | | - Cassie L. Kemmler
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Susan Nieuwenhuize
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Raymundo Lerma
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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7
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Mi J, Ren L, Andersson O. Leveraging zebrafish to investigate pancreatic development, regeneration, and diabetes. Trends Mol Med 2024:S1471-4914(24)00124-2. [PMID: 38825440 DOI: 10.1016/j.molmed.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024]
Abstract
The zebrafish has become an outstanding model for studying organ development and tissue regeneration, which is prominently leveraged for studies of pancreatic development, insulin-producing β-cells, and diabetes. Although studied for more than two decades, many aspects remain elusive and it has only recently been possible to investigate these due to technical advances in transcriptomics, chemical-genetics, genome editing, drug screening, and in vivo imaging. Here, we review recent findings on zebrafish pancreas development, β-cell regeneration, and how zebrafish can be used to provide novel insights into gene functions, disease mechanisms, and therapeutic targets in diabetes, inspiring further use of zebrafish for the development of novel therapies for diabetes.
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Affiliation(s)
- Jiarui Mi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China.
| | - Lipeng Ren
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Cell Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Cell Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden.
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8
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Cardeira-da-Silva J, Wang Q, Sagvekar P, Mintcheva J, Latting S, Günther S, Ramadass R, Yekelchyk M, Preussner J, Looso M, Junker JP, Stainier DYR. Antigen presentation plays positive roles in the regenerative response to cardiac injury in zebrafish. Nat Commun 2024; 15:3637. [PMID: 38684665 PMCID: PMC11058276 DOI: 10.1038/s41467-024-47430-1] [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: 04/25/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
In contrast to adult mammals, adult zebrafish can fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which components of the immune response are required during regeneration is unclear. Here, we report positive roles for the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. We find that following the initial innate immune response, activated endocardial cells (EdCs), as well as immune cells, start expressing antigen presentation genes. We also observe that T helper cells, a.k.a. Cd4+ T cells, lie in close physical proximity to these antigen-presenting EdCs. We targeted Major Histocompatibility Complex (MHC) class II antigen presentation by generating cd74a; cd74b mutants, which display a defective immune response. In these mutants, Cd4+ T cells and activated EdCs fail to efficiently populate the injured tissue and EdC proliferation is significantly decreased. cd74a; cd74b mutants exhibit additional defects in cardiac regeneration including reduced cardiomyocyte dedifferentiation and proliferation. Notably, Cd74 also becomes activated in neonatal mouse EdCs following cardiac injury. Altogether, these findings point to positive roles for antigen presentation during cardiac regeneration, potentially involving interactions between activated EdCs, classical antigen-presenting cells, and Cd4+ T cells.
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Affiliation(s)
- João Cardeira-da-Silva
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
| | - Qianchen Wang
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Pooja Sagvekar
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Janita Mintcheva
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Humboldt University of Berlin, Berlin, Germany
| | - Stephan Latting
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Radhan Ramadass
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michail Yekelchyk
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jens Preussner
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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9
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Carey CM, Hollins HL, Schmid AV, Gagnon JA. Distinct features of the regenerating heart uncovered through comparative single-cell profiling. Biol Open 2024; 13:bio060156. [PMID: 38526188 PMCID: PMC11007736 DOI: 10.1242/bio.060156] [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: 09/18/2023] [Accepted: 03/14/2024] [Indexed: 03/26/2024] Open
Abstract
Adult humans respond to heart injury by forming a permanent scar, yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians, the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features, we compared cardiac injury responses in zebrafish and medaka, two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single-cell transcriptional profiling to create a time-resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach, we identified several key features that distinguish cardiac injury response in the non-regenerating medaka heart. By comparing immune responses to injury, we found altered cell recruitment and a distinct pro-inflammatory gene program in medaka leukocytes, and an absence of the injury-induced interferon response seen in zebrafish. In addition, we found a lack of pro-regenerative signals, including nrg1 and retinoic acid, from medaka endothelial and epicardial cells. Finally, we identified alterations in the myocardial structure in medaka, where they lack primordial layer cardiomyocytes and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka, demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates.
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Affiliation(s)
- Clayton M. Carey
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Hailey L. Hollins
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Alexis V. Schmid
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - James A. Gagnon
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
- Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
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10
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Usui Y, Hanashima A, Hashimoto K, Kimoto M, Ohira M, Mohri S. Comparative analysis of ventricular stiffness across species. Physiol Rep 2024; 12:e16013. [PMID: 38644486 PMCID: PMC11033294 DOI: 10.14814/phy2.16013] [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: 09/20/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/23/2024] Open
Abstract
Investigating ventricular diastolic properties is crucial for understanding the physiological cardiac functions in organisms and unraveling the pathological mechanisms of cardiovascular disorders. Ventricular stiffness, a fundamental parameter that defines ventricular diastolic functions in chordates, is typically analyzed using the end-diastolic pressure-volume relationship (EDPVR). However, comparing ventricular stiffness accurately across chambers of varying maximum volume capacities has been a long-standing challenge. As one of the solutions to this problem, we propose calculating a relative ventricular stiffness index by applying an exponential approximation formula to the EDPVR plot data of the relationship between ventricular pressure and values of normalized ventricular volume by the ventricular weight. This article reviews the potential, utility, and limitations of using normalized EDPVR analysis in recent studies. Herein, we measured and ranked ventricular stiffness in differently sized and shaped chambers using ex vivo ventricular pressure-volume analysis data from four animals: Wistar rats, red-eared slider turtles, masu salmon, and cherry salmon. Furthermore, we have discussed the mechanical effects of intracellular and extracellular viscoelastic components, Titin (Connectin) filaments, collagens, physiological sarcomere length, and other factors that govern ventricular stiffness. Our review provides insights into the comparison of ventricular stiffness in different-sized ventricles between heterologous and homologous species, including non-model organisms.
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Grants
- JP22K15155 Japan Society for the Promotion of Science, Grant/Award Number
- JP20K21453 Japan Society for the Promotion of Science, Grant/Award Number
- JP20H04508 Japan Society for the Promotion of Science, Grant/Award Number
- JP21K19933 Japan Society for the Promotion of Science, Grant/Award Number
- JP20H04521 Japan Society for the Promotion of Science, Grant/Award Number
- JP17H02092 Japan Society for the Promotion of Science, Grant/Award Number
- JP23H00556 Japan Society for the Promotion of Science, Grant/Award Number
- JP17H06272 Japan Society for the Promotion of Science, Grant/Award Number
- JP17H00859 Japan Society for the Promotion of Science, Grant/Award Number
- JP25560214 Japan Society for the Promotion of Science, Grant/Award Number
- JP16K01385 Japan Society for the Promotion of Science, Grant/Award Number
- JP26282127 Japan Society for the Promotion of Science, Grant/Award Number
- The Futaba research grant program
- Research Grant from the Kawasaki Foundation in 2016 from Medical Science and Medical Welfare
- Medical Research Grant in 2010 from Takeda Science Foundation
- R03S005 Research Project Grant from Kawasaki Medical School
- R03B050 Research Project Grant from Kawasaki Medical School
- R01B054 Research Project Grant from Kawasaki Medical School
- H30B041 Research Project Grant from Kawasaki Medical School
- H30B016 Research Project Grant from Kawasaki Medical School
- H27B10 Research Project Grant from Kawasaki Medical School
- R02B039 Research Project Grant from Kawasaki Medical School
- H28B80 Research Project Grant from Kawasaki Medical School
- R05B016 Research Project Grant from Kawasaki Medical School
- Japan Society for the Promotion of Science, Grant/Award Number
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Affiliation(s)
- Yuu Usui
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Akira Hanashima
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Ken Hashimoto
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Misaki Kimoto
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Momoko Ohira
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
| | - Satoshi Mohri
- First Department of PhysiologyKawasaki Medical SchoolKurashikiOkayamaJapan
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11
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van Doorn ECH, Amesz JH, Sadeghi AH, de Groot NMS, Manintveld OC, Taverne YJHJ. Preclinical Models of Cardiac Disease: A Comprehensive Overview for Clinical Scientists. Cardiovasc Eng Technol 2024; 15:232-249. [PMID: 38228811 PMCID: PMC11116217 DOI: 10.1007/s13239-023-00707-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
For recent decades, cardiac diseases have been the leading cause of death and morbidity worldwide. Despite significant achievements in their management, profound understanding of disease progression is limited. The lack of biologically relevant and robust preclinical disease models that truly grasp the molecular underpinnings of cardiac disease and its pathophysiology attributes to this stagnation, as well as the insufficiency of platforms that effectively explore novel therapeutic avenues. The area of fundamental and translational cardiac research has therefore gained wide interest of scientists in the clinical field, while the landscape has rapidly evolved towards an elaborate array of research modalities, characterized by diverse and distinctive traits. As a consequence, current literature lacks an intelligible and complete overview aimed at clinical scientists that focuses on selecting the optimal platform for translational research questions. In this review, we present an elaborate overview of current in vitro, ex vivo, in vivo and in silico platforms that model cardiac health and disease, delineating their main benefits and drawbacks, innovative prospects, and foremost fields of application in the scope of clinical research incentives.
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Affiliation(s)
- Elisa C H van Doorn
- Translational Cardiothoracic Surgery Research Lab, Department of Cardiothoracic Surgery, Erasmus Medical Center, Rotterdam, The Netherlands
- Translational Electrophysiology Laboratory, Department of Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jorik H Amesz
- Translational Cardiothoracic Surgery Research Lab, Department of Cardiothoracic Surgery, Erasmus Medical Center, Rotterdam, The Netherlands
- Translational Electrophysiology Laboratory, Department of Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Amir H Sadeghi
- Translational Cardiothoracic Surgery Research Lab, Department of Cardiothoracic Surgery, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Natasja M S de Groot
- Translational Electrophysiology Laboratory, Department of Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Yannick J H J Taverne
- Translational Cardiothoracic Surgery Research Lab, Department of Cardiothoracic Surgery, Erasmus Medical Center, Rotterdam, The Netherlands.
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12
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Feng J, Li Y, Li Y, Yin Q, Li H, Li J, Zhou B, Meng J, Lian H, Wu M, Li Y, Dou K, Song W, Lu B, Liu L, Hu S, Nie Y. Versican Promotes Cardiomyocyte Proliferation and Cardiac Repair. Circulation 2024; 149:1004-1015. [PMID: 37886839 DOI: 10.1161/circulationaha.123.066298] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND The adult mammalian heart is incapable of regeneration, whereas a transient regenerative capacity is maintained in the neonatal heart, primarily through the proliferation of preexisting cardiomyocytes. Neonatal heart regeneration after myocardial injury is accompanied by an expansion of cardiac fibroblasts and compositional changes in the extracellular matrix. Whether and how these changes influence cardiomyocyte proliferation and heart regeneration remains to be investigated. METHODS We used apical resection and myocardial infarction surgical models in neonatal and adult mice to investigate extracellular matrix components involved in heart regeneration after injury. Single-cell RNA sequencing and liquid chromatography-mass spectrometry analyses were used for versican identification. Cardiac fibroblast-specific Vcan deletion was achieved using the mouse strains Col1a2-2A-CreER and Vcanfl/fl. Molecular signaling pathways related to the effects of versican were assessed through Western blot, immunostaining, and quantitative reverse transcription polymerase chain reaction. Cardiac fibrosis and heart function were evaluated by Masson trichrome staining and echocardiography, respectively. RESULTS Versican, a cardiac fibroblast-derived extracellular matrix component, was upregulated after neonatal myocardial injury and promoted cardiomyocyte proliferation. Conditional knockout of Vcan in cardiac fibroblasts decreased cardiomyocyte proliferation and impaired neonatal heart regeneration. In adult mice, intramyocardial injection of versican after myocardial infarction enhanced cardiomyocyte proliferation, reduced fibrosis, and improved cardiac function. Furthermore, versican augmented the proliferation of human induced pluripotent stem cell-derived cardiomyocytes. Mechanistically, versican activated integrin β1 and downstream signaling molecules, including ERK1/2 and Akt, thereby promoting cardiomyocyte proliferation and cardiac repair. CONCLUSIONS Our study identifies versican as a cardiac fibroblast-derived pro-proliferative proteoglycan and clarifies the role of versican in promoting adult cardiac repair. These findings highlight its potential as a therapeutic factor for ischemic heart diseases.
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Affiliation(s)
- Jie Feng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Yandong Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Yan Li
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China (Y.L.)
| | - Qianqian Yin
- Institute of Medical Innovation and Research, Peking University Third Hospital, Peking University, Beijing, China (Q.Q.Y.)
| | - Haotong Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Jun Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Bin Zhou
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academic of Sciences, Shanghai (B.Z.)
| | - Jian Meng
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Hong Lian
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Mengge Wu
- Experimental Animal Center, Fuwai Central-China Hospital, Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou (M.G.W.)
| | - Yahuan Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Kefei Dou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Weihua Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Bin Lu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Lihui Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing (J.F., Y.D.L., H.T.L., J.L., J.M., H.L., Y.H.L., K.F.D., W.H.S., B.L., L.H.L., S.S.H., Y.N.)
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences (Y.N.)
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou (Y.N.)
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13
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Constanty F, Wu B, Wei KH, Lin IT, Dallmann J, Guenther S, Lautenschlaeger T, Priya R, Lai SL, Stainier DYR, Beisaw A. Border-zone cardiomyocytes and macrophages contribute to remodeling of the extracellular matrix to promote cardiomyocyte invasion during zebrafish cardiac regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584570. [PMID: 38559277 PMCID: PMC10980021 DOI: 10.1101/2024.03.12.584570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Despite numerous advances in our understanding of zebrafish cardiac regeneration, an aspect that remains less studied is how regenerating cardiomyocytes invade, and eventually replace, the collagen-containing fibrotic tissue following injury. Here, we provide an in-depth analysis of the process of cardiomyocyte invasion using live-imaging and histological approaches. We observed close interactions between protruding cardiomyocytes and macrophages at the wound border zone, and macrophage-deficient irf8 mutant zebrafish exhibited defects in extracellular matrix (ECM) remodeling and cardiomyocyte protrusion into the injured area. Using a resident macrophage ablation model, we show that defects in ECM remodeling at the border zone and subsequent cardiomyocyte protrusion can be partly attributed to a population of resident macrophages. Single-cell RNA-sequencing analysis of cells at the wound border revealed a population of cardiomyocytes and macrophages with fibroblast-like gene expression signatures, including the expression of genes encoding ECM structural proteins and ECM-remodeling proteins. The expression of mmp14b , which encodes a membrane-anchored matrix metalloproteinase, was restricted to cells in the border zone, including cardiomyocytes, macrophages, fibroblasts, and endocardial/endothelial cells. Genetic deletion of mmp14b led to a decrease in 1) macrophage recruitment to the border zone, 2) collagen degradation at the border zone, and 3) subsequent cardiomyocyte invasion. Furthermore, cardiomyocyte-specific overexpression of mmp14b was sufficient to enhance cardiomyocyte invasion into the injured tissue and along the apical surface of the wound. Altogether, our data shed important insights into the process of cardiomyocyte invasion of the collagen-containing injured tissue during cardiac regeneration. They further suggest that cardiomyocytes and resident macrophages contribute to ECM remodeling at the border zone to promote cardiomyocyte replenishment of the fibrotic injured tissue.
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14
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Tan FH, Bronner ME. Regenerative loss in the animal kingdom as viewed from the mouse digit tip and heart. Dev Biol 2024; 507:44-63. [PMID: 38145727 PMCID: PMC10922877 DOI: 10.1016/j.ydbio.2023.12.008] [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: 08/06/2023] [Revised: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
The myriad regenerative abilities across the animal kingdom have fascinated us for centuries. Recent advances in developmental, molecular, and cellular biology have allowed us to unearth a surprising diversity of mechanisms through which these processes occur. Developing an all-encompassing theory of animal regeneration has thus proved a complex endeavor. In this chapter, we frame the evolution and loss of animal regeneration within the broad developmental constraints that may physiologically inhibit regenerative ability across animal phylogeny. We then examine the mouse as a model of regeneration loss, specifically the experimental systems of the digit tip and heart. We discuss the digit tip and heart as a positionally-limited system of regeneration and a temporally-limited system of regeneration, respectively. We delve into the physiological processes involved in both forms of regeneration, and how each phase of the healing and regenerative process may be affected by various molecular signals, systemic changes, or microenvironmental cues. Lastly, we also discuss the various approaches and interventions used to induce or improve the regenerative response in both contexts, and the implications they have for our understanding regenerative ability more broadly.
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Affiliation(s)
- Fayth Hui Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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15
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Nguyen T, Rosa-Garrido M, Sadek H, Garry DJ, Zhang JJ. Promoting cardiomyocyte proliferation for myocardial regeneration in large mammals. J Mol Cell Cardiol 2024; 188:52-60. [PMID: 38340541 PMCID: PMC11018144 DOI: 10.1016/j.yjmcc.2024.01.005] [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: 10/21/2023] [Revised: 12/29/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
From molecular and cellular perspectives, heart failure is caused by the loss of cardiomyocytes-the fundamental contractile units of the heart. Because mammalian cardiomyocytes exit the cell cycle shortly after birth, the cardiomyocyte damage induced by myocardial infarction (MI) typically leads to dilatation of the left ventricle (LV) and often progresses to heart failure. However, recent findings indicate that the hearts of neonatal pigs completely regenerated the cardiomyocytes that were lost to MI when the injury occurred on postnatal day 1 (P1). This recovery was accompanied by increases in the expression of markers for cell-cycle activity in cardiomyocytes. These results suggest that the repair process was driven by cardiomyocyte proliferation. This review summarizes findings from recent studies that found evidence of cardiomyocyte proliferation in 1) the uninjured hearts of newborn pigs on P1, 2) neonatal pig hearts after myocardial injury on P1, and 3) the hearts of pigs that underwent apical resection surgery (AR) on P1 followed by MI on postnatal day 28 (P28). Analyses of cardiomyocyte single-nucleus RNA sequencing data collected from the hearts of animals in these three experimental groups, their corresponding control groups, and fetal pigs suggested that although the check-point regulators and other molecules that direct cardiomyocyte cell-cycle progression and proliferation in fetal, newborn, and postnatal pigs were identical, the mechanisms that activated cardiomyocyte proliferation in response to injury may differ from those that regulate cardiomyocyte proliferation during development.
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Affiliation(s)
- Thanh Nguyen
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Hesham Sadek
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel J Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jianyi Jay Zhang
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35233, USA; Department of Medicine, Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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16
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Dong Y, Yang Y, Wang H, Feng D, Nist E, Yapundich N, Spurlock B, Craft M, Qian L, Liu J. Single-cell chromatin profiling reveals genetic programs activating proregenerative states in nonmyocyte cells. SCIENCE ADVANCES 2024; 10:eadk4694. [PMID: 38381829 PMCID: PMC10881044 DOI: 10.1126/sciadv.adk4694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Cardiac regeneration requires coordinated participation of multiple cell types whereby their communications result in transient activation of proregenerative cell states. Although the molecular characteristics and lineage origins of these activated cell states and their contribution to cardiac regeneration have been studied, the extracellular signaling and the intrinsic genetic program underlying the activation of the transient functional cell states remain largely unexplored. In this study, we delineated the chromatin landscapes of the noncardiomyocytes (nonCMs) of the regenerating heart at the single-cell level and inferred the cis-regulatory architectures and trans-acting factors that control cell type-specific gene expression programs. Moreover, further motif analysis and cell-specific genetic manipulations suggest that the macrophage-derived inflammatory signal tumor necrosis factor-α, acting via its downstream transcription factor complex activator protein-1, functions cooperatively with discrete transcription regulators to activate respective nonCM cell types critical for cardiac regeneration. Thus, our study defines the regulatory architectures and intercellular communication principles in zebrafish heart regeneration.
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Affiliation(s)
- Yanhan Dong
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Haofei Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dong Feng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elizabeth Nist
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nicholas Yapundich
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Brian Spurlock
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Madison Craft
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
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17
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Weinberger M, Riley PR. Animal models to study cardiac regeneration. Nat Rev Cardiol 2024; 21:89-105. [PMID: 37580429 DOI: 10.1038/s41569-023-00914-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/16/2023]
Abstract
Permanent fibrosis and chronic deterioration of heart function in patients after myocardial infarction present a major health-care burden worldwide. In contrast to the restricted potential for cellular and functional regeneration of the adult mammalian heart, a robust capacity for cardiac regeneration is seen during the neonatal period in mammals as well as in the adults of many fish and amphibian species. However, we lack a complete understanding as to why cardiac regeneration takes place more efficiently in some species than in others. The capacity of the heart to regenerate after injury is controlled by a complex network of cellular and molecular mechanisms that form a regulatory landscape, either permitting or restricting regeneration. In this Review, we provide an overview of the diverse array of vertebrates that have been studied for their cardiac regenerative potential and discuss differential heart regeneration outcomes in closely related species. Additionally, we summarize current knowledge about the core mechanisms that regulate cardiac regeneration across vertebrate species.
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Affiliation(s)
- Michael Weinberger
- Institute of Developmental & Regenerative Medicine, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Paul R Riley
- Institute of Developmental & Regenerative Medicine, University of Oxford, Oxford, UK.
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18
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Zheng S, Liu T, Chen M, Sun F, Fei Y, Chen Y, Tian X, Wu Z, Zhu Z, Zheng W, Wang Y, Wang W. Morroniside induces cardiomyocyte cell cycle activity and promotes cardiac repair after myocardial infarction in adult rats. Front Pharmacol 2024; 14:1260674. [PMID: 38273822 PMCID: PMC10808748 DOI: 10.3389/fphar.2023.1260674] [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: 08/07/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction: Acute myocardial infarction (AMI) is characterized by the loss of cardiomyocytes, which impairs cardiac function and eventually leads to heart failure. The induction of cardiomyocyte cell cycle activity provides a new treatment strategy for the repair of heart damage. Our previous study demonstrated that morroniside exerts cardioprotective effects. This study investigated the effects and underlying mechanisms of action of morroniside on cardiomyocyte cell cycle activity and cardiac repair following AMI. Methods: Neonatal rat cardiomyocytes (NRCMs) were isolated and exposed to oxygen-glucose deprivation (OGD) in vitro. A rat model of AMI was established by ligation of the left anterior descending coronary artery (LAD) in vivo. Immunofluorescence staining was performed to detect newly generated cardiomyocytes. Western blotting was performed to assess the expression of cell cycle-related proteins. Electrocardiography (ECG) was used to examine pathological Q waves. Masson's trichrome and wheat germ agglutinin (WGA) staining assessed myocardial fibrosis and hypertrophy. Results: The results showed that morroniside induced cardiomyocyte cell cycle activity and increased the levels of cell cycle proteins, including cyclin D1, CDK4, cyclin A2, and cyclin B1, both in vitro and in vivo. Moreover, morroniside reduced myocardial fibrosis and remodeling. Discussion: In conclusion, our study demonstrated that morroniside stimulates cardiomyocyte cell cycle activity and cardiac repair in adult rats, and that these effects may be related to the upregulation of cell cycle proteins.
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Affiliation(s)
- Songyang Zheng
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Tingting Liu
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Mengqi Chen
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Fangling Sun
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yihuan Fei
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei, China
| | - Yanxi Chen
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, Shijiazhuang, Hebei, China
| | - Xin Tian
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Zheng Wu
- Department of Functional Neurosurgery, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Zixin Zhu
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Wenrong Zheng
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yufeng Wang
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Wen Wang
- Department of Experimental Animal Laboratory, Xuanwu Hospital of Capital Medical University, Beijing, China
- Beijing Institute for Brain Disorders, Beijing, China
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19
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Cook SA. Understanding interleukin 11 as a disease gene and therapeutic target. Biochem J 2023; 480:1987-2008. [PMID: 38054591 PMCID: PMC10754292 DOI: 10.1042/bcj20220160] [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: 09/16/2023] [Revised: 11/13/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023]
Abstract
Interleukin 11 (IL11) is an elusive member of the IL6 family of cytokines. While initially thought to be a haematopoietic and cytoprotective factor, more recent data show instead that IL11 is redundant for haematopoiesis and toxic. In this review, the reasons that led to the original misunderstandings of IL11 biology, which are now understandable, are explained with particular attention on the use of recombinant human IL11 in mice and humans. Following tissue injury, as part of an evolutionary ancient homeostatic response, IL11 is secreted from damaged mammalian cells to signal via JAK/STAT3, ERK/P90RSK, LKB1/mTOR and GSK3β/SNAI1 in autocrine and paracrine. This activates a program of mesenchymal transition of epithelial, stromal, and endothelial cells to cause inflammation, fibrosis, and stalled endogenous tissue repair, leading to organ failure. The role of IL11 signalling in cell- and organ-specific pathobiology is described, the large unknowns about IL11 biology are discussed and the promise of targeting IL11 signalling as a therapeutic approach is reviewed.
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Affiliation(s)
- Stuart A Cook
- MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London, U.K
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
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20
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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570868. [PMID: 38106217 PMCID: PMC10723424 DOI: 10.1101/2023.12.08.570868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Standard methods for transgenesis in zebrafish depend on random transgene integration into the genome followed by resource-intensive screening and validation. Targeted vector integration into validated genomic loci using phiC31 integrase-based attP/attB recombination has transformed mouse and Drosophila transgenesis. However, while the phiC31 system functions in zebrafish, validated loci carrying attP-based landing or safe harbor sites suitable for universal transgenesis applications in zebrafish have not been established. Here, using CRISPR-Cas9, we converted two well-validated single insertion Tol2-based zebrafish transgenes with long-standing genetic stability into two attP landing sites, called phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET). Generating fluorescent reporters, loxP-based Switch lines, CreERT2 drivers, and gene-regulatory variant reporters in the pIGLET14a and pIGLET24b landing site alleles, we document their suitability for transgenesis applications across cell types and developmental stages. For both landing sites, we routinely achieve 25-50% germline transmission of targeted transgene integrations, drastically reducing the number of required animals and necessary resources to generate individual transgenic lines. We document that phiC31 integrase-based transgenesis into pIGLET14a and pIGLET24b reproducibly results in representative reporter expression patterns in injected F0 zebrafish embryos suitable for enhancer discovery and qualitative and quantitative comparison of gene-regulatory element variants. Taken together, our new phiC31 integrase-based transgene landing sites establish reproducible, targeted zebrafish transgenesis for numerous applications while greatly reducing the workload of generating new transgenic zebrafish lines.
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Affiliation(s)
- Robert L. Lalonde
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Harrison H. Wells
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Cassie L. Kemmler
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Susan Nieuwenhuize
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Raymundo Lerma
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Alexa Burger
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado, School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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21
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Apaydin O, Altaikyzy A, Filosa A, Sawamiphak S. Alpha-1 adrenergic signaling drives cardiac regeneration via extracellular matrix remodeling transcriptional program in zebrafish macrophages. Dev Cell 2023; 58:2460-2476.e7. [PMID: 37875117 DOI: 10.1016/j.devcel.2023.09.011] [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: 06/27/2022] [Revised: 06/24/2023] [Accepted: 09/29/2023] [Indexed: 10/26/2023]
Abstract
The autonomic nervous system plays a pivotal role in cardiac repair. Here, we describe the mechanistic underpinning of adrenergic signaling in fibrotic and regenerative response of the heart to be dependent on immunomodulation. A pharmacological approach identified adrenergic receptor alpha-1 as a key regulator of macrophage phenotypic diversification following myocardial damage in zebrafish. Genetic manipulation and single-cell transcriptomics showed that the receptor signals activation of an "extracellular matrix remodeling" transcriptional program in a macrophage subset, which serves as a key regulator of matrix composition and turnover. Mechanistically, adrenergic receptor alpha-1-activated macrophages determine activation of collagen-12-expressing fibroblasts, a cellular determinant of cardiac regenerative niche, through midkine-mediated paracrine crosstalk, allowing lymphatic and blood vessel growth and cardiomyocyte proliferation at the lesion site. These findings identify the mechanism of adrenergic signaling in macrophage phenotypic and functional determination and highlight the potential of neural modulation for regulation of fibrosis and coordination of myocardial regenerative response.
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Affiliation(s)
- Onur Apaydin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Akerke Altaikyzy
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Alessandro Filosa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Suphansa Sawamiphak
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
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22
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Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA. The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration. Development 2023; 150:dev201376. [PMID: 37306388 PMCID: PMC10281269 DOI: 10.1242/dev.201376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
The eIF4E family of translation initiation factors bind 5' methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability, yet other related eIF4E families exist and are utilized in specific contexts or tissues. Here, we describe a family called Eif4e1c, for which we find roles during heart development and regeneration in zebrafish. The Eif4e1c family is present in all aquatic vertebrates but is lost in all terrestrial species. A core group of amino acids shared over 500 million years of evolution forms an interface along the protein surface, suggesting that Eif4e1c functions in a novel pathway. Deletion of eif4e1c in zebrafish caused growth deficits and impaired survival in juveniles. Mutants surviving to adulthood had fewer cardiomyocytes and reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although eif4e1c is broadly expressed, its disruption had most notable impact on the heart and at juvenile stages. Our findings reveal context-dependent requirements for translation initiation regulators during heart regeneration.
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Affiliation(s)
- Anupama Rao
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Baken Lyu
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Ishrat Jahan
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Anna Lubertozzi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Gao Zhou
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Frank Tedeschi
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Bryan Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kedryn Baskin
- Department of Cell Biology and Physiology, The Ohio State University Medical Center, Columbus, OH 43210, USA
| | - Joseph Aaron Goldman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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23
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Anderson T, Mo J, Gagarin E, Sherwood D, Blumenkrantz M, Mao E, Leon G, Levitz H, Chen HJ, Tseng KC, Fabian P, Crump JG, Smeeton J. Ligament injury in adult zebrafish triggers ECM remodeling and cell dedifferentiation for scar-free regeneration. NPJ Regen Med 2023; 8:51. [PMID: 37726321 PMCID: PMC10509200 DOI: 10.1038/s41536-023-00329-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023] Open
Abstract
After traumatic injury, healing of mammalian ligaments is typically associated with fibrotic scarring as opposed to scar-free regeneration. In contrast, here we show that the ligament supporting the jaw joint of adult zebrafish is capable of rapid and complete scar-free healing. Following surgical transection of the jaw joint ligament, we observe breakdown of ligament tissue adjacent to the cut sites, expansion of mesenchymal tissue within the wound site, and then remodeling of extracellular matrix (ECM) to a normal ligament morphology. Lineage tracing of mature ligamentocytes following transection shows that they dedifferentiate, undergo cell cycle re-entry, and contribute to the regenerated ligament. Single-cell RNA sequencing of the regenerating ligament reveals dynamic expression of ECM genes in neural-crest-derived mesenchymal cells, as well as diverse immune cells expressing the endopeptidase-encoding gene legumain. Analysis of legumain mutant zebrafish shows a requirement for early ECM remodeling and efficient ligament regeneration. Our study establishes a new model of adult scar-free ligament regeneration and highlights roles of immune-mesenchyme cross-talk in ECM remodeling that initiates regeneration.
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Affiliation(s)
- Troy Anderson
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
| | - Julia Mo
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
| | - Ernesto Gagarin
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
| | - Desmarie Sherwood
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
| | - Maria Blumenkrantz
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
| | - Eric Mao
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
- Department of Biological Sciences, Columbia College, Columbia University, New York, NY, 10027, USA
| | - Gianna Leon
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
- Packer Collegiate Institute, New York, NY, 11201, USA
| | - Hailey Levitz
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
- Department of Chemistry, Barnard College, Columbia University, New York, NY, 10027, USA
| | - Hung-Jhen Chen
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Kuo-Chang Tseng
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Peter Fabian
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Joanna Smeeton
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, and Department of Genetics and Development, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA.
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24
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Chodkowski M, Zielezinski A, Anbalagan S. A ligand-receptor interactome atlas of the zebrafish. iScience 2023; 26:107309. [PMID: 37539027 PMCID: PMC10393773 DOI: 10.1016/j.isci.2023.107309] [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: 01/24/2023] [Revised: 05/25/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Studies in zebrafish can unravel the functions of cellular communication and thus identify novel bench-to-bedside drugs targeting cellular communication signaling molecules. Due to the incomplete annotation of zebrafish proteome, the knowledge of zebrafish receptors, ligands, and tools to explore their interactome is limited. To address this gap, we de novo predicted the cellular localization of zebrafish reference proteome using deep learning algorithm. We combined the predicted and existing annotations on cellular localization of zebrafish proteins and created repositories of zebrafish ligands, membrane receptome, and interactome as well as associated diseases and targeting drugs. Unlike other tools, our interactome atlas is based on both the physical interaction data of zebrafish proteome and existing human ligand-receptor pair databases. The resources are available as R and Python scripts. DanioTalk provides a novel resource for researchers interested in targeting cellular communication in zebrafish, as we demonstrate in applications studying synapse and axo-glial interactome. DanioTalk methodology can be applied to build and explore the ligand-receptor atlas of other non-mammalian model organisms.
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Affiliation(s)
- Milosz Chodkowski
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Andrzej Zielezinski
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Savani Anbalagan
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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25
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Tajer B, Savage AM, Whited JL. The salamander blastema within the broader context of metazoan regeneration. Front Cell Dev Biol 2023; 11:1206157. [PMID: 37635872 PMCID: PMC10450636 DOI: 10.3389/fcell.2023.1206157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Throughout the animal kingdom regenerative ability varies greatly from species to species, and even tissue to tissue within the same organism. The sheer diversity of structures and mechanisms renders a thorough comparison of molecular processes truly daunting. Are "blastemas" found in organisms as distantly related as planarians and axolotls derived from the same ancestral process, or did they arise convergently and independently? Is a mouse digit tip blastema orthologous to a salamander limb blastema? In other fields, the thorough characterization of a reference model has greatly facilitated these comparisons. For example, the amphibian Spemann-Mangold organizer has served as an amazingly useful comparative template within the field of developmental biology, allowing researchers to draw analogies between distantly related species, and developmental processes which are superficially quite different. The salamander limb blastema may serve as the best starting point for a comparative analysis of regeneration, as it has been characterized by over 200 years of research and is supported by a growing arsenal of molecular tools. The anatomical and evolutionary closeness of the salamander and human limb also add value from a translational and therapeutic standpoint. Tracing the evolutionary origins of the salamander blastema, and its relatedness to other regenerative processes throughout the animal kingdom, will both enhance our basic biological understanding of regeneration and inform our selection of regenerative model systems.
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Affiliation(s)
| | | | - Jessica L. Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
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26
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Jimenez Gonzalez A, Baranasic D, Müller F. Zebrafish regulatory genomic resources for disease modelling and regeneration. Dis Model Mech 2023; 16:dmm050280. [PMID: 37529920 PMCID: PMC10417509 DOI: 10.1242/dmm.050280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
In the past decades, the zebrafish has become a disease model with increasing popularity owing to its advantages that include fast development, easy genetic manipulation, simplicity for imaging, and sharing conserved disease-associated genes and pathways with those of human. In parallel, studies of disease mechanisms are increasingly focusing on non-coding mutations, which require genome annotation maps of regulatory elements, such as enhancers and promoters. In line with this, genomic resources for zebrafish research are expanding, producing a variety of genomic data that help in defining regulatory elements and their conservation between zebrafish and humans. Here, we discuss recent developments in generating functional annotation maps for regulatory elements of the zebrafish genome and how this can be applied to human diseases. We highlight community-driven developments, such as DANIO-CODE, in generating a centralised and standardised catalogue of zebrafish genomics data and functional annotations; consider the advantages and limitations of current annotation maps; and offer considerations for interpreting and integrating existing maps with comparative genomics tools. We also discuss the need for developing standardised genomics protocols and bioinformatic pipelines and provide suggestions for the development of analysis and visualisation tools that will integrate various multiomic bulk sequencing data together with fast-expanding data on single-cell methods, such as single-cell assay for transposase-accessible chromatin with sequencing. Such integration tools are essential to exploit the multiomic chromatin characterisation offered by bulk genomics together with the cell-type resolution offered by emerging single-cell methods. Together, these advances will build an expansive toolkit for interrogating the mechanisms of human disease in zebrafish.
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Affiliation(s)
- Ada Jimenez Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London SW7 2AZ, UK
- MRC London Institute of Medical Sciences, London W12 0NN, UK
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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27
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Wei KH, Lin IT, Chowdhury K, Lim KL, Liu KT, Ko TM, Chang YM, Yang KC, Lai SL(B. Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration. eLife 2023; 12:e84679. [PMID: 37498060 PMCID: PMC10411971 DOI: 10.7554/elife.84679] [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: 11/22/2022] [Accepted: 07/26/2023] [Indexed: 07/28/2023] Open
Abstract
Zebrafish exhibit a robust ability to regenerate their hearts following injury, and the immune system plays a key role in this process. We previously showed that delaying macrophage recruitment by clodronate liposome (-1d_CL, macrophage-delayed model) impairs neutrophil resolution and heart regeneration, even when the infiltrating macrophage number was restored within the first week post injury (Lai et al., 2017). It is thus intriguing to learn the regenerative macrophage property by comparing these late macrophages vs. control macrophages during cardiac repair. Here, we further investigate the mechanistic insights of heart regeneration by comparing the non-regenerative macrophage-delayed model with regenerative controls. Temporal RNAseq analyses revealed that -1d_CL treatment led to disrupted inflammatory resolution, reactive oxygen species homeostasis, and energy metabolism during cardiac repair. Comparative single-cell RNAseq profiling of inflammatory cells from regenerative vs. non-regenerative hearts further identified heterogeneous macrophages and neutrophils, showing alternative activation and cellular crosstalk leading to neutrophil retention and chronic inflammation. Among macrophages, two residential subpopulations (hbaa+ Mac and timp4.3+ Mac 3) were enriched only in regenerative hearts and barely recovered after +1d_CL treatment. To deplete the resident macrophage without delaying the circulating macrophage recruitment, we established the resident macrophage-deficient model by administrating CL earlier at 8 d (-8d_CL) before cryoinjury. Strikingly, resident macrophage-deficient zebrafish still exhibited defects in revascularization, cardiomyocyte survival, debris clearance, and extracellular matrix remodeling/scar resolution without functional compensation from the circulating/monocyte-derived macrophages. Our results characterized the diverse function and interaction between inflammatory cells and identified unique resident macrophages prerequisite for zebrafish heart regeneration.
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Affiliation(s)
- Ke-Hsuan Wei
- Graduate Institute of Life Sciences, National Defense Medical CenterTaipeiTaiwan
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - I-Ting Lin
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Kaushik Chowdhury
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Khai Lone Lim
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Kuan-Ting Liu
- Department of Biological Science & Technology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Tai-Ming Ko
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Department of Biological Science & Technology, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
| | - Kai-Chien Yang
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Department and Graduate Institute of Pharmacology, National Taiwan University College of MedicineTaipeiTaiwan
| | - Shih-Lei (Ben) Lai
- Graduate Institute of Life Sciences, National Defense Medical CenterTaipeiTaiwan
- Institute of Biomedical Sciences, Academia SinicaTaipeiTaiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung UniversityTaipeiTaiwan
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28
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Carey CM, Hollins HL, Schmid AV, Gagnon JA. Distinct features of the regenerating heart uncovered through comparative single-cell profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547574. [PMID: 37461520 PMCID: PMC10349989 DOI: 10.1101/2023.07.04.547574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Adult humans respond to heart injury by forming a permanent scar, yet other vertebrates are capable of robust and complete cardiac regeneration. Despite progress towards characterizing the mechanisms of cardiac regeneration in fish and amphibians, the large evolutionary gulf between mammals and regenerating vertebrates complicates deciphering which cellular and molecular features truly enable regeneration. To better define these features, we compared cardiac injury responses in zebrafish and medaka, two fish species that share similar heart anatomy and common teleost ancestry but differ in regenerative capability. We used single-cell transcriptional profiling to create a time-resolved comparative cell atlas of injury responses in all major cardiac cell types across both species. With this approach, we identified several key features that distinguish cardiac injury response in the non-regenerating medaka heart. By comparing immune responses to injury, we found altered cell recruitment and a distinct pro-inflammatory gene program in medaka leukocytes, and an absence of the injury-induced interferon response seen in zebrafish. In addition, we found a lack of pro-regenerative signals, including nrg1 and retinoic acid, from medaka endothelial and epicardial cells. Finally, we identified alterations in the myocardial structure in medaka, where they lack embryonic-like primordial layer cardiomyocytes, and fail to employ a cardioprotective gene program shared by regenerating vertebrates. Our findings reveal notable variation in injury response across nearly all major cardiac cell types in zebrafish and medaka, demonstrating how evolutionary divergence influences the hidden cellular features underpinning regenerative potential in these seemingly similar vertebrates.
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Affiliation(s)
- Clayton M. Carey
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Hailey L. Hollins
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Alexis V. Schmid
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - James A. Gagnon
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
- Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT 84112, USA
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29
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Lu J, Zhang C, Wang W, Xu W, Chen W, Tao L, Li Z, Zhang Y, Cheng J. Exposure to environmental concentrations of glyphosate induces cardiotoxicity through cellular senescence and reduced cell proliferation capacity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 261:115112. [PMID: 37290295 DOI: 10.1016/j.ecoenv.2023.115112] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/01/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Glyphosate (GLY), the preeminent herbicide utilized globally, is known to be exposed to the environment and population on a chronic basis. Exposure to GLY and the consequent health risks are alarming public health problems that are attracting international attention. However, the cardiotoxicity of GLY has been a matter of dispute and uncertainty. Here, AC16 cardiomyocytes and zebrafish were exposed to GLY. This study found that low concentrations of GLY lead to morphological enlargement of AC16 human cardiomyocytes, indicating a senescent state. The increased expression of P16, P21, and P53 following exposure to GLY demonstrated that GLY causes senescence in AC16. Moreover, it was mechanistically confirmed that GLY-induced senescence in AC16 cardiomyocytes was produced by ROS-mediated DNA damage. In terms of in vivo cardiotoxicity, GLY decreased the proliferative capacity of cardiomyocytes in zebrafish through the notch signaling pathway, resulting in a reduction of cardiomyocytes. It was also found that GLY caused zebrafish cardiotoxicity associated with DNA damage and mitochondrial damage. KEGG analysis after RNA-seq shows a significant enrichment of protein processing pathways in the endoplasmic reticulum (ER) after GLY exposure. Importantly, GLY induced ER stress in AC16 cells and zebrafish by activating PERK-eIF2α-ATF4 pathway. Our study has thus provided the first novel insights into the mechanism underlying GLY-induced cardiotoxicity. Furthermore, our findings emphasize the need for increased attention to the potential cardiotoxic effects of GLY.
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Affiliation(s)
- Jian Lu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Cheng Zhang
- Department of Pathology,UT southwestern Medical Center, Dallas, TX 75390, United States
| | - Weiguo Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weidong Chen
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Liming Tao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yang Zhang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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30
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Zhu D, Liu S, Huang K, Li J, Mei X, Li Z, Cheng K. Intrapericardial long non-coding RNA-Tcf21 antisense RNA inducing demethylation administration promotes cardiac repair. Eur Heart J 2023; 44:1748-1760. [PMID: 36916305 PMCID: PMC10411945 DOI: 10.1093/eurheartj/ehad114] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 02/01/2023] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
AIMS Epicardium and epicardium-derived cells are critical players in myocardial fibrosis. Mesenchymal stem cell-derived extracellular vesicles (EVs) have been studied for cardiac repair to improve cardiac remodelling, but the actual mechanisms remain elusive. The aim of this study is to investigate the mechanisms of EV therapy for improving cardiac remodelling and develop a promising treatment addressing myocardial fibrosis. METHODS AND RESULTS Extracellular vesicles were intrapericardially injected for mice myocardial infarction treatment. RNA-seq, in vitro gain- and loss-of-function experiments, and in vivo studies were performed to identify targets that can be used for myocardial fibrosis treatment. Afterward, a lipid nanoparticle-based long non-coding RNA (lncRNA) therapy was prepared for mouse and porcine models of myocardial infarction treatment. Intrapericardial injection of EVs improved adverse myocardial remodelling in mouse models of myocardial infarction. Mechanistically, Tcf21 was identified as a potential target to improve cardiac remodelling. Loss of Tcf21 function in epicardium-derived cells caused increased myofibroblast differentiation, whereas forced Tcf21 overexpression suppressed transforming growth factor-β signalling and myofibroblast differentiation. LncRNA-Tcf21 antisense RNA inducing demethylation (TARID) that enriched in EVs was identified to up-regulate Tcf21 expression. Formulated lncRNA-TARID-laden lipid nanoparticles up-regulated Tcf21 expression in epicardium-derived cells and improved cardiac function and histology in mouse and porcine models of myocardial infarction. CONCLUSION This study identified Tcf21 as a critical target for improving cardiac fibrosis. Up-regulating Tcf21 by using lncRNA-TARID-laden lipid nanoparticles could be a promising way to treat myocardial fibrosis. This study established novel mechanisms underlying EV therapy for improving adverse remodelling and proposed a lncRNA therapy for cardiac fibrosis.
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Affiliation(s)
- Dashuai Zhu
- Joint Department of Biomedical Engineering, North Carolina State University & University of North Carolina at Chapel Hill, 1001 William Moore Drive, Raleigh, NC 27607, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, 1001 William Moore Drive, Raleigh, NC 27607, USA
| | - Shuo Liu
- Joint Department of Biomedical Engineering, North Carolina State University & University of North Carolina at Chapel Hill, 1001 William Moore Drive, Raleigh, NC 27607, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, 1001 William Moore Drive, Raleigh, NC 27607, USA
| | - Ke Huang
- Joint Department of Biomedical Engineering, North Carolina State University & University of North Carolina at Chapel Hill, 1001 William Moore Drive, Raleigh, NC 27607, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, 1001 William Moore Drive, Raleigh, NC 27607, USA
| | - Junlang Li
- Joint Department of Biomedical Engineering, North Carolina State University & University of North Carolina at Chapel Hill, 1001 William Moore Drive, Raleigh, NC 27607, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, 1001 William Moore Drive, Raleigh, NC 27607, USA
| | - Xuan Mei
- Joint Department of Biomedical Engineering, North Carolina State University & University of North Carolina at Chapel Hill, 1001 William Moore Drive, Raleigh, NC 27607, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, 1001 William Moore Drive, Raleigh, NC 27607, USA
| | - Zhenhua Li
- Joint Department of Biomedical Engineering, North Carolina State University & University of North Carolina at Chapel Hill, 1001 William Moore Drive, Raleigh, NC 27607, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, 1001 William Moore Drive, Raleigh, NC 27607, USA
| | - Ke Cheng
- Joint Department of Biomedical Engineering, North Carolina State University & University of North Carolina at Chapel Hill, 1001 William Moore Drive, Raleigh, NC 27607, USA
- Department of Molecular Biomedical Sciences, North Carolina State University, 1001 William Moore Drive, Raleigh, NC 27607, USA
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31
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Li H, Weng W, Zhou B. Perfect duet: Dual recombinases improve genetic resolution. Cell Prolif 2023; 56:e13446. [PMID: 37060165 PMCID: PMC10212704 DOI: 10.1111/cpr.13446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 04/16/2023] Open
Abstract
As a powerful genetic tool, site-specific recombinases (SSRs) have been widely used in genomic manipulation to elucidate cell fate plasticity in vivo, advancing research in stem cell and regeneration medicine. However, the low resolution of conventional single-recombinase-mediated lineage tracing strategies, which rely heavily on the specificity of one marker gene, has led to controversial conclusions in many scientific questions. Therefore, different SSRs systems are combined to improve the accuracy of lineage tracing. Here we review the recent advances in dual-recombinase-mediated genetic approaches, including the development of novel genetic recombination technologies and their applications in cell differentiation, proliferation, and genetic manipulation. In comparison with the single-recombinase system, we also discuss the advantages of dual-genetic strategies in solving scientific issues as well as their technical limitations.
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Affiliation(s)
- Hongxin Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Wendong Weng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of SciencesHangzhouChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- New Cornerstone Science LaboratoryShenzhenChina
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32
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Ji L, Shi Y, Bian Q. Comparative genomics analyses reveal sequence determinants underlying interspecies variations in injury-responsive enhancers. BMC Genomics 2023; 24:177. [PMID: 37020217 PMCID: PMC10077677 DOI: 10.1186/s12864-023-09283-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Injury induces profound transcriptional remodeling events, which could lead to only wound healing, partial tissue repair, or perfect regeneration in different species. Injury-responsive enhancers (IREs) are cis-regulatory elements activated in response to injury signals, and have been demonstrated to promote tissue regeneration in some organisms such as zebrafish and flies. However, the functional significances of IREs in mammals remain elusive. Moreover, whether the transcriptional responses elicited by IREs upon injury are conserved or specialized in different species, and what sequence features may underlie the functional variations of IREs have not been elucidated. RESULTS We identified a set of IREs that are activated in both regenerative and non-regenerative neonatal mouse hearts upon myocardial ischemia-induced damage by integrative epigenomic and transcriptomic analyses. Motif enrichment analysis showed that AP-1 and ETS transcription factor binding motifs are significantly enriched in both zebrafish and mouse IREs. However, the IRE-associated genes vary considerably between the two species. We further found that the IRE-related sequences in zebrafish and mice diverge greatly, with the loss of IRE inducibility accompanied by a reduction in AP-1 and ETS motif frequencies. The functional turnover of IREs between zebrafish and mice is correlated with changes in transcriptional responses of the IRE-associated genes upon injury. Using mouse cardiomyocytes as a model, we demonstrated that the reduction in AP-1 or ETS motif frequency attenuates the activation of IREs in response to hypoxia-induced damage. CONCLUSIONS By performing comparative genomics analyses on IREs, we demonstrated that inter-species variations in AP-1 and ETS motifs may play an important role in defining the functions of enhancers during injury response. Our findings provide important insights for understanding the molecular mechanisms of transcriptional remodeling in response to injury across species.
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Affiliation(s)
- Luzhang Ji
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Yuanyuan Shi
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Qian Bian
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.
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33
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Uscategui Calderon M, Gonzalez BA, Yutzey KE. Cardiomyocyte-fibroblast crosstalk in the postnatal heart. Front Cell Dev Biol 2023; 11:1163331. [PMID: 37077417 PMCID: PMC10106698 DOI: 10.3389/fcell.2023.1163331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
During the postnatal period in mammals, the heart undergoes significant remodeling in response to increased circulatory demands. In the days after birth, cardiac cells, including cardiomyocytes and fibroblasts, progressively lose embryonic characteristics concomitant with the loss of the heart’s ability to regenerate. Moreover, postnatal cardiomyocytes undergo binucleation and cell cycle arrest with induction of hypertrophic growth, while cardiac fibroblasts proliferate and produce extracellular matrix (ECM) that transitions from components that support cellular maturation to production of the mature fibrous skeleton of the heart. Recent studies have implicated interactions of cardiac fibroblasts and cardiomyocytes within the maturing ECM environment to promote heart maturation in the postnatal period. Here, we review the relationships of different cardiac cell types and the ECM as the heart undergoes both structural and functional changes during development. Recent advances in the field, particularly in several recently published transcriptomic datasets, have highlighted specific signaling mechanisms that underlie cellular maturation and demonstrated the biomechanical interdependence of cardiac fibroblast and cardiomyocyte maturation. There is increasing evidence that postnatal heart development in mammals is dependent on particular ECM components and that resulting changes in biomechanics influence cell maturation. These advances, in definition of cardiac fibroblast heterogeneity and function in relation to cardiomyocyte maturation and the extracellular environment provide, support for complex cell crosstalk in the postnatal heart with implications for heart regeneration and disease mechanisms.
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Affiliation(s)
- Maria Uscategui Calderon
- Division of Molecular Cardiovascular Biology, The Heart Institute, Cincinnati Children’s Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Brittany A. Gonzalez
- Division of Molecular Cardiovascular Biology, The Heart Institute, Cincinnati Children’s Medical Center, Cincinnati, OH, United States
| | - Katherine E. Yutzey
- Division of Molecular Cardiovascular Biology, The Heart Institute, Cincinnati Children’s Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- *Correspondence: Katherine E. Yutzey,
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34
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Botos MA, Arora P, Chouvardas P, Mercader N. Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart. Sci Rep 2023; 13:5418. [PMID: 37012284 PMCID: PMC10070245 DOI: 10.1038/s41598-023-32272-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signaling pathways and gene regulatory networks in the zebrafish heart regeneration process. This process has been studied in response to different types of injuries namely: ventricular resection, ventricular cryoinjury, and genetic ablation of cardiomyocytes. However, there exists no database to compare injury specific and core cardiac regeneration responses. Here, we present a meta-analysis of transcriptomic data of regenerating zebrafish hearts in response to these three injury models at 7 days post injury (7dpi). We reanalyzed 36 samples and analyzed the differentially expressed genes (DEG) followed by downstream Gene Ontology Biological Processes (GO:BP) analysis. We found that the three injury models share a common core of DEG encompassing genes involved in cell proliferation, the Wnt signaling pathway and genes that are enriched in fibroblasts. We also found injury-specific gene signatures for resection and genetic ablation, and to a lower extent the cryoinjury model. Finally, we present our data in a user-friendly web interface that displays gene expression signatures across different injury types and highlights the importance to consider injury-specific gene regulatory networks when interpreting the results related to cardiac regeneration in the zebrafish. The analysis is freely available at: https://mybinder.org/v2/gh/MercaderLabAnatomy/PUB_Botos_et_al_2022_shinyapp_binder/HEAD?urlpath=shiny/bus-dashboard/ .
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Affiliation(s)
- Marius Alexandru Botos
- Institute of Anatomy, University of Bern, 3012, Bern, Switzerland
- Department for Biomedical Research, University of Bern, 3012, Bern, Switzerland
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Prateek Arora
- Institute of Anatomy, University of Bern, 3012, Bern, Switzerland
- Department for Biomedical Research, University of Bern, 3012, Bern, Switzerland
| | - Panagiotis Chouvardas
- Department for Biomedical Research, University of Bern, 3012, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, 3010, Bern, Switzerland
| | - Nadia Mercader
- Institute of Anatomy, University of Bern, 3012, Bern, Switzerland.
- Department for Biomedical Research, University of Bern, 3012, Bern, Switzerland.
- Centro Nacional de Investigaciones Cardiovasculares CNIC, 28029, Madrid, Spain.
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35
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Amrute JM, Lai L, Ma P, Koenig AL, Kamimoto K, Bredemeyer A, Shankar TS, Kuppe C, Kadyrov FF, Schulte LJ, Stoutenburg D, Kopecky BJ, Navankasattusas S, Visker J, Morris SA, Kramann R, Leuschner F, Mann DL, Drakos SG, Lavine KJ. Defining cardiac functional recovery in end-stage heart failure at single-cell resolution. NATURE CARDIOVASCULAR RESEARCH 2023; 2:399-416. [PMID: 37583573 PMCID: PMC10426763 DOI: 10.1038/s44161-023-00260-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/01/2023] [Indexed: 08/17/2023]
Abstract
Recovery of cardiac function is the holy grail of heart failure therapy yet is infrequently observed and remains poorly understood. In this study, we performed single-nucleus RNA sequencing from patients with heart failure who recovered left ventricular systolic function after left ventricular assist device implantation, patients who did not recover and non-diseased donors. We identified cell-specific transcriptional signatures of recovery, most prominently in macrophages and fibroblasts. Within these cell types, inflammatory signatures were negative predictors of recovery, and downregulation of RUNX1 was associated with recovery. In silico perturbation of RUNX1 in macrophages and fibroblasts recapitulated the transcriptional state of recovery. Cardiac recovery mediated by BET inhibition in mice led to decreased macrophage and fibroblast Runx1 expression and diminished chromatin accessibility within a Runx1 intronic peak and acquisition of human recovery signatures. These findings suggest that cardiac recovery is a unique biological state and identify RUNX1 as a possible therapeutic target to facilitate cardiac recovery.
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Affiliation(s)
- Junedh M. Amrute
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- These authors contributed equally: Junedh M. Amrute, Lulu Lai
| | - Lulu Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- These authors contributed equally: Junedh M. Amrute, Lulu Lai
| | - Pan Ma
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew L. Koenig
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Bredemeyer
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Thirupura S. Shankar
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology and Division of Nephrology, RWTH Aachen University, Aachen, Germany
| | - Farid F. Kadyrov
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Linda J. Schulte
- Division of Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Dylan Stoutenburg
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin J. Kopecky
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sutip Navankasattusas
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Joseph Visker
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Samantha A. Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology and Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Florian Leuschner
- Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg, Heidelberg, Germany
| | - Douglas L. Mann
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Stavros G. Drakos
- Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT, USA
| | - Kory J. Lavine
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
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36
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Xia Y, Duca S, Perder B, Dündar F, Zumbo P, Qiu M, Yao J, Cao Y, Harrison MRM, Zangi L, Betel D, Cao J. Activation of a transient progenitor state in the epicardium is required for zebrafish heart regeneration. Nat Commun 2022; 13:7704. [PMID: 36513650 PMCID: PMC9747719 DOI: 10.1038/s41467-022-35433-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The epicardium, a mesothelial cell tissue that encompasses vertebrate hearts, supports heart regeneration after injury through paracrine effects and as a source of multipotent progenitors. However, the progenitor state in the adult epicardium has yet to be defined. Through single-cell RNA-sequencing of isolated epicardial cells from uninjured and regenerating adult zebrafish hearts, we define the epithelial and mesenchymal subsets of the epicardium. We further identify a transiently activated epicardial progenitor cell (aEPC) subpopulation marked by ptx3a and col12a1b expression. Upon cardiac injury, aEPCs emerge from the epithelial epicardium, migrate to enclose the wound, undergo epithelial-mesenchymal transition (EMT), and differentiate into mural cells and pdgfra+hapln1a+ mesenchymal epicardial cells. These EMT and differentiation processes are regulated by the Tgfβ pathway. Conditional ablation of aEPCs blocks heart regeneration through reduced nrg1 expression and mesenchymal cell number. Our findings identify a transient progenitor population of the adult epicardium that is indispensable for heart regeneration and highlight it as a potential target for enhancing cardiac repair.
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Affiliation(s)
- Yu Xia
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Sierra Duca
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Björn Perder
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Miaoyan Qiu
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Jun Yao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Yingxi Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Michael R M Harrison
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Lior Zangi
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Institute for Computational Biomedicine, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
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37
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Comparative single-cell analysis of the adult heart and coronary vasculature. Mamm Genome 2022:10.1007/s00335-022-09968-7. [DOI: 10.1007/s00335-022-09968-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/07/2022] [Indexed: 11/21/2022]
Abstract
AbstractThe structure and function of the circulatory system, including the heart, have undergone substantial changes with the vertebrate evolution. Although the basic function of the heart is to pump blood through the body, its size, shape, speed, regeneration capacity, etc. vary considerably across species. Here, we address the differences among vertebrate hearts using a single-cell transcriptomics approach. Published datasets of macaque (Macaca fascicularis), mouse, and zebrafish hearts were integrated and compared to the human heart as a reference. While the three mammalian hearts integrated well, the zebrafish heart showed very little overlap with the other species. Our analysis revealed a mouse-specific cell subpopulation of ventricular cardiomyocytes (CM), represented by strikingly different expression patterns of specific genes related to high-energy metabolism. Interestingly, the observed differences between mouse and human CM coincided with actual biological differences between the two species. Smooth muscle and endothelial cells (EC) exhibited species-specific differences in clustering and gene expression, respectively, which we attribute to the tissues selected for sequencing, given different focuses of the original studies. Finally, we compared human and zebrafish heart-specific fibroblasts (FB) and identified a distinctively high expression of genes associated with heart regeneration following injury in zebrafish. Together, our results show that integration of numerous datasets of different species and different sequencing technologies is feasible and that this approach can identify species-specific differences and similarities in the heart.
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38
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Single-Cell RNA Sequencing Reveals Distinct Cardiac-Derived Stromal Cell Subpopulations. J Cardiovasc Dev Dis 2022; 9:jcdd9110374. [DOI: 10.3390/jcdd9110374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Human cardiac-derived c-kit+ stromal cells (CSCs) have demonstrated efficacy in preclinical trials for the treatment of heart failure and myocardial dysfunction. Unfortunately, large variability in patient outcomes and cell populations remains a problem. Previous research has demonstrated that the reparative capacity of CSCs may be linked to the age of the cells: CSCs derived from neonate patients increase cardiac function and reduce fibrosis. However, age-dependent differences between CSC populations have primarily been explored with bulk sequencing methods. In this work, we hypothesized that differences in CSC populations and subsequent cell therapy outcomes may arise from differing cell subtypes within donor CSC samples. We performed single-cell RNA sequencing on four neonatal CSC (nCSC) and five child CSC (cCSC) samples. Subcluster analysis revealed cCSC-enriched clusters upregulated in several fibrosis- and immune response-related genes. Module-based analysis identified upregulation of chemotaxis and ribosomal activity-related genes in nCSCs and upregulation of immune response and fiber synthesis genes in cCSCs. Further, we identified versican and integrin alpha 2 as potential markers for a fibrotic cell subtype. By investigating differences in patient-derived CSC populations at the single-cell level, this research aims to identify and characterize CSC subtypes to better optimize CSC-based therapy and improve patient outcomes.
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