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Ex uno, plures-From One Tissue to Many Cells: A Review of Single-Cell Transcriptomics in Cardiovascular Biology. Int J Mol Sci 2021; 22:ijms22042071. [PMID: 33669808 PMCID: PMC7922347 DOI: 10.3390/ijms22042071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/17/2022] Open
Abstract
Recent technological advances have revolutionized the study of tissue biology and garnered a greater appreciation for tissue complexity. In order to understand cardiac development, heart tissue homeostasis, and the effects of stress and injury on the cardiovascular system, it is essential to characterize the heart at high cellular resolution. Single-cell profiling provides a more precise definition of tissue composition, cell differentiation trajectories, and intercellular communication, compared to classical bulk approaches. Here, we aim to review how recent single-cell multi-omic studies have changed our understanding of cell dynamics during cardiac development, and in the healthy and diseased adult myocardium.
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2
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Chirikian O, Goodyer WR, Dzilic E, Serpooshan V, Buikema JW, McKeithan W, Wu H, Li G, Lee S, Merk M, Galdos F, Beck A, Ribeiro AJS, Paige S, Mercola M, Wu JC, Pruitt BL, Wu SM. CRISPR/Cas9-based targeting of fluorescent reporters to human iPSCs to isolate atrial and ventricular-specific cardiomyocytes. Sci Rep 2021; 11:3026. [PMID: 33542270 PMCID: PMC7862643 DOI: 10.1038/s41598-021-81860-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 01/12/2021] [Indexed: 01/08/2023] Open
Abstract
Generating cardiomyocytes (CMs) from human induced pluripotent stem cells (hiPSCs) has represented a significant advance in our ability to model cardiac disease. Current differentiation protocols, however, have limited use due to their production of heterogenous cell populations, primarily consisting of ventricular-like CMs. Here we describe the creation of two chamber-specific reporter hiPSC lines by site-directed genomic integration using CRISPR-Cas9 technology. In the MYL2-tdTomato reporter, the red fluorescent tdTomato was inserted upstream of the 3′ untranslated region of the Myosin Light Chain 2 (MYL2) gene in order faithfully label hiPSC-derived ventricular-like CMs while avoiding disruption of endogenous gene expression. Similarly, in the SLN-CFP reporter, Cyan Fluorescent Protein (CFP) was integrated downstream of the coding region of the atrial-specific gene, Sarcolipin (SLN). Purification of tdTomato+ and CFP+ CMs using flow cytometry coupled with transcriptional and functional characterization validated these genetic tools for their use in the isolation of bona fide ventricular-like and atrial-like CMs, respectively. Finally, we successfully generated a double reporter system allowing for the isolation of both ventricular and atrial CM subtypes within a single hiPSC line. These tools provide a platform for chamber-specific hiPSC-derived CM purification and analysis in the context of atrial- or ventricular-specific disease and therapeutic opportunities.
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Affiliation(s)
- Orlando Chirikian
- Stanford Cardiovascular Institute, Stanford, CA, USA.,Biotechnology Graduate Program, California State University Channel Islands, Camarillo, CA, USA.,Biomolecular, Science, and Engineering, University California, Santa Barbara, CA, USA
| | - William R Goodyer
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA.,Department of Pediatrics, Division of Cardiology, Stanford, CA, USA
| | - Elda Dzilic
- Stanford Cardiovascular Institute, Stanford, CA, USA.,Department of Cardiovascular Surgery, German Heart Center Munich, Technische Universität München, Lazarettstraße 36, 80636, Munich, Germany.,Insure (Institute for Translational Cardiac Surgery), Department of Cardiovascular Surgery, German Heart Center, Technische Universität München, Lothstraße 11, 80636, Munich, Germany
| | - Vahid Serpooshan
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA
| | - Jan W Buikema
- Stanford Cardiovascular Institute, Stanford, CA, USA.,Department of Cardiology, Utrecht Regenerative Medicine Center, University Medical Center Utrecht, Utrecht University, 3508 GA, Utrecht, The Netherlands
| | - Wesley McKeithan
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA
| | - HaoDi Wu
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA
| | - Guang Li
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA
| | - Soah Lee
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA
| | - Markus Merk
- Biomolecular, Science, and Engineering, University California, Santa Barbara, CA, USA
| | - Francisco Galdos
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA
| | - Aimee Beck
- Stanford Cardiovascular Institute, Stanford, CA, USA.,Biotechnology Graduate Program, California State University Channel Islands, Camarillo, CA, USA
| | - Alexandre J S Ribeiro
- Stanford University, Stanford, CA, USA.,Departments of Bioengineering and of Mechanical Engineering, Stanford University, Stanford, USA
| | - Sharon Paige
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA.,Department of Pediatrics, Division of Cardiology, Stanford, CA, USA
| | - Mark Mercola
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA.,Stanford University School of Medicine, Stanford, CA, USA.,Department of Medicine, Division of Cardiovascular Medicine, Stanford University , Stanford, CA, 94305, USA
| | - Joseph C Wu
- Stanford University, Stanford, CA, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA.,Stanford University School of Medicine, Stanford, CA, USA.,Department of Medicine, Division of Cardiovascular Medicine, Stanford University , Stanford, CA, 94305, USA
| | - Beth L Pruitt
- Stanford University, Stanford, CA, USA.,Departments of Bioengineering and of Mechanical Engineering, Stanford University, Stanford, USA.,Department of Mechanical Engineering, University California, Santa Barbara, CA, USA
| | - Sean M Wu
- Stanford University, Stanford, CA, USA. .,Stanford Cardiovascular Institute, Stanford, CA, USA. .,Stanford University School of Medicine, Stanford, CA, USA. .,Department of Pediatrics, Division of Cardiology, Stanford, CA, USA. .,Department of Medicine, Division of Cardiovascular Medicine, Stanford University , Stanford, CA, 94305, USA.
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3
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Reading the heart at single-cell resolution. J Mol Cell Cardiol 2020; 148:34-45. [PMID: 32871159 DOI: 10.1016/j.yjmcc.2020.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 12/21/2022]
Abstract
The burgeoning field of single-cell transcriptomics augments our ability to scrutinize organ systems at unprecedented resolutions. Single-cell RNA sequencing (scRNA-seq) and analytical techniques have shed light on the cellular heterogeneity, developmental trajectories, intercellular communications of the cardiac system, and thus contributed much to the understanding of cardiac development, homeostasis and disorders. Although generalized protocols are well established for scRNA-seq pipelines, customized sample preparation, quality control, and data interpretation are still needed in cardiac research. In this article, we highlight major steps that impact data quality in scRNA-seq experiments, with particular focus on sample and data processing of cardiomyocytes. We also summarize popular applications of scRNA-seq, outlining general tools, caveats and examples in cardiac research.
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Abstract
PURPOSE OF REVIEW Cardiomyocytes are the chief cell type in the heart, and are central to the pathogenesis of many cardiac diseases. Increasing recognition of its cellular, molecular, and functional heterogeneity prompted us to review the latest advancements in cardiac health and disease at single-cell resolution. RECENT FINDINGS Single-cell RNA profiling of cardiac lineage commitment events uncovered immense heterogeneity amongst ostensibly homogeneous cell populations. Classic cardiac transcription factors and new regulatory genes exhibit cell subtype-specific and temporally controlled expression patterns that serve the phenotypic changes in development, disease progression, and regeneration. Dissection of dynamically changing cell-cell communications and cardiac cell plasticity offers new opportunities in disease intervention and cardiac repair. Finally, updates in research models, platforms, and pipelines are continuously increasing the efficiency and reliability in data generation and interpretation. Transcriptional profiling of cardiac lineage cells, especially cardiomyocytes, has tremendously enriched our knowledge of the cellular milieu and the transcriptional network in the heart. Implementing technical standards and interrogating underexplored research areas will further our understanding of this organ and increase the likelihood of finding tractable therapeutic targets.
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Affiliation(s)
- Bingying Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 North Lishi Road, Beijing, 100037, People's Republic of China
| | - Li Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 North Lishi Road, Beijing, 100037, People's Republic of China.
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5
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Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart. Cell Rep 2020; 26:1934-1950.e5. [PMID: 30759401 DOI: 10.1016/j.celrep.2019.01.079] [Citation(s) in RCA: 287] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/14/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
The heart is the central organ of the circulatory system, and its proper development is vital for maintaining human life. Here, we used single-cell RNA sequencing to profile the gene expression landscapes of ∼4,000 cardiac cells from human embryos and identified four major types of cells: cardiomyocytes (CMs), cardiac fibroblasts, endothelial cells (ECs), and valvar interstitial cells (VICs). Atrial and ventricular CMs acquired distinct features early in heart development. Furthermore, both CMs and fibroblasts show stepwise changes in gene expression. As development proceeds, VICs may be involved in the remodeling phase, and ECs display location-specific characteristics. Finally, we compared gene expression profiles between humans and mice and identified a series of unique features of human heart development. Our study lays the groundwork for elucidating the mechanisms of in vivo human cardiac development and provides potential clues to understand cardiac regeneration.
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6
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miR-128a Acts as a Regulator in Cardiac Development by Modulating Differentiation of Cardiac Progenitor Cell Populations. Int J Mol Sci 2020; 21:ijms21031158. [PMID: 32050579 PMCID: PMC7038042 DOI: 10.3390/ijms21031158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRs) appear to be major, yet poorly understood players in regulatory networks guiding cardiogenesis. We sought to identify miRs with unknown functions during cardiogenesis analyzing the miR-profile of multipotent Nkx2.5 enhancer cardiac progenitor cells (NkxCE-CPCs). Besides well-known candidates such as miR-1, we found about 40 miRs that were highly enriched in NkxCE-CPCs, four of which were chosen for further analysis. Knockdown in zebrafish revealed that only miR-128a affected cardiac development and function robustly. For a detailed analysis, loss-of-function and gain-of-function experiments were performed during in vitro differentiations of transgenic murine pluripotent stem cells. MiR-128a knockdown (1) increased Isl1, Sfrp5, and Hcn4 (cardiac transcription factors) but reduced Irx4 at the onset of cardiogenesis, (2) upregulated Isl1-positive CPCs, whereas NkxCE-positive CPCs were downregulated, and (3) increased the expression of the ventricular cardiomyocyte marker Myl2 accompanied by a reduced beating frequency of early cardiomyocytes. Overexpression of miR-128a (4) diminished the expression of Isl1, Sfrp5, Nkx2.5, and Mef2c, but increased Irx4, (5) enhanced NkxCE-positive CPCs, and (6) favored nodal-like cardiomyocytes (Tnnt2+, Myh6+, Shox2+) accompanied by increased beating frequencies. In summary, we demonstrated that miR-128a plays a so-far unknown role in early heart development by affecting the timing of CPC differentiation into various cardiomyocyte subtypes.
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7
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Feng W, Przysinda A, Li G. Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells. J Vis Exp 2020. [PMID: 31984954 DOI: 10.3791/60647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Single cell mRNA sequencing has made significant progress in the last several years and has become an important tool in the field of developmental biology. It has been successfully used to identify rare cell populations, discover novel marker genes, and decode spatial and temporal developmental information. The single cell method has also evolved from the microfluidic based Fluidigm C1 technology to the droplet-based solutions in the last two to three years. Here we used the heart as an example to demonstrate how to profile the mouse embryonic tissue cells using the droplet based scRNA-Seq method. In addition, we have integrated two strategies into the workflow to profile multiple samples in a single experiment. Using one of the integrated methods, we have simultaneously profiled more than 9,000 cells from eight heart samples. These methods will be valuable to the developmental biology field by providing a cost-effective way to simultaneously profile single cells from different genetic backgrounds, developmental stages, or anatomical locations.
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Affiliation(s)
- Wei Feng
- Department of Developmental Biology, University of Pittsburgh School of Medicine
| | - Andrew Przysinda
- Department of Developmental Biology, University of Pittsburgh School of Medicine
| | - Guang Li
- Department of Developmental Biology, University of Pittsburgh School of Medicine;
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8
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Echeagaray O, Sussman MA. Transcribing the heart: faithfully interpreting cardiac transcriptional insights. Regen Med 2019; 14:805-810. [PMID: 31464566 PMCID: PMC6770408 DOI: 10.2217/rme-2019-0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/07/2019] [Indexed: 12/12/2022] Open
Abstract
Transcriptional profiling continues to produce phenotypical data essential for understanding of basic cardiac biology and required to improve efficiency of cardiac regenerative and therapeutic approaches after injury. Accurate interpretation of cardiac transcriptional data comes with the unique challenges of heart biology including cardiomyocyte morphology, cryopreservation of limited samples and adequate selection of transcriptional platform at a single-cell resolution. Consequently, development and implementation of novel transcriptional platforms and creative bioinformatic analysis are essential to resolve standing questions in the field of cardiac regenerative medicine. Targeted bioinformatic approaches, advancing technological access, increase technical availability and fostering communication between interdisciplinary groups is critical to improve therapeutic approaches and to overcome challenges inherent to transcriptomic cardiac research.
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Affiliation(s)
- Oscar Echeagaray
- San Diego Heart Research Institute and Integrated Regenerative Research Institute, San Diego State University, San Diego, CA 92182-4650, USA
| | - Mark A Sussman
- San Diego Heart Research Institute and Integrated Regenerative Research Institute, San Diego State University, San Diego, CA 92182-4650, USA
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9
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Deutsch MA, Doppler SA, Li X, Lahm H, Santamaria G, Cuda G, Eichhorn S, Ratschiller T, Dzilic E, Dreßen M, Eckart A, Stark K, Massberg S, Bartels A, Rischpler C, Gilsbach R, Hein L, Fleischmann BK, Wu SM, Lange R, Krane M. Reactivation of the Nkx2.5 cardiac enhancer after myocardial infarction does not presage myogenesis. Cardiovasc Res 2019; 114:1098-1114. [PMID: 29579159 DOI: 10.1093/cvr/cvy069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022] Open
Abstract
Aims The contribution of resident stem or progenitor cells to cardiomyocyte renewal after injury in adult mammalian hearts remains a matter of considerable debate. We evaluated a cell population in the adult mouse heart induced by myocardial infarction (MI) and characterized by an activated Nkx2.5 enhancer element that is specific for multipotent cardiac progenitor cells (CPCs) during embryonic development. We hypothesized that these MI-induced cells (MICs) harbour cardiomyogenic properties similar to their embryonic counterparts. Methods and results MICs reside in the heart and mainly localize to the infarction area and border zone. Interestingly, gene expression profiling of purified MICs 1 week after infarction revealed increased expression of stem cell markers and embryonic cardiac transcription factors (TFs) in these cells as compared to the non-mycoyte cell fraction of adult hearts. A subsequent global transcriptome comparison with embryonic CPCs and fibroblasts and in vitro culture of MICs unveiled that (myo-)fibroblastic features predominated and that cardiac TFs were only expressed at background levels. Conclusions Adult injury-induced reactivation of a cardiac-specific Nkx2.5 enhancer element known to specifically mark myocardial progenitor cells during embryonic development does not reflect hypothesized embryonic cardiomyogenic properties. Our data suggest a decreasing plasticity of cardiac progenitor (-like) cell populations with increasing age. A re-expression of embryonic, stem or progenitor cell features in the adult heart must be interpreted very carefully with respect to the definition of cardiac resident progenitor cells. Albeit, the abundance of scar formation after cardiac injury suggests a potential to target predestinated activated profibrotic cells to push them towards cardiomyogenic differentiation to improve regeneration.
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Affiliation(s)
- Marcus-André Deutsch
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Stefanie A Doppler
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany
| | - Xinghai Li
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany
| | - Harald Lahm
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany
| | - Gianluca Santamaria
- Stem Cell Laboratory, Department of Experimental and Clinical Medicine, Research Center of Advanced Biochemistry and Molecular Biology.,CIS (Centro Interdisciplinare Servizi), University 'Magna Graecia' of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Giovanni Cuda
- Stem Cell Laboratory, Department of Experimental and Clinical Medicine, Research Center of Advanced Biochemistry and Molecular Biology
| | - Stefan Eichhorn
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany
| | - Thomas Ratschiller
- Department of Cardiothoracic and Vascular Surgery, Kepler University Hospital, 4021 Linz, Austria
| | - Elda Dzilic
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany
| | - Annekathrin Eckart
- Medizinische Klinik und Poliklinik I, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Konstantin Stark
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.,Medizinische Klinik und Poliklinik I, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Steffen Massberg
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.,Medizinische Klinik und Poliklinik I, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Anna Bartels
- Nuklearmedizinische Klinik des Klinikums Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Christoph Rischpler
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.,Nuklearmedizinische Klinik des Klinikums Rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Ralf Gilsbach
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
| | - Bernd K Fleischmann
- Institute of Physiology I, Life and Brain Center, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Sean M Wu
- Division of Cardiovascular Medicine, Department of Medicine, Stanford Cardiovascular Institute, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, German Heart Center Munich at the Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany.,Department of Cardiovascular Surgery, German Heart Center, Insure (Institute for Translational Cardiac Surgery), Technische Universität München, Lothstraße 11, 80636 Munich, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
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10
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Goodyer WR, Beyersdorf BM, Paik DT, Tian L, Li G, Buikema JW, Chirikian O, Choi S, Venkatraman S, Adams EL, Tessier-Lavigne M, Wu JC, Wu SM. Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution. Circ Res 2019; 125:379-397. [PMID: 31284824 DOI: 10.1161/circresaha.118.314578] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RATIONALE The cardiac conduction system (CCS) consists of distinct components including the sinoatrial node, atrioventricular node, His bundle, bundle branches, and Purkinje fibers. Despite an essential role for the CCS in heart development and function, the CCS has remained challenging to interrogate because of inherent obstacles including small cell numbers, large cell-type heterogeneity, complex anatomy, and difficulty in isolation. Single-cell RNA-sequencing allows for genome-wide analysis of gene expression at single-cell resolution. OBJECTIVE Assess the transcriptional landscape of the entire CCS at single-cell resolution by single-cell RNA-sequencing within the developing mouse heart. METHODS AND RESULTS Wild-type, embryonic day 16.5 mouse hearts (n=6 per zone) were harvested and 3 zones of microdissection were isolated, including: Zone I-sinoatrial node region; Zone II-atrioventricular node/His region; and Zone III-bundle branch/Purkinje fiber region. Tissue was digested into single-cell suspensions, cells isolated, mRNA reverse transcribed, and barcoded before high-throughput sequencing and bioinformatics analyses. Single-cell RNA-sequencing was performed on over 22 000 cells, and all major cell types of the murine heart were successfully captured including bona fide clusters of cells consistent with each major component of the CCS. Unsupervised weighted gene coexpression network analysis led to the discovery of a host of novel CCS genes, a subset of which were validated using fluorescent in situ hybridization as well as whole-mount immunolabeling with volume imaging (iDISCO+) in 3 dimensions on intact mouse hearts. Further, subcluster analysis unveiled isolation of distinct CCS cell subtypes, including the clinically relevant but poorly characterized transitional cells that bridge the CCS and surrounding myocardium. CONCLUSIONS Our study represents the first comprehensive assessment of the transcriptional profiles from the entire CCS at single-cell resolution and provides a characterization in the context of development and disease.
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Affiliation(s)
- William R Goodyer
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA.,Department of Pediatrics (W.R.G., S.M.W.), Stanford University, CA
| | - Benjamin M Beyersdorf
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA.,Department of Cardiovascular Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich at the Technical University of Munich, Germany (B.M.B.)
| | - David T Paik
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA
| | - Lei Tian
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA
| | - Guang Li
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA.,Department of Developmental Biology, University of Pittsburgh School of Medicine, PA (G.L.)
| | - Jan W Buikema
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA.,Department of Cardiology, Utrecht Regenerative Medicine Center, University Medical Center Utrecht, Utrecht University, The Netherlands (J.W.B.)
| | - Orlando Chirikian
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA.,Department of Molecular, Cellular, and Developmental Biology, UC Santa Barbara, CA (O.C.)
| | - Shannon Choi
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA
| | - Sneha Venkatraman
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA
| | - Eliza L Adams
- Department of Biology (E.L.A., M.T.-L.), Stanford University, CA
| | | | - Joseph C Wu
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA.,Department of Medicine, Cardiovascular Medicine (J.C.W., S.M.W.), Stanford University School of Medicine, CA
| | - Sean M Wu
- From the Cardiovascular Institute (W.R.G., B.M.B., D.T.P., L.T., G.L., J.W.B., O.C., S.C., S.V., J.C.W., S.M.W.), Stanford University School of Medicine, CA.,Department of Medicine, Cardiovascular Medicine (J.C.W., S.M.W.), Stanford University School of Medicine, CA.,Department of Pediatrics (W.R.G., S.M.W.), Stanford University, CA
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11
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Saint-Jean L, Barkas N, Harmelink C, Tompkins KL, Oakey RJ, Baldwin HS. Myocardial differentiation is dependent upon endocardial signaling during early cardiogenesis in vitro. Development 2019; 146:dev.172619. [PMID: 31023876 DOI: 10.1242/dev.172619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/10/2019] [Indexed: 01/18/2023]
Abstract
The endocardium interacts with the myocardium to promote proliferation and morphogenesis during the later stages of heart development. However, the role of the endocardium in early cardiac ontogeny remains under-explored. Given the shared origin, subsequent juxtaposition, and essential cell-cell interactions of endocardial and myocardial cells throughout heart development, we hypothesized that paracrine signaling from the endocardium to the myocardium is crucial for initiating early differentiation of myocardial cells. To test this, we generated an in vitro, endocardial-specific ablation model using the diphtheria toxin receptor under the regulatory elements of the Nfat c1 genomic locus (NFATc1-DTR). Early treatment of NFATc1-DTR mouse embryoid bodies with diphtheria toxin efficiently ablated endocardial cells, which significantly attenuated the percentage of beating EBs in culture and expression of early and late myocardial differentiation markers. The addition of Bmp2 during endocardial ablation partially rescued myocyte differentiation, maturation and function. Therefore, we conclude that early stages of myocardial differentiation rely on endocardial paracrine signaling mediated in part by Bmp2. Our findings provide novel insight into early endocardial-myocardial interactions that can be explored to promote early myocardial development and growth.
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Affiliation(s)
- Leshana Saint-Jean
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Nikolaos Barkas
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - Cristina Harmelink
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kevin L Tompkins
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Rebecca J Oakey
- Department of Medical & Molecular Genetics, King's College London, London, SE1 9RT, UK
| | - H Scott Baldwin
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA .,Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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12
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Kim YH, Kim BJ, Kim SM, Kim SU, Ryu BY. Induction of cardiomyocyte‑like cells from hair follicle cells in mice. Int J Mol Med 2019; 43:2230-2240. [PMID: 30864673 DOI: 10.3892/ijmm.2019.4133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/08/2019] [Indexed: 11/05/2022] Open
Abstract
Hair follicles (HFs) are a well‑characterized niche for adult stem cells (SCs), and include epithelial and melanocytic SCs. HF cells are an accessible source of multipotent adult SCs for the generation of the interfollicular epidermis, HF structures and sebaceous glands in addition to the reconstitution of novel HFs in vivo. In the present study, it was demonstrated that HF cells are able to be induced to differentiate into cardiomyocyte‑like cells in vitro under specific conditions. It was determined that HF cells cultured on OP9 feeder cells in KnockOut‑Dulbecco's modified Eagle's medium/B27 in the presence of vascular endothelial growth factors differentiated into cardiomyocyte‑like cells that express markers specific to cardiac lineage, but do not express non‑cardiac lineage markers including neural stem/progenitor cell, HF bulge cells or undifferentiated spermatogonia markers. These cardiomyocyte‑like cells exhibited a spindle‑ and filament‑shaped morphology similar to that presented by cardiac muscles and exhibited spontaneous beating that persisted for over 3 months. These results demonstrate that SC reprogramming and differentiation may be induced without resulting in any genetic modification, which is important for the clinical applications of SCs including tissue and organ regeneration.
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Affiliation(s)
- Yong-Hee Kim
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung‑Ang University, Anseong, Gyeonggi‑do 17546, Republic of Korea
| | - Bang-Jin Kim
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Seok-Man Kim
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung‑Ang University, Anseong, Gyeonggi‑do 17546, Republic of Korea
| | - Sun-Uk Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk‑do 28116, Republic of Korea
| | - Buom-Yong Ryu
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung‑Ang University, Anseong, Gyeonggi‑do 17546, Republic of Korea
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13
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Vahdat S, Pahlavan S, Aghdami N, Bakhshandeh B, Baharvand H. Establishment of A Protocol for In Vitro Culture of Cardiogenic Mesodermal Cells Derived from Human Embryonic Stem Cells. CELL JOURNAL 2018; 20:496-504. [PMID: 30123995 PMCID: PMC6099148 DOI: 10.22074/cellj.2019.5661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 02/19/2017] [Indexed: 11/11/2022]
Abstract
Objective Cardiovascular progenitor cells (CPCs) are introduced as one of the promising cell sources for preclinical studies
and regenerative medicine. One of the earliest type of CPCs is cardiogenic mesoderm cells (CMCs), which have the capability
to generate all types of cardiac lineage derivatives. In order to benefit from CMCs, development of an efficient culture strategy
is required. We aim to explore an optimized culture condition that uses human embryonic stem cell (hESC)-derived CMCs.
Materials and Methods In this experimental study, hESCs were expanded and induced toward cardiac lineage in a
suspension culture. Mesoderm posterior 1-positive (MESP1+) CMCs were subjected to four different culture conditions: i.
Suspension culture of CMC spheroids, ii. Adherent culture of CMC spheroids, iii. Adherent culture of single CMCs using
gelatin, and iv. Adherent culture of single CMCs using Matrigel.
Results Although, we observed no substantial changes in the percentage of MESP1+ cells in different culture
conditions, there were significantly higher viability and total cell numbers in CMCs cultured on Matrigel (condition iv)
compared to the other groups. CMCs cultivated on Matrigel maintained their progenitor cell signature, which included
the tendency for cardiogenic differentiation.
Conclusion These results showed the efficacy of an adherent culture on Matrigel for hESC-derived CMCs, which would
facilitate their use for future applications.
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Affiliation(s)
- Sadaf Vahdat
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Nasser Aghdami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Behnaz Bakhshandeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, Tehran, Iran.
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14
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Massaia A, Chaves P, Samari S, Miragaia RJ, Meyer K, Teichmann SA, Noseda M. Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart. Front Cardiovasc Med 2018; 5:167. [PMID: 30525044 PMCID: PMC6258739 DOI: 10.3389/fcvm.2018.00167] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/29/2018] [Indexed: 12/21/2022] Open
Abstract
The recent development of single cell gene expression technologies, and especially single cell transcriptomics, have revolutionized the way biologists and clinicians investigate organs and organisms, allowing an unprecedented level of resolution to the description of cell demographics in both healthy and diseased states. Single cell transcriptomics provide information on prevalence, heterogeneity, and gene co-expression at the individual cell level. This enables a cell-centric outlook to define intracellular gene regulatory networks and to bridge toward the definition of intercellular pathways otherwise masked in bulk analysis. The technologies have developed at a fast pace producing a multitude of different approaches, with several alternatives to choose from at any step, including single cell isolation and capturing, lysis, RNA reverse transcription and cDNA amplification, library preparation, sequencing, and computational analyses. Here, we provide guidelines for the experimental design of single cell RNA sequencing experiments, exploring the current options for the crucial steps. Furthermore, we provide a complete overview of the typical data analysis workflow, from handling the raw sequencing data to making biological inferences. Significantly, advancements in single cell transcriptomics have already contributed to outstanding exploratory and functional studies of cardiac development and disease models, as summarized in this review. In conclusion, we discuss achievable outcomes of single cell transcriptomics' applications in addressing unanswered questions and influencing future cardiac clinical applications.
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Affiliation(s)
- Andrea Massaia
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Patricia Chaves
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sara Samari
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Kerstin Meyer
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Sarah Amalia Teichmann
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Michela Noseda
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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15
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Zhao YT, Wang J, Yano N, Zhang LX, Wang H, Zhang S, Qin G, Dubielecka PM, Zhuang S, Liu PY, Chin YE, Zhao TC. Irisin promotes cardiac progenitor cell-induced myocardial repair and functional improvement in infarcted heart. J Cell Physiol 2018; 234:1671-1681. [PMID: 30171682 DOI: 10.1002/jcp.27037] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023]
Abstract
Irisin, a newly identified hormone and cardiokine, is critical for modulating body metabolism. New evidence indicates that irisin protects the heart against myocardial ischemic injury. However, whether irisin enhances cardiac progenitor cell (CPC)-induced cardiac repair remains unknown. This study examines the effect of irisin on CPC-induced cardiac repair when these cells are introduced into the infarcted myocardium. Nkx2.5+ CPC stable cells were isolated from mouse embryonic stem cells. Nkx2.5 + CPCs (0.5 × 10 6 ) were reintroduced into the infarcted myocardium using PEGlylated fibrin delivery. The mouse myocardial infarction model was created by permanent ligation of the left anterior descending (LAD) artery. Nkx2.5 + CPCs were pretreated with irisin at a concentration of 5 ng/ml in vitro for 24 hr before transplantation. Myocardial functions were evaluated by echocardiographic measurement. Eight weeks after engraftment, Nkx2.5 + CPCs improved ventricular function as evident by an increase in ejection fraction and fractional shortening. These findings are concomitant with the suppression of cardiac hypertrophy and attenuation of myocardial interstitial fibrosis. Transplantation of Nkx2.5 + CPCs promoted cardiac regeneration and neovascularization, which were increased with the pretreatment of Nkx2.5 + CPCs with irisin. Furthermore, irisin treatment promoted myocyte proliferation as indicated by proliferative markers Ki67 and phosphorylated histone 3 and decreased apoptosis. Additionally, irisin resulted in a marked reduction of histone deacetylase 4 and increased p38 acetylation in cultured CPCs. These results indicate that irisin promoted Nkx2.5 + CPC-induced cardiac regeneration and functional improvement and that irisin serves as a novel therapeutic approach for stem cells in cardiac repair.
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Affiliation(s)
- Yu Tina Zhao
- Department of Surgery, Roger Williams Medical Center, Boston University School of Medicine, Providence, Rhode Island
| | - Jianguo Wang
- Department of Surgery, Roger Williams Medical Center, Boston University School of Medicine, Providence, Rhode Island
| | | | - Ling X Zhang
- Department of Medicine, Rhode Island Hospital, Brown University, Providence, Rhode Island
| | - Hao Wang
- Department of Surgery, Roger Williams Medical Center, Boston University School of Medicine, Providence, Rhode Island
| | - Shouyan Zhang
- Department of Medicine, Luoyang Central Hospital, Zhengzhou University, Luoyang, China
| | - Gangjian Qin
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, Alabama
| | - Patrycja M Dubielecka
- Department of Medicine, Rhode Island Hospital, Brown University, Providence, Rhode Island
| | - Shougang Zhuang
- Department of Medicine, Rhode Island Hospital, Brown University, Providence, Rhode Island
| | - Paul Y Liu
- Department of Plastic Surgery, Rhode Island Hospital, Brown University, Providence, Rhode Island
| | - Y Eugene Chin
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Chinese Academy of Sciences-Jiaotong University School of Medicine, Shanghai, China
| | - Ting C Zhao
- Department of Surgery, Roger Williams Medical Center, Boston University School of Medicine, Providence, Rhode Island
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16
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Anderson DJ, Kaplan DI, Bell KM, Koutsis K, Haynes JM, Mills RJ, Phelan DG, Qian EL, Leitoguinho AR, Arasaratnam D, Labonne T, Ng ES, Davis RP, Casini S, Passier R, Hudson JE, Porrello ER, Costa MW, Rafii A, Curl CL, Delbridge LM, Harvey RP, Oshlack A, Cheung MM, Mummery CL, Petrou S, Elefanty AG, Stanley EG, Elliott DA. NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network. Nat Commun 2018; 9:1373. [PMID: 29636455 PMCID: PMC5893543 DOI: 10.1038/s41467-018-03714-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/05/2018] [Indexed: 12/19/2022] Open
Abstract
Congenital heart defects can be caused by mutations in genes that guide cardiac lineage formation. Here, we show deletion of NKX2-5, a critical component of the cardiac gene regulatory network, in human embryonic stem cells (hESCs), results in impaired cardiomyogenesis, failure to activate VCAM1 and to downregulate the progenitor marker PDGFRα. Furthermore, NKX2-5 null cardiomyocytes have abnormal physiology, with asynchronous contractions and altered action potentials. Molecular profiling and genetic rescue experiments demonstrate that the bHLH protein HEY2 is a key mediator of NKX2-5 function during human cardiomyogenesis. These findings identify HEY2 as a novel component of the NKX2-5 cardiac transcriptional network, providing tangible evidence that hESC models can decipher the complex pathways that regulate early stage human heart development. These data provide a human context for the evaluation of pathogenic mutations in congenital heart disease. A gene regulatory network, including the transcription factor Nkx2-5, regulates cardiac development. Here, the authors show that on deletion of NKX2-5 from human embryonic stem cells, there is impaired cardiomyogenesis and changes in action potentials, and that this is regulated via HEY2.
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Affiliation(s)
- David J Anderson
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - David I Kaplan
- The Florey Institute of Neuroscience and Mental Health; Centre for Neuroscience, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Katrina M Bell
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Katerina Koutsis
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - John M Haynes
- Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade Parkville, Victoria, 3052, Australia
| | - Richard J Mills
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dean G Phelan
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Elizabeth L Qian
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Ana Rita Leitoguinho
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Deevina Arasaratnam
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Tanya Labonne
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Elizabeth S Ng
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Richard P Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Simona Casini
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Robert Passier
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - James E Hudson
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Enzo R Porrello
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Arash Rafii
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medical College in Qatar Qatar Foundation, Doha, Qatar.,Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Clare L Curl
- Department of Physiology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Lea M Delbridge
- Department of Physiology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2052, Australia.,St. Vincent's Clinical School and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, 2052, Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
| | - Michael M Cheung
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.,Department of Pediatrics, The Royal Children's Hospital, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Christine L Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Stephen Petrou
- The Florey Institute of Neuroscience and Mental Health; Centre for Neuroscience, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Andrew G Elefanty
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.,Department of Pediatrics, The Royal Children's Hospital, University of Melbourne, Parkville, VIC, 3052, Australia.,Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Edouard G Stanley
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia.,Department of Pediatrics, The Royal Children's Hospital, University of Melbourne, Parkville, VIC, 3052, Australia.,Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - David A Elliott
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia. .,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. .,School of Biosciences, University of Melbourne, Parkville, VIC, 3052, Australia.
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17
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Liu T, Wu H, Wu S, Wang C. Single-Cell Sequencing Technologies for Cardiac Stem Cell Studies. Stem Cells Dev 2017; 26:1540-1551. [PMID: 28859577 DOI: 10.1089/scd.2017.0050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Today with the rapid advancements in stem cell studies and the promising potential of using stem cells in clinical therapy, there is an increasing demand for in-depth comprehensive analysis on individual cell transcriptome and epigenome, as they play critical roles in a number of cell functions such as cell differentiation, growth, and reprogramming. The development of single-cell sequencing technologies has helped in revealing some exciting new perspectives in stem cells and regenerative medicine research. Among the various potential applications, single-cell analysis for cardiac stem cells (CSCs) holds tremendous promises in understanding the mechanisms of heart development and regeneration, which might light up the path toward cell therapy for cardiovascular diseases. This review briefly highlights the recent progresses in single-cell sequencing analysis technologies and their applications in CSC research.
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Affiliation(s)
- Tiantian Liu
- 1 Center for Genomics & Department of Basic Sciences, School of Medicine, Loma Linda University , Loma Linda, California
| | - Hongjin Wu
- 1 Center for Genomics & Department of Basic Sciences, School of Medicine, Loma Linda University , Loma Linda, California.,2 Cancer Research Institute, Hangzhou Cancer Hospital , Hangzhou, Zhejiang Province, P.R. China
| | - Shixiu Wu
- 2 Cancer Research Institute, Hangzhou Cancer Hospital , Hangzhou, Zhejiang Province, P.R. China
| | - Charles Wang
- 1 Center for Genomics & Department of Basic Sciences, School of Medicine, Loma Linda University , Loma Linda, California
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18
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Zamir L, Singh R, Nathan E, Patrick R, Yifa O, Yahalom-Ronen Y, Arraf AA, Schultheiss TM, Suo S, Han JDJ, Peng G, Jing N, Wang Y, Palpant N, Tam PP, Harvey RP, Tzahor E. Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta. eLife 2017; 6:20994. [PMID: 28271994 PMCID: PMC5400512 DOI: 10.7554/elife.20994] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/06/2017] [Indexed: 01/10/2023] Open
Abstract
Novel regenerative therapies may stem from deeper understanding of the mechanisms governing cardiovascular lineage diversification. Using enhancer mapping and live imaging in avian embryos, and genetic lineage tracing in mice, we investigated the spatio-temporal dynamics of cardiovascular progenitor populations. We show that expression of the cardiac transcription factor Nkx2.5 marks a mesodermal population outside of the cardiac crescent in the extraembryonic and lateral plate mesoderm, with characteristics of hemogenic angioblasts. Extra-cardiac Nkx2.5 lineage progenitors migrate into the embryo and contribute to clusters of CD41+/CD45+ and RUNX1+ cells in the endocardium, the aorta-gonad-mesonephros region of the dorsal aorta and liver. We also demonstrated that ectopic expression of Nkx2.5 in chick embryos activates the hemoangiogenic gene expression program. Taken together, we identified a hemogenic angioblast cell lineage characterized by transient Nkx2.5 expression that contributes to hemogenic endothelium and endocardium, suggesting a novel role for Nkx2.5 in hemoangiogenic lineage specification and diversification. DOI:http://dx.doi.org/10.7554/eLife.20994.001 As an animal embryo develops, it establishes a circulatory system that includes the heart, vessels and blood. Vessels and blood initially form in the yolk sac, a membrane that surrounds the embryo. These yolk sac vessels act as a rudimentary circulatory system, connecting to the heart and blood vessels within the embryo itself. In older embryos, cells in the inner layer of the largest blood vessel (known as the dorsal aorta) generate blood stem cells that give rise to the different types of blood cells. A gene called Nkx2.5 encodes a protein that controls the activity of a number of complex genetic programs and has been long studied as a key player in the development of the heart. Nkx2.5 is essential for forming normal heart muscle cells and for shaping the primitive heart and its surrounding vessels into a working organ. Interfering with the normal activity of the Nkx2.5 gene results in severe defects in blood vessels and the heart. However, many details are missing on the role played by Nkx2.5 in specifying the different cellular components of the circulatory system and heart. Zamir et al. genetically engineered chick and mouse embryos to produce fluorescent markers that could be used to trace the cells that become part of blood vessels and heart. The experiments found that some of the cells that form the blood and vessels in the yolk sac originate from within the membranes surrounding the embryo, outside of the areas previously reported to give rise to the heart. The Nkx2.5 gene is active in these cells for only a short period of time as they migrate toward the heart and dorsal aorta, where they give rise to blood stem cells These findings suggest that Nkx2.5 plays an important role in triggering developmental processes that eventually give rise to blood vessels and blood cells. The next step following on from this work will be to find out what genes the protein encoded by Nkx2.5 regulates to drive these processes. Mapping the genes that control the early origins of blood and blood-forming vessels will help biologists understand this complex and vital tissue system, and develop new treatments for patients with conditions that affect their circulatory system. In the future, this knowledge may also help to engineer synthetic blood and blood products for use in trauma and genetic diseases. DOI:http://dx.doi.org/10.7554/eLife.20994.002
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Affiliation(s)
- Lyad Zamir
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Reena Singh
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Elisha Nathan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ralph Patrick
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Oren Yifa
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yfat Yahalom-Ronen
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alaa A Arraf
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Thomas M Schultheiss
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shengbao Suo
- Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing-Dong Jackie Han
- Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guangdun Peng
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, The University of Washington, Seattle, United States
| | - Nathan Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Patrick Pl Tam
- School of Medical Sciences, Sydney Medical School, The University of Sydney, Westmead, Australia.,Embryology Unit, Children's Medical Research Institute, Westmead, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, Australia.,St. Vincent's Clinical School, School of Biological and Biomolecular Sciences, University of New South Wales, Kensington, Australia
| | - Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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19
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Li G, Dzilic E, Flores N, Shieh A, Wu SM. Strategies for the acquisition of transcriptional and epigenetic information in single cells. J Thorac Dis 2017; 9:S9-S16. [PMID: 28446964 DOI: 10.21037/jtd.2016.08.17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
As the basic unit of living organisms, each single cell has unique molecular signatures and functions. Our ability to uncover the transcriptional and epigenetic signature of single cells has been hampered by the lack of tools to explore this area of research. The advent of microfluidic single cell technology along with single cell genome-wide DNA amplification methods had greatly improved our understanding of the expression variation in single cells. Transcriptional expression profile by multiplex qPCR or genome-wide RNA sequencing has enabled us to examine genes expression in single cells in different tissues. With the new tools, the identification of new cellular heterogeneity, novel marker genes, unique subpopulations, and spatial locations of each single cell can be acquired successfully. Epigenetic modifications for each single cell can also be obtained via similar methods. Based on single cell genome sequencing, single cell epigenetic information including histone modifications, DNA methylation, and chromatin accessibility have been explored and provided valuable insights regarding gene regulation and disease prognosis. In this article, we review the development of strategies to obtain single cell transcriptional and epigenetic data. Furthermore, we discuss ways in which single cell studies may help to provide greater understanding of the mechanisms of basic cardiovascular biology that will eventually lead to improvement in our ability to diagnose disease and develop new therapies.
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Affiliation(s)
- Guang Li
- Cardiovascular Institute, School of Medicine, Stanford, CA 94305, USA
| | - Elda Dzilic
- Cardiovascular Institute, School of Medicine, Stanford, CA 94305, USA.,Department of Cardiovascular Surgery, German Heart Centre Munich, Technical University Munich, Munich, Germany
| | - Nick Flores
- Cardiovascular Institute, School of Medicine, Stanford, CA 94305, USA
| | - Alice Shieh
- Cardiovascular Institute, School of Medicine, Stanford, CA 94305, USA
| | - Sean M Wu
- Cardiovascular Institute, School of Medicine, Stanford, CA 94305, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Department of Medicine, School of Medicine, Stanford, CA 94305, USA.,Division of Cardiovascular Medicine, Department of Medicine, School of Medicine, Stanford, CA 94305, USA
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20
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DeLaughter DM, Bick AG, Wakimoto H, McKean D, Gorham JM, Kathiriya IS, Hinson JT, Homsy J, Gray J, Pu W, Bruneau BG, Seidman JG, Seidman CE. Single-Cell Resolution of Temporal Gene Expression during Heart Development. Dev Cell 2016; 39:480-490. [PMID: 27840107 PMCID: PMC5198784 DOI: 10.1016/j.devcel.2016.10.001] [Citation(s) in RCA: 295] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 03/30/2016] [Accepted: 09/30/2016] [Indexed: 12/29/2022]
Abstract
Activation of complex molecular programs in specific cell lineages governs mammalian heart development, from a primordial linear tube to a four-chamber organ. To characterize lineage-specific, spatiotemporal developmental programs, we performed single-cell RNA sequencing of >1,200 murine cells isolated at seven time points spanning embryonic day 9.5 (primordial heart tube) to postnatal day 21 (mature heart). Using unbiased transcriptional data, we classified cardiomyocytes, endothelial cells, and fibroblast-enriched cells, thus identifying markers for temporal and chamber-specific developmental programs. By harnessing these datasets, we defined developmental ages of human and mouse pluripotent stem-cell-derived cardiomyocytes and characterized lineage-specific maturation defects in hearts of mice with heterozygous mutations in Nkx2.5 that cause human heart malformations. This spatiotemporal transcriptome analysis of heart development reveals lineage-specific gene programs underlying normal cardiac development and congenital heart disease.
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Affiliation(s)
| | - Alexander G. Bick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - David McKean
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Irfan S. Kathiriya
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA
- Department of Anesthesia and Perioperative Care, University of California, San Francisco
| | - John T. Hinson
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jesse Gray
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - William Pu
- Department of Cardiology, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Benoit G. Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA
- Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute and Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
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21
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Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells. Dev Cell 2016; 39:491-507. [PMID: 27840109 DOI: 10.1016/j.devcel.2016.10.014] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 09/29/2016] [Accepted: 10/17/2016] [Indexed: 02/06/2023]
Abstract
Embryonic gene expression intricately reflects anatomical context, developmental stage, and cell type. To address whether the precise spatial origins of cardiac cells can be deduced solely from their transcriptional profiles, we established a genome-wide expression database from 118, 949, and 1,166 single murine heart cells at embryonic day 8.5 (e8.5), e9.5, and e10.5, respectively. We segregated these cells by type using unsupervised bioinformatics analysis and identified chamber-specific genes. Using a random forest algorithm, we reconstructed the spatial origin of single e9.5 and e10.5 cardiomyocytes with 92.0% ± 3.2% and 91.2% ± 2.8% accuracy, respectively (99.4% ± 1.0% and 99.1% ± 1.1% if a ±1 zone margin is permitted) and predicted the second heart field distribution of Isl-1-lineage descendants. When applied to Nkx2-5-/- cardiomyocytes from murine e9.5 hearts, we showed their transcriptional alteration and lack of ventricular phenotype. Our database and zone classification algorithm will enable the discovery of novel mechanisms in early cardiac development and disease.
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22
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Campbell KA, Terzic A, Nelson TJ. Induced pluripotent stem cells for cardiovascular disease: from product-focused disease modeling to process-focused disease discovery. Regen Med 2015; 10:773-83. [PMID: 26439809 DOI: 10.2217/rme.15.41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Induced pluripotent stem (iPS) cell technology offers an unprecedented opportunity to study patient-specific disease. This biotechnology platform enables recapitulation of individualized disease signatures in a dish through differentiation of patient-derived iPS cells. Beyond disease modeling, the in vitro process of differentiation toward genuine patient tissue offers a blueprint to inform disease etiology and molecular pathogenesis. Here, we highlight recent advances in patient-specific cardiac disease modeling and outline the future promise of iPS cell-based disease discovery applications.
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Affiliation(s)
- Katherine A Campbell
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, USA.,Division of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Andre Terzic
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.,Department of Medical Genetics, Mayo Clinic, Rochester, MN, USA
| | - Timothy J Nelson
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, USA.,Division of General Internal Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.,Center for Transplantation & Clinical Regeneration, Mayo Clinic, Rochester, MN, USA.,Division of Pediatric Cardiology, Mayo Clinic, Rochester, MN, USA
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