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Snabel RR, Cofiño-Fabrés C, Baltissen M, Schwach V, Passier R, Veenstra GJC. Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment. Stem Cell Reports 2025; 20:102422. [PMID: 40020683 PMCID: PMC11960529 DOI: 10.1016/j.stemcr.2025.102422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 01/27/2025] [Accepted: 01/28/2025] [Indexed: 03/03/2025] Open
Abstract
Stem cell-based models of human heart tissue and cardiac differentiation employ monolayer and 3D organoid cultures with different properties, cell type composition, and maturity. Here we show how cardiac monolayer, embryoid body, and engineered heart tissue trajectories compare in a single-cell roadmap of atrial and ventricular differentiation conditions. Using a multiomic approach and gene-regulatory network inference, we identified regulators of the epicardial, atrial, and ventricular cardiomyocyte lineages. We identified ZNF711 as a regulatory switch and safeguard for cardiomyocyte commitment. We show that ZNF711 ablation prevents cardiomyocyte differentiation in the absence of retinoic acid, causing progenitors to be diverted more prominently to epicardial and other lineages. Retinoic acid rescues this shift in lineage commitment and promotes atrial cardiomyocyte differentiation by regulation of shared and complementary target genes, showing interplay between ZNF711 and retinoic acid in cardiac lineage commitment.
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Affiliation(s)
- Rebecca R Snabel
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Carla Cofiño-Fabrés
- Department of Bioengineering Technologies, Applied Stem Cell Technologies Group, TechMed Centre, University of Twente, Enschede, the Netherlands
| | - Marijke Baltissen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, Oncode Institute, Radboud University, Nijmegen, the Netherlands
| | - Verena Schwach
- Department of Bioengineering Technologies, Applied Stem Cell Technologies Group, TechMed Centre, University of Twente, Enschede, the Netherlands
| | - Robert Passier
- Department of Bioengineering Technologies, Applied Stem Cell Technologies Group, TechMed Centre, University of Twente, Enschede, the Netherlands.
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science, Radboud University, Nijmegen, the Netherlands.
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2
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Zhou W, He K, Wang C, Wang P, Wang D, Wang B, Geng H, Lian H, Ma T, Nie Y, Ding S. Pharmacologically inducing regenerative cardiac cells by small molecule drugs. eLife 2024; 13:RP93405. [PMID: 39651957 PMCID: PMC11627505 DOI: 10.7554/elife.93405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2024] Open
Abstract
Adult mammals, unlike some lower organisms, lack the ability to regenerate damaged hearts through cardiomyocytes (CMs) dedifferentiation into cells with regenerative capacity. Developing conditions to induce such naturally unavailable cells with potential to proliferate and differentiate into CMs, that is, regenerative cardiac cells (RCCs), in mammals will provide new insights and tools for heart regeneration research. In this study, we demonstrate that a two-compound combination, CHIR99021 and A-485 (2C), effectively induces RCCs from human embryonic stem cell-derived TNNT2+ CMs in vitro, as evidenced by lineage tracing experiments. Functional analysis shows that these RCCs express a broad spectrum of cardiogenesis genes and have the potential to differentiate into functional CMs, endothelial cells, and smooth muscle cells. Importantly, similar results were observed in neonatal rat CMs both in vitro and in vivo. Remarkably, administering 2C in adult mouse hearts significantly enhances survival and improves heart function post-myocardial infarction. Mechanistically, CHIR99021 is crucial for the transcriptional and epigenetic activation of genes essential for RCC development, while A-485 primarily suppresses H3K27Ac and particularly H3K9Ac in CMs. Their synergistic effect enhances these modifications on RCC genes, facilitating the transition from CMs to RCCs. Therefore, our findings demonstrate the feasibility and reveal the mechanisms of pharmacological induction of RCCs from endogenous CMs, which could offer a promising regenerative strategy to repair injured hearts.
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Affiliation(s)
- Wei Zhou
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua UniversityBeijingChina
| | - Kezhang He
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Chiyin Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Pengqi Wang
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Dan Wang
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Bowen Wang
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua UniversityBeijingChina
| | - Han Geng
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Hong Lian
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Tianhua Ma
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijingChina
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua UniversityBeijingChina
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3
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Seeler S, Arnarsson K, Dreßen M, Krane M, Doppler SA. Beyond the Heartbeat: Single-Cell Omics Redefining Cardiovascular Research. Curr Cardiol Rep 2024; 26:1183-1196. [PMID: 39158785 DOI: 10.1007/s11886-024-02117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/07/2024] [Indexed: 08/20/2024]
Abstract
PURPOSE OF REVIEW This review aims to explore recent advances in single-cell omics techniques as applied to various regions of the human heart, illuminating cellular diversity, regulatory networks, and disease mechanisms. We examine the contributions of single-cell transcriptomics, genomics, proteomics, epigenomics, and spatial transcriptomics in unraveling the complexity of cardiac tissues. RECENT FINDINGS Recent strides in single-cell omics technologies have revolutionized our understanding of the heart's cellular composition, cell type heterogeneity, and molecular dynamics. These advancements have elucidated pathological conditions as well as the cellular landscape in heart development. We highlight emerging applications of integrated single-cell omics, particularly for cardiac regeneration, disease modeling, and precision medicine, and emphasize the transformative potential of these technologies to advance cardiovascular research and clinical practice.
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Affiliation(s)
- Sabine Seeler
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Kristjan Arnarsson
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Division of Cardiac Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Stefanie A Doppler
- Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Lazarettstr. 36, 80636, Munich, Germany.
- Institute for Translational Cardiac Surgery (INSURE), Department of Cardiovascular Surgery, German Heart Center Munich, School of Medicine and Health, TUM University Hospital, Technical University Munich, Munich, Germany.
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Lam YY, Chan CH, Geng L, Wong N, Keung W, Cheung YF. APLNR marks a cardiac progenitor derived with human induced pluripotent stem cells. Heliyon 2023; 9:e18243. [PMID: 37539315 PMCID: PMC10395470 DOI: 10.1016/j.heliyon.2023.e18243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/05/2023] Open
Abstract
Cardiomyocytes can be readily derived from human induced pluripotent stem cell (hiPSC) lines, yet its efficacy varies across different batches of the same and different hiPSC lines. To unravel the inconsistencies of in vitro cardiac differentiation, we utilized single cell transcriptomics on hiPSCs undergoing cardiac differentiation and identified cardiac and extra-cardiac lineages throughout differentiation. We further identified APLNR as a surface marker for in vitro cardiac progenitors and immunomagnetically isolated them. Differentiation of isolated in vitro APLNR+ cardiac progenitors derived from multiple hiPSC lines resulted in predominantly cardiomyocytes accompanied with cardiac mesenchyme. Transcriptomic analysis of differentiating in vitro APLNR+ cardiac progenitors revealed transient expression of cardiac progenitor markers before further commitment into cardiomyocyte and cardiac mesenchyme. Analysis of in vivo human and mouse embryo single cell transcriptomic datasets have identified APLNR expression in early cardiac progenitors of multiple lineages. This platform enables generation of in vitro cardiac progenitors from multiple hiPSC lines without genetic manipulation, which has potential applications in studying cardiac development, disease modelling and cardiac regeneration.
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Affiliation(s)
- Yin-Yu Lam
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, China
| | - Chun-Ho Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, China
| | - Lin Geng
- – Dr. Li Dak-Sum Research Centre, HKU-KI Collaboration in Regenerative Medicine, The University of Hong Kong, China
| | - Nicodemus Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, China
| | - Wendy Keung
- – Dr. Li Dak-Sum Research Centre, HKU-KI Collaboration in Regenerative Medicine, The University of Hong Kong, China
| | - Yiu-Fai Cheung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, China
- – Dr. Li Dak-Sum Research Centre, HKU-KI Collaboration in Regenerative Medicine, The University of Hong Kong, China
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5
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Identification of SALL4 Expressing Islet-1+ Cardiovascular Progenitor Cell Clones. Int J Mol Sci 2023; 24:ijms24021780. [PMID: 36675298 PMCID: PMC9863009 DOI: 10.3390/ijms24021780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/23/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023] Open
Abstract
The utilization of cardiac progenitor cells (CPCs) has been shown to induce favorable regenerative effects. While there are various populations of endogenous CPCs in the heart, there is no consensus regarding which population is ideal for cell-based regenerative therapy. Early-stage progenitor cells can be differentiated into all cardiovascular lineages, including cardiomyocytes and endothelial cells. Identifying an Islet-1+ (Isl-1+) early-stage progenitor population with enhanced stemness, multipotency and differentiation potential would be beneficial for the development of novel regenerative therapies. Here, we investigated the transcriptome of human neonatal Isl-1+ CPCs. Isl-1+ human neonatal CPCs exhibit enhanced stemness properties and were found to express Spalt-like transcription factor 4 (SALL4). SALL4 plays a role in embryonic development as well as proliferation and expansion of hematopoietic progenitor cells. SALL4, SOX2, EpCAM and TBX5 are co-expressed in the majority of Isl-1+ clones isolated from neonatal patients. The pre-mesendodermal transcript TFAP2C was identified in select Isl-1, SALL4, SOX2, EpCAM and TBX5 expressing clones. The ability to isolate and expand pre-mesendodermal stage cells from human patients is a novel finding that holds potential value for applications in regenerative medicine.
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Panfilio KA, Chuva de Sousa Lopes SM. The extended analogy of extraembryonic development in insects and amniotes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210268. [PMID: 36252225 PMCID: PMC9574626 DOI: 10.1098/rstb.2021.0268] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/14/2022] [Indexed: 12/22/2022] Open
Abstract
It is fascinating that the amnion and serosa/chorion, two extraembryonic (EE) tissues that are characteristic of the amniote vertebrates (mammals, birds and reptiles), have also independently evolved in insects. In this review, we offer the first detailed, macroevolutionary comparison of EE development and tissue biology across these animal groups. Some commonalities represent independent solutions to shared challenges for protecting the embryo (environmental assaults, risk of pathogens) and supporting its development, including clear links between cellular properties (e.g. polyploidy) and physiological function. Further parallels encompass developmental features such as the early segregation of the serosa/chorion compared to later, progressive differentiation of the amnion and formation of the amniotic cavity from serosal-amniotic folds as a widespread morphogenetic mode across species. We also discuss common developmental roles for orthologous transcription factors and BMP signalling in EE tissues of amniotes and insects, and between EE and cardiac tissues, supported by our exploration of new resources for global and tissue-specific gene expression. This highlights the degree to which general developmental principles and protective tissue features can be deduced from each of these animal groups, emphasizing the value of broad comparative studies to reveal subtle developmental strategies and answer questions that are common across species. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.
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Affiliation(s)
| | - Susana M. Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Department for Reproductive Medicine, Ghent University Hospital, 9000 Ghent, Belgium
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7
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Identification of the Potential Molecular Mechanism of TGFBI Gene in Persistent Atrial Fibrillation. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1643674. [PMID: 36398072 PMCID: PMC9666036 DOI: 10.1155/2022/1643674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/12/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Background Transforming growth factor beta-induced protein (TGFBI, encoded by TGFBI gene), is an extracellular matrix protein, widely expressed in variety of tissues. It binds to collagens type I, II, and IV and plays important roles in the interactions of cell with cell, collagen, and matrix. It has been reported to be associated with myocardial fibrosis, and the latter is an important pathophysiologyical basis of atrial fibrillation (AF). However, the mechanism of TGFBI in AF remains unclear. We aimed to detect the potential mechanism of TGFBI in AF via bioinformatics analysis. Methods The microarray dataset of GSE115574 was examined to detect the genes coexpressed with TGFBI from 14 left atrial tissue samples of AF patients. TGFBI coexpression genes were then screened using the R package. Using online analytical tools, we determined the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, Gene Ontology (GO) annotation, and protein-protein interaction (PPI) network of TGFBI and its coexpression genes. The modules and hub genes of the PPI-network were then identified. Another dataset, GSE79768 was examined to verify the hub genes. DrugBank was used to detect the potential target drugs. Results In GSE115574 dataset, a total of 1818 coexpression genes (769 positive and 1049 negative) were identified, enriched in 120 biological processes (BP), 38 cellular components (CC), 36 molecular functions (MF), and 39 KEGG pathways. A PPI-network with average 12.2-degree nodes was constructed. The genes clustered in the top module constructed from this network mainly play a role in PI3K-Akt signaling pathway, viral myocarditis, inflammatory bowel disease, and platelet activation. CXCL12, C3, FN1, COL1A2, ACTB, VCAM1, and MMP2 were identified and finally verified as the hub genes, mainly enriched in pathways like leukocyte transendothelial migration, PI3K-Akt signaling pathway, viral myocarditis, rheumatoid arthritis, and platelet activation. Pegcetacoplan, ocriplasmin, and carvedilol were the potential target drugs. Conclusions We used microdataset to identify the potential functions and mechanisms of the TGFBI and its coexpression genes in AF patients. Our findings suggest that CXCL12, C3, FN1, COL1A2, ACTB, VCAM1, and MMP2 may be the hub genes.
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8
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Destici E, Zhu F, Tran S, Preissl S, Farah EN, Zhang Y, Hou X, Poirion OB, Lee AY, Grinstein JD, Bloomekatz J, Kim HS, Hu R, Evans SM, Ren B, Benner C, Chi NC. Human-gained heart enhancers are associated with species-specific cardiac attributes. NATURE CARDIOVASCULAR RESEARCH 2022; 1:830-843. [PMID: 36817700 PMCID: PMC9937543 DOI: 10.1038/s44161-022-00124-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
The heart, a vital organ which is first to develop, has adapted its size, structure and function in order to accommodate the circulatory demands for a broad range of animals. Although heart development is controlled by a relatively conserved network of transcriptional/chromatin regulators, how the human heart has evolved species-specific features to maintain adequate cardiac output and function remains to be defined. Here, we show through comparative epigenomic analysis the identification of enhancers and promoters that have gained activity in humans during cardiogenesis. These cis-regulatory elements (CREs) are associated with genes involved in heart development and function, and may account for species-specific differences between human and mouse hearts. Supporting these findings, genetic variants that are associated with human cardiac phenotypic/disease traits, particularly those differing between human and mouse, are enriched in human-gained CREs. During early stages of human cardiogenesis, these CREs are also gained within genomic loci of transcriptional regulators, potentially expanding their role in human heart development. In particular, we discovered that gained enhancers in the locus of the early human developmental regulator ZIC3 are selectively accessible within a subpopulation of mesoderm cells which exhibits cardiogenic potential, thus possibly extending the function of ZIC3 beyond its conserved left-right asymmetry role. Genetic deletion of these enhancers identified a human gained enhancer that was required for not only ZIC3 and early cardiac gene expression at the mesoderm stage but also cardiomyocyte differentiation. Overall, our results illuminate how human gained CREs may contribute to human-specific cardiac attributes, and provide insight into how transcriptional regulators may gain cardiac developmental roles through the evolutionary acquisition of enhancers.
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Affiliation(s)
- Eugin Destici
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Fugui Zhu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaina Tran
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elie N. Farah
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Xiameng Hou
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olivier B. Poirion
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Jonathan D. Grinstein
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Hong Sook Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Hu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sylvia M. Evans
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Neil C. Chi
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
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9
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Choudhury TZ, Garg V. Molecular genetic mechanisms of congenital heart disease. Curr Opin Genet Dev 2022; 75:101949. [PMID: 35816939 PMCID: PMC9673038 DOI: 10.1016/j.gde.2022.101949] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/28/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Abstract
Congenital heart disease (CHD) affects ~1% of all live births, but a definitive etiology is identified in only ~50%. The causes include chromosomal aneuploidies and copy-number variations, pathogenic variation in single genes, and exposure to environmental factors. High-throughput sequencing of large CHD patient cohorts and continued expansion of the complex molecular regulation of cardiac morphogenesis has uncovered numerous disease-causing genes, but the previously held monogenic model for CHD etiology does not sufficiently explain the heterogeneity and incomplete penetrance of CHD phenotypes. Here, we provide a summary of well-known genetic contributors to CHD and discuss emerging concepts supporting complex genetic mechanisms that may provide explanations for cases that currently lack a molecular diagnosis.
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Affiliation(s)
- Talita Z Choudhury
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Heart Center, Nationwide Children's Hospital, Columbus, OH, USA.
| | - Vidu Garg
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Heart Center, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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10
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Marbán E, Liao K. On the cellular origin of cardiosphere-derived cells (CDCs). Basic Res Cardiol 2022; 117:12. [PMID: 35258685 DOI: 10.1007/s00395-022-00914-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/31/2023]
Affiliation(s)
- Eduardo Marbán
- Cedars-Sinai Medical Center, Smidt Heart Institute, 127 South San Vicente Boulevard, AHSP A3600, Los Angeles, CA, 90048, USA.
| | - Ke Liao
- Cedars-Sinai Medical Center, Smidt Heart Institute, 127 South San Vicente Boulevard, AHSP A3600, Los Angeles, CA, 90048, USA
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11
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Kogan PS, Wirth F, Tomar A, Darr J, Teperino R, Lahm H, Dreßen M, Puluca N, Zhang Z, Neb I, Beck N, Luzius T, de la Osa de la Rosa L, Gärtner K, Hüls C, Zeidler R, Ramanujam D, Engelhardt S, Wenk C, Holdt LM, Mononen M, Sahara M, Cleuziou J, Hörer J, Lange R, Krane M, Doppler SA. Uncovering the molecular identity of cardiosphere-derived cells (CDCs) by single-cell RNA sequencing. Basic Res Cardiol 2022; 117:11. [PMID: 35258704 PMCID: PMC8902493 DOI: 10.1007/s00395-022-00913-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 01/31/2023]
Abstract
Cardiosphere-derived cells (CDCs) generated from human cardiac biopsies have been shown to have disease-modifying bioactivity in clinical trials. Paradoxically, CDCs' cellular origin in the heart remains elusive. We studied the molecular identity of CDCs using single-cell RNA sequencing (sc-RNAseq) in comparison to cardiac non-myocyte and non-hematopoietic cells (cardiac fibroblasts/CFs, smooth muscle cells/SMCs and endothelial cells/ECs). We identified CDCs as a distinct and mitochondria-rich cell type that shared biological similarities with non-myocyte cells but not with cardiac progenitor cells derived from human-induced pluripotent stem cells. CXCL6 emerged as a new specific marker for CDCs. By analysis of sc-RNAseq data from human right atrial biopsies in comparison with CDCs we uncovered transcriptomic similarities between CDCs and CFs. By direct comparison of infant and adult CDC sc-RNAseq data, infant CDCs revealed GO-terms associated with cardiac development. To analyze the beneficial effects of CDCs (pro-angiogenic, anti-fibrotic, anti-apoptotic), we performed functional in vitro assays with CDC-derived extracellular vesicles (EVs). CDC EVs augmented in vitro angiogenesis and did not stimulate scarring. They also reduced the expression of pro-apoptotic Bax in NRCMs. In conclusion, CDCs were disclosed as mitochondria-rich cells with unique properties but also with similarities to right atrial CFs. CDCs displayed highly proliferative, secretory and immunomodulatory properties, characteristics that can also be found in activated or inflammatory cell types. By special culture conditions, CDCs earn some bioactivities, including angiogenic potential, which might modify disease in certain disorders.
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Affiliation(s)
- Palgit-S. Kogan
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Felix Wirth
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Archana Tomar
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Jonatan Darr
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Raffaele Teperino
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Harald Lahm
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Martina Dreßen
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Nazan Puluca
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Zhong Zhang
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Irina Neb
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Nicole Beck
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Tatjana Luzius
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Luis de la Osa de la Rosa
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
| | - Kathrin Gärtner
- Research Unit Gene Vectors, Helmholtz Center Munich German Research Center for Environmental Health, Munich, Germany
| | - Corinna Hüls
- Research Unit Gene Vectors, Helmholtz Center Munich German Research Center for Environmental Health, Munich, Germany
| | - Reinhard Zeidler
- Research Unit Gene Vectors, Helmholtz Center Munich German Research Center for Environmental Health, Munich, Germany ,Department of Otorhinolaryngology, Klinikum der Universität (KUM), Munich, Germany
| | - Deepak Ramanujam
- DZHK (German Center for Cardiovascular Research)-Partner Site Munich Heart Alliance, Biedersteiner Straße 29, 80802 Munich, Germany ,Institute of Pharmacology and Toxicology, Technische Universität München, Biedersteiner Str. 29, 80802 Munich, Germany
| | - Stefan Engelhardt
- DZHK (German Center for Cardiovascular Research)-Partner Site Munich Heart Alliance, Biedersteiner Straße 29, 80802 Munich, Germany ,Institute of Pharmacology and Toxicology, Technische Universität München, Biedersteiner Str. 29, 80802 Munich, Germany
| | - Catharina Wenk
- Institute of Laboratory Medicine, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Lesca M. Holdt
- Institute of Laboratory Medicine, University Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Mimmi Mononen
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden ,Department of Surgery, Yale University School of Medicine, CN06510 New Haven, CT USA
| | - Julie Cleuziou
- School of Medicine and Health, Department of Pediatric and Congenital Heart Surgery, Institute Insure, Technical University of Munich, Lazarettstraße 36, 80636 Munich, Germany
| | - Jürgen Hörer
- School of Medicine and Health, Department of Pediatric and Congenital Heart Surgery, Technical University of Munich, German Heart Center Munich, Lazarettstraße 36, 80636 Munich, Germany ,Division of Congenital and Pediatric Heart Surgery, University Hospital of Munich, Ludwig-Maximilians-Universität, Munich, Germany
| | - Rüdiger Lange
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany ,DZHK (German Center for Cardiovascular Research)-Partner Site Munich Heart Alliance, Biedersteiner Straße 29, 80802 Munich, Germany
| | - Markus Krane
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany ,DZHK (German Center for Cardiovascular Research)-Partner Site Munich Heart Alliance, Biedersteiner Straße 29, 80802 Munich, Germany ,Division of Cardiac Surgery, Department of Surgery, Yale University School of Medicine, New Haven, CT USA
| | - Stefanie A. Doppler
- School of Medicine and Health, Department of Cardiovascular Surgery, Institute Insure, Technical University of Munich, German Heart Center Munich, Lazarettstrasse 36, 80636 Munich, Germany
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12
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Tang CSM, Mononen M, Lam WY, Jin SC, Zhuang X, Garcia-Barcelo MM, Lin Q, Yang Y, Sahara M, Eroglu E, Chien KR, Hong H, Tam PK, Gruber PJ. Sequencing of a Chinese tetralogy of fallot cohort reveals clustering mutations in myogenic heart progenitors. JCI Insight 2021; 7:152198. [PMID: 34905512 PMCID: PMC8855809 DOI: 10.1172/jci.insight.152198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic heart defect, yet the underlying genetic mechanisms remain poorly understood. Here, we performed whole-genome sequencing analysis on 146 nonsyndromic TOF parent-offspring trios of Chinese ethnicity. Comparison of de novo variants and recessive genotypes of this data set with data from a European cohort identified both overlapping and potentially novel gene loci and revealed differential functional enrichment between cohorts. To assess the impact of these mutations on early cardiac development, we integrated single-cell and spatial transcriptomics of early human heart development with our genetic findings. We discovered that the candidate gene expression was enriched in the myogenic progenitors of the cardiac outflow tract. Moreover, subsets of the candidate genes were found in specific gene coexpression modules along the cardiomyocyte differentiation trajectory. These integrative functional analyses help dissect the pathogenesis of TOF, revealing cellular hotspots in early heart development resulting in cardiac malformations.
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Affiliation(s)
- Clara Sze Man Tang
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Mimmi Mononen
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Wai-Yee Lam
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, United States of America
| | - Xuehan Zhuang
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Qiongfen Lin
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yujia Yang
- Department of Surgery, Yale University School of Medicine, New Haven, United States of America
| | - Makoto Sahara
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Elif Eroglu
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Haifa Hong
- Department of Cardiovascular Surgery, Shanghai Children's Medical Center, Shanghai, China
| | - Paul Kh Tam
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Peter J Gruber
- Yale University School of Medicine, New Haven, United States of America
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13
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In vitro CSC-derived cardiomyocytes exhibit the typical microRNA-mRNA blueprint of endogenous cardiomyocytes. Commun Biol 2021; 4:1146. [PMID: 34593953 PMCID: PMC8484596 DOI: 10.1038/s42003-021-02677-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/15/2021] [Indexed: 02/08/2023] Open
Abstract
miRNAs modulate cardiomyocyte specification by targeting mRNAs of cell cycle regulators and acting in cardiac muscle lineage gene regulatory loops. It is unknown if or to-what-extent these miRNA/mRNA networks are operative during cardiomyocyte differentiation of adult cardiac stem/progenitor cells (CSCs). Clonally-derived mouse CSCs differentiated into contracting cardiomyocytes in vitro (iCMs). Comparison of "CSCs vs. iCMs" mRNome and microRNome showed a balanced up-regulation of CM-related mRNAs together with a down-regulation of cell cycle and DNA replication mRNAs. The down-regulation of cell cycle genes and the up-regulation of the mature myofilament genes in iCMs reached intermediate levels between those of fetal and neonatal cardiomyocytes. Cardiomyo-miRs were up-regulated in iCMs. The specific networks of miRNA/mRNAs operative in iCMs closely resembled those of adult CMs (aCMs). miR-1 and miR-499 enhanced myogenic commitment toward terminal differentiation of iCMs. In conclusions, CSC specification/differentiation into contracting iCMs follows known cardiomyo-MiR-dependent developmental cardiomyocyte differentiation trajectories and iCMs transcriptome/miRNome resembles that of CMs.
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14
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Diab NS, Barish S, Dong W, Zhao S, Allington G, Yu X, Kahle KT, Brueckner M, Jin SC. Molecular Genetics and Complex Inheritance of Congenital Heart Disease. Genes (Basel) 2021; 12:1020. [PMID: 34209044 PMCID: PMC8307500 DOI: 10.3390/genes12071020] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 01/09/2023] Open
Abstract
Congenital heart disease (CHD) is the most common congenital malformation and the leading cause of mortality therein. Genetic etiologies contribute to an estimated 90% of CHD cases, but so far, a molecular diagnosis remains unsolved in up to 55% of patients. Copy number variations and aneuploidy account for ~23% of cases overall, and high-throughput genomic technologies have revealed additional types of genetic variation in CHD. The first CHD risk genotypes identified through high-throughput sequencing were de novo mutations, many of which occur in chromatin modifying genes. Murine models of cardiogenesis further support the damaging nature of chromatin modifying CHD mutations. Transmitted mutations have also been identified through sequencing of population scale CHD cohorts, and many transmitted mutations are enriched in cilia genes and Notch or VEGF pathway genes. While we have come a long way in identifying the causes of CHD, more work is required to end the diagnostic odyssey for all CHD families. Complex genetic explanations of CHD are emerging but will require increasingly sophisticated analysis strategies applied to very large CHD cohorts before they can come to fruition in providing molecular diagnoses to genetically unsolved patients. In this review, we discuss the genetic architecture of CHD and biological pathways involved in its pathogenesis.
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Affiliation(s)
- Nicholas S. Diab
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Syndi Barish
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Shujuan Zhao
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
| | - Garrett Allington
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Xiaobing Yu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA
| | - Kristopher T. Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06510, USA;
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; (N.S.D.); (S.B.); (W.D.)
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sheng Chih Jin
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (S.Z.); (X.Y.)
- Department of Pediatrics, School of Medicine, Washington University, St. Louis, MO 63110, USA
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