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Kapuria S, Bai H, Fierros J, Huang Y, Ma F, Yoshida T, Aguayo A, Kok F, Wiens KM, Yip JK, McCain ML, Pellegrini M, Nagashima M, Hitchcock PF, Mochizuki N, Lawson ND, Harrison MMR, Lien CL. Heterogeneous pdgfrb+ cells regulate coronary vessel development and revascularization during heart regeneration. Development 2022; 149:274137. [PMID: 35088848 PMCID: PMC8918812 DOI: 10.1242/dev.199752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022]
Abstract
Endothelial cells emerge from the atrioventricular canal to form coronary blood vessels in juvenile zebrafish hearts. We find that pdgfrb is first expressed in the epicardium around the atrioventricular canal and later becomes localized mainly in the mural cells. pdgfrb mutant fish show severe defects in mural cell recruitment and coronary vessel development. Single-cell RNA sequencing analyses identified pdgfrb+ cells as epicardium-derived cells (EPDCs) and mural cells. Mural cells associated with coronary arteries also express cxcl12b and smooth muscle cell markers. Interestingly, these mural cells remain associated with coronary arteries even in the absence of Pdgfrβ, although smooth muscle gene expression is downregulated. We find that pdgfrb expression dynamically changes in EPDCs of regenerating hearts. Differential gene expression analyses of pdgfrb+ EPDCs and mural cells suggest that they express genes that are important for regeneration after heart injuries. mdka was identified as a highly upregulated gene in pdgfrb+ cells during heart regeneration. However, pdgfrb but not mdka mutants show defects in heart regeneration after amputation. Our results demonstrate that heterogeneous pdgfrb+ cells are essential for coronary development and heart regeneration.
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Affiliation(s)
- Subir Kapuria
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Authors for correspondence (; ; )
| | - Haipeng Bai
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, People's Republic of China
| | - Juancarlos Fierros
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Department of Biology, California State University, San Bernardino, San Bernardino, CA 92407, USA
| | - Ying Huang
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, College of Letters and Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tyler Yoshida
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90007, USA
| | - Antonio Aguayo
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Fatma Kok
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Katie M. Wiens
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Science Department, Bay Path University, Longmeadow, MA 01106, USA
| | - Joycelyn K. Yip
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Megan L. McCain
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, College of Letters and Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mikiko Nagashima
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Peter F. Hitchcock
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Naoki Mochizuki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Osaka, 564-8565, Japan
| | - Nathan D. Lawson
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael M. R. Harrison
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Authors for correspondence (; ; )
| | - Ching-Ling Lien
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Authors for correspondence (; ; )
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2
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Nepomuceno-Chamorro IA, Nepomuceno JA, Galván-Rojas JL, Vega-Márquez B, Rubio-Escudero C. Using prior knowledge in the inference of gene association networks. APPL INTELL 2020. [DOI: 10.1007/s10489-020-01705-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Juul Belling H, Hofmeister W, Andersen DC. A Systematic Exposition of Methods used for Quantification of Heart Regeneration after Apex Resection in Zebrafish. Cells 2020; 9:cells9030548. [PMID: 32111059 PMCID: PMC7140516 DOI: 10.3390/cells9030548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 02/06/2023] Open
Abstract
Myocardial infarction (MI) is a worldwide condition that affects millions of people. This is mainly caused by the adult human heart lacking the ability to regenerate upon injury, whereas zebrafish have the capacity through cardiomyocyte proliferation to fully regenerate the heart following injury such as apex resection (AR). But a systematic overview of the methods used to evidence heart regrowth and regeneration in the zebrafish is lacking. Herein, we conducted a systematical search in Embase and Pubmed for studies on heart regeneration in the zebrafish following injury and identified 47 AR studies meeting the inclusion criteria. Overall, three different methods were used to assess heart regeneration in zebrafish AR hearts. 45 out of 47 studies performed qualitative (37) and quantitative (8) histology, whereas immunohistochemistry for various cell cycle markers combined with cardiomyocyte specific proteins was used in 34 out of 47 studies to determine cardiomyocyte proliferation qualitatively (6 studies) or quantitatively (28 studies). For both methods, analysis was based on selected heart sections and not the whole heart, which may bias interpretations. Likewise, interstudy comparison of reported cardiomyocyte proliferation indexes seems complicated by distinct study designs and reporting manners. Finally, six studies performed functional analysis to determine heart function, a hallmark of human heart injury after MI. In conclusion, our data implies that future studies should consider more quantitative methods eventually taking the 3D of the zebrafish heart into consideration when evidencing myocardial regrowth after AR. Furthermore, standardized guidelines for reporting cardiomyocyte proliferation and sham surgery details may be considered to enable inter study comparisons and robustly determine the effect of given genes on the process of heart regeneration.
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Affiliation(s)
- Helene Juul Belling
- Laboratory of Molecular and Cellular Cardiology, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense C, Denmark; (H.J.B.); (W.H.)
- Clinical Institute, University of Southern Denmark, Winsloewparken 25, 1. floor, 5000 Odense C, Denmark
| | - Wolfgang Hofmeister
- Laboratory of Molecular and Cellular Cardiology, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense C, Denmark; (H.J.B.); (W.H.)
- Clinical Institute, University of Southern Denmark, Winsloewparken 25, 1. floor, 5000 Odense C, Denmark
- Faculty of Health and Medical Sciences, DanStem, Novo Nordisk Foundation Center for Stem Cell Biology, 2200 København H, Denmark
| | - Ditte Caroline Andersen
- Laboratory of Molecular and Cellular Cardiology, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense C, Denmark; (H.J.B.); (W.H.)
- Clinical Institute, University of Southern Denmark, Winsloewparken 25, 1. floor, 5000 Odense C, Denmark
- Correspondence:
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4
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Zuppo DA, Tsang M. Zebrafish heart regeneration: Factors that stimulate cardiomyocyte proliferation. Semin Cell Dev Biol 2019; 100:3-10. [PMID: 31563389 DOI: 10.1016/j.semcdb.2019.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 02/07/2023]
Abstract
Myocardial infarctions (MI) remain a leading cause of global morbidity and mortality, and a reason for this is the inability of adult, mammalian cardiomyocytes to divide post-MI. Recent studies demonstrate a limited population of cardiomyocytes retain their proliferative capacity and understanding how endogenous cardiomyocytes can be stimulated to re-enter the cell cycle is a focus of current research. In this review we discuss the history of zebrafish cardiac regeneration and highlight how different models reveal the molecular pathways important in driving cardiomyocyte proliferation after injury. Understanding the molecules that regulate cell cycle re-entry can provide insights into promoting cardiac repair in humans.
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Affiliation(s)
- D A Zuppo
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - M Tsang
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA.
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5
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González-Rosa JM, Burns CE, Burns CG. Zebrafish heart regeneration: 15 years of discoveries. ACTA ACUST UNITED AC 2017; 4:105-123. [PMID: 28979788 PMCID: PMC5617908 DOI: 10.1002/reg2.83] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 12/12/2022]
Abstract
Cardiovascular disease is the leading cause of death worldwide. Compared to other organs such as the liver, the adult human heart lacks the capacity to regenerate on a macroscopic scale after injury. As a result, myocardial infarctions are responsible for approximately half of all cardiovascular related deaths. In contrast, the zebrafish heart regenerates efficiently upon injury through robust myocardial proliferation. Therefore, deciphering the mechanisms that underlie the zebrafish heart's endogenous regenerative capacity represents an exciting avenue to identify novel therapeutic strategies for inducing regeneration of the human heart. This review provides a historical overview of adult zebrafish heart regeneration. We summarize 15 years of research, with a special focus on recent developments from this fascinating field. We discuss experimental findings that address fundamental questions of regeneration research. What is the origin of regenerated muscle? How is regeneration controlled from a genetic and molecular perspective? How do different cell types interact to achieve organ regeneration? Understanding natural models of heart regeneration will bring us closer to answering the ultimate question: how can we stimulate myocardial regeneration in humans?
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Affiliation(s)
- Juan Manuel González-Rosa
- Cardiovascular Research Center Massachusetts General Hospital Charlestown MA 02129 USA.,Harvard Medical School Boston MA 02115 USA
| | - Caroline E Burns
- Cardiovascular Research Center Massachusetts General Hospital Charlestown MA 02129 USA.,Harvard Medical School Boston MA 02115 USA.,Harvard Stem Cell Institute Cambridge MA 02138 USA
| | - C Geoffrey Burns
- Cardiovascular Research Center Massachusetts General Hospital Charlestown MA 02129 USA.,Harvard Medical School Boston MA 02115 USA
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6
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Koth J, Maguire ML, McClymont D, Diffley L, Thornton VL, Beech J, Patient RK, Riley PR, Schneider JE. High-Resolution Magnetic Resonance Imaging of the Regenerating Adult Zebrafish Heart. Sci Rep 2017; 7:2917. [PMID: 28592901 PMCID: PMC5462770 DOI: 10.1038/s41598-017-03050-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 04/24/2017] [Indexed: 02/08/2023] Open
Abstract
The adult zebrafish is a well-established model for studying heart regeneration, but due to its tissue opaqueness, repair has been primarily assessed using destructive histology, precluding repeated investigations of the same animal. We present a high-resolution, non-invasive in vivo magnetic resonance imaging (MRI) method incorporating a miniature respiratory and anaesthetic perfusion set-up for live adult zebrafish, allowing for visualization of scar formation and heart regeneration in the same animal over time at an isotropic 31 µm voxel resolution. To test the method, we compared well and poorly healing cardiac ventricles using a transgenic fish model that exhibits heat-shock (HS) inducible impaired heart regeneration. HS-treated groups revealed persistent scar tissue for 10 weeks, while control groups were healed after 4 weeks. Application of the advanced MRI technique allowed clear discrimination of levels of repair following cryo- and resection injury for several months. It further provides a novel tool for in vivo time-lapse imaging of adult fish for non-cardiac studies, as the method can be readily applied to image wound healing in other injured or diseased tissues, or to monitor tissue changes over time, thus expanding the range of questions that can be addressed in adult zebrafish and other small aquatic species.
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Affiliation(s)
- Jana Koth
- Weatherall Institute of Molecular Medicine, JR Hospital, Oxford University, Oxford, OX3 9DS, UK.
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, OX1 3PT, UK.
| | - Mahon L Maguire
- BHF Experimental MR Unit, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK
| | - Darryl McClymont
- BHF Experimental MR Unit, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK
| | - Leonie Diffley
- BHF Experimental MR Unit, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK
| | - Victoria L Thornton
- BHF Experimental MR Unit, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK
| | - John Beech
- Department of Oncology, Oxford University, Oxford, OX3 7DQ, UK
| | - Roger K Patient
- Weatherall Institute of Molecular Medicine, JR Hospital, Oxford University, Oxford, OX3 9DS, UK
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford, OX1 3PT, UK
| | - Jürgen E Schneider
- BHF Experimental MR Unit, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, OX3 7BN, UK.
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7
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Abstract
The hearts of lower vertebrates such as fish and salamanders display scarless regeneration following injury, although this feature is lost in adult mammals. The remarkable capacity of the neonatal mammalian heart to regenerate suggests that the underlying machinery required for the regenerative process is evolutionarily retained. Recent studies highlight the epicardial covering of the heart as an important source of the signalling factors required for the repair process. The developing epicardium is also a major source of cardiac fibroblasts, smooth muscle, endothelial cells and stem cells. Here, we examine animal models that are capable of scarless regeneration, the role of the epicardium as a source of cells, signalling mechanisms implicated in the regenerative process and how these mechanisms influence cardiomyocyte proliferation. We also discuss recent advances in cardiac stem cell research and potential therapeutic targets arising from these studies.
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Affiliation(s)
| | - Nadia Rosenthal
- National Heart and Lung Institute, Imperial College London, London, UK Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia The Jackson Laboratory, Bar Harbor, ME, USA
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8
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Rodius S, Fournier A, Götz L, Liechti R, Crespo I, Merz S, Nazarov PV, de Klein N, Jeanty C, González-Rosa JM, Muller A, Bernardin F, Niclou SP, Vallar L, Mercader N, Ibberson M, Xenarios I, Azuaje F. Analysis of the dynamic co-expression network of heart regeneration in the zebrafish. Sci Rep 2016; 6:26822. [PMID: 27241320 PMCID: PMC4886216 DOI: 10.1038/srep26822] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022] Open
Abstract
The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration.
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Affiliation(s)
- Sophie Rodius
- Oncology Department, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, L-1526 Luxembourg
| | - Anna Fournier
- Oncology Department, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, L-1526 Luxembourg
- Present Address: Present address: Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg.,
| | - Lou Götz
- Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015 Switzerland
| | - Robin Liechti
- Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015 Switzerland
| | - Isaac Crespo
- Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015 Switzerland
| | - Susanne Merz
- Oncology Department, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, L-1526 Luxembourg
| | - Petr V. Nazarov
- Oncology Department, Genomics Research Unit, LIH, L-1526 Luxembourg Luxembourg
| | - Niek de Klein
- Oncology Department, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, L-1526 Luxembourg
- Vrije Universiteit Amsterdam, 1081 HV Amsterdam The Netherlands
- Present Address: Present address: Department of Genetics, University of Groningen, Groningen, 9700 RB, The Netherlands.,
| | - Céline Jeanty
- Oncology Department, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, L-1526 Luxembourg
| | - Juan M. González-Rosa
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114 USA
| | - Arnaud Muller
- Oncology Department, Genomics Research Unit, LIH, L-1526 Luxembourg Luxembourg
| | - Francois Bernardin
- Oncology Department, Genomics Research Unit, LIH, L-1526 Luxembourg Luxembourg
| | - Simone P. Niclou
- Oncology Department, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, L-1526 Luxembourg
| | - Laurent Vallar
- Oncology Department, Genomics Research Unit, LIH, L-1526 Luxembourg Luxembourg
| | - Nadia Mercader
- Epicardium Development and Regeneration group, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC-ISCIII), 28029 Madrid Spain
- Present Address: Present address: Department of Development and Regeneration, Institute of Anatomy, Faculty of Medicine, University of Bern, Bern, Switzerland.,
| | - Mark Ibberson
- Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015 Switzerland
| | - Ioannis Xenarios
- Vital-IT Systems Biology Division, SIB Swiss Institute of Bioinformatics, Lausanne, CH-1015 Switzerland
- Center for Integrative Genomics, University of Lausanne, Lausanne, CH-1015 Switzerland
- Department of Biochemistry, University of Geneva, 1211 Geneva 4, Switzerland
| | - Francisco Azuaje
- Oncology Department, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, L-1526 Luxembourg
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9
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Nepomuceno-Chamorro IA. Model tree to improve the inference of gene association networks. AI COMMUN 2016. [DOI: 10.3233/aic-160700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Singh AR, Sivadas A, Sabharwal A, Vellarikal SK, Jayarajan R, Verma A, Kapoor S, Joshi A, Scaria V, Sivasubbu S. Chamber Specific Gene Expression Landscape of the Zebrafish Heart. PLoS One 2016; 11:e0147823. [PMID: 26815362 PMCID: PMC4729522 DOI: 10.1371/journal.pone.0147823] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/08/2016] [Indexed: 01/01/2023] Open
Abstract
The organization of structure and function of cardiac chambers in vertebrates is defined by chamber-specific distinct gene expression. This peculiarity and uniqueness of the genetic signatures demonstrates functional resolution attributed to the different chambers of the heart. Altered expression of the cardiac chamber genes can lead to individual chamber related dysfunctions and disease patho-physiologies. Information on transcriptional repertoire of cardiac compartments is important to understand the spectrum of chamber specific anomalies. We have carried out a genome wide transcriptome profiling study of the three cardiac chambers in the zebrafish heart using RNA sequencing. We have captured the gene expression patterns of 13,396 protein coding genes in the three cardiac chambers—atrium, ventricle and bulbus arteriosus. Of these, 7,260 known protein coding genes are highly expressed (≥10 FPKM) in the zebrafish heart. Thus, this study represents nearly an all-inclusive information on the zebrafish cardiac transcriptome. In this study, a total of 96 differentially expressed genes across the three cardiac chambers in zebrafish were identified. The atrium, ventricle and bulbus arteriosus displayed 20, 32 and 44 uniquely expressing genes respectively. We validated the expression of predicted chamber-restricted genes using independent semi-quantitative and qualitative experimental techniques. In addition, we identified 23 putative novel protein coding genes that are specifically restricted to the ventricle and not in the atrium or bulbus arteriosus. In our knowledge, these 23 novel genes have either not been investigated in detail or are sparsely studied. The transcriptome identified in this study includes 68 differentially expressing zebrafish cardiac chamber genes that have a human ortholog. We also carried out spatiotemporal gene expression profiling of the 96 differentially expressed genes throughout the three cardiac chambers in 11 developmental stages and 6 tissue types of zebrafish. We hypothesize that clustering the differentially expressed genes with both known and unknown functions will deliver detailed insights on fundamental gene networks that are important for the development and specification of the cardiac chambers. It is also postulated that this transcriptome atlas will help utilize zebrafish in a better way as a model for studying cardiac development and to explore functional role of gene networks in cardiac disease pathogenesis.
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Affiliation(s)
- Angom Ramcharan Singh
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Ankit Sabharwal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Shamsudheen Karuthedath Vellarikal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Ankit Verma
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Shruti Kapoor
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Adita Joshi
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
- * E-mail: (VS); (SS)
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
- * E-mail: (VS); (SS)
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