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Zhang H, Sen P, Hamers J, Sittig T, Woestenburg B, Moretti A, Dendorfer A, Merkus D. Retinoic acid modulation guides human-induced pluripotent stem cell differentiation towards left or right ventricle-like cardiomyocytes. Stem Cell Res Ther 2024; 15:184. [PMID: 38902843 PMCID: PMC11191368 DOI: 10.1186/s13287-024-03741-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/23/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Cardiomyocytes (CMs) derived from human induced pluripotent stem cells (hiPSCs) by traditional methods are a mix of atrial and ventricular CMs and many other non-cardiomyocyte cells. Retinoic acid (RA) plays an important role in regulation of the spatiotemporal development of the embryonic heart. METHODS CMs were derived from hiPSC (hi-PCS-CM) using different concentrations of RA (Control without RA, LRA with 0.05μM and HRA with 0.1 μM) between day 3-6 of the differentiation process. Engineered heart tissues (EHTs) were generated by assembling hiPSC-CM at high cell density in a low collagen hydrogel. RESULTS In the HRA group, hiPSC-CMs exhibited highest expression of contractile proteins MYH6, MYH7 and cTnT. The expression of TBX5, NKX2.5 and CORIN, which are marker genes for left ventricular CMs, was also the highest in the HRA group. In terms of EHT, the HRA group displayed the highest contraction force, the lowest beating frequency, and the highest sensitivity to hypoxia and isoprenaline, which means it was functionally more similar to the left ventricle. RNAsequencing revealed that the heightened contractility of EHT within the HRA group can be attributed to the promotion of augmented extracellular matrix strength by RA. CONCLUSION By interfering with the differentiation process of hiPSC with a specific concentration of RA at a specific time, we were able to successfully induce CMs and EHTs with a phenotype similar to that of the left ventricle or right ventricle.
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Affiliation(s)
- Hengliang Zhang
- Walter Brendel Center for Experimental Medicine (WBex), University Clinic Munich, LMU Munich, 81377, Munich, Germany
- Center for Cardiovascular Research (DZHK), Munich Heart Alliance (MHA), Partner Site Munich, 81377, Munich, Germany
- The First Affiliated Hospital, College of Clinical Medicine of Henan, University of Science and Technology, Luoyang, China
| | - Payel Sen
- Walter Brendel Center for Experimental Medicine (WBex), University Clinic Munich, LMU Munich, 81377, Munich, Germany
- Center for Cardiovascular Research (DZHK), Munich Heart Alliance (MHA), Partner Site Munich, 81377, Munich, Germany
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany
| | - Jules Hamers
- Walter Brendel Center for Experimental Medicine (WBex), University Clinic Munich, LMU Munich, 81377, Munich, Germany
- Center for Cardiovascular Research (DZHK), Munich Heart Alliance (MHA), Partner Site Munich, 81377, Munich, Germany
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany
| | - Theresa Sittig
- Walter Brendel Center for Experimental Medicine (WBex), University Clinic Munich, LMU Munich, 81377, Munich, Germany
- Center for Cardiovascular Research (DZHK), Munich Heart Alliance (MHA), Partner Site Munich, 81377, Munich, Germany
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany
| | - Brent Woestenburg
- Walter Brendel Center for Experimental Medicine (WBex), University Clinic Munich, LMU Munich, 81377, Munich, Germany
| | - Allessandra Moretti
- Center for Cardiovascular Research (DZHK), Munich Heart Alliance (MHA), Partner Site Munich, 81377, Munich, Germany
- First Department of Medicine, Klinikum Rechts der Isar, School of Medicine and Health, Technical University of Munich, Cardiology, Munich, Germany
- Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum Rechts der Isar, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Andreas Dendorfer
- Walter Brendel Center for Experimental Medicine (WBex), University Clinic Munich, LMU Munich, 81377, Munich, Germany
- Center for Cardiovascular Research (DZHK), Munich Heart Alliance (MHA), Partner Site Munich, 81377, Munich, Germany
| | - Daphne Merkus
- Walter Brendel Center for Experimental Medicine (WBex), University Clinic Munich, LMU Munich, 81377, Munich, Germany.
- Center for Cardiovascular Research (DZHK), Munich Heart Alliance (MHA), Partner Site Munich, 81377, Munich, Germany.
- Interfaculty Center for Endocrine and Cardiovascular Disease Network Modelling and Clinical Transfer (ICONLMU), LMU Munich, Munich, Germany.
- Division of Experimental Cardiology, Dept of Cardiology, Erasmus University Medical Center, 3000CA, Rotterdam, The Netherlands.
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Reilly K, Sonner S, McCay N, Rolnik DL, Casey F, Seale AN, Watson CJ, Kan A, Lai THT, Chung BHY, Diderich KEM, Srebniak MI, Dempsey E, Drury S, Giordano J, Wapner R, Kilby MD, Chitty LS, Mone F. The incremental yield of prenatal exome sequencing over chromosome microarray for congenital heart abnormalities: A systematic review and meta-analysis. Prenat Diagn 2024; 44:821-831. [PMID: 38708840 DOI: 10.1002/pd.6581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 05/07/2024]
Abstract
OBJECTIVES To determine the incremental yield of prenatal exome sequencing (PES) over standard testing in fetuses with an isolated congenital heart abnormality (CHA), CHA associated with extra-cardiac malformations (ECMs) and CHA dependent upon anatomical subclassification. METHODS A systematic review of the literature was performed using MEDLINE, EMBASE, Web of Science and grey literature January 2010-February 2023. Studies were selected if they included greater than 20 cases of prenatally diagnosed CHA when standard testing (QF-PCR/chromosome microarray/karyotype) was negative. Pooled incremental yield was determined. PROSPERO CRD 42022364747. RESULTS Overall, 21 studies, incorporating 1957 cases were included. The incremental yield of PES (causative pathogenic and likely pathogenic variants) over standard testing was 17.4% (95% CI, 13.5%-21.6%), 9.3% (95% CI, 6.6%-12.3%) and 35.9% (95% CI, 21.0%-52.3%) for all CHAs, isolated CHAs and CHAs associated with ECMs. The subgroup with the greatest yield was complex lesions/heterotaxy; 35.2% (95% CI 9.7%-65.3%). The most common syndrome was Kabuki syndrome (31/256, 12.1%) and most pathogenic variants occurred de novo and in autosomal dominant (monoallelic) disease causing genes (114/224, 50.9%). CONCLUSION The likelihood of a monogenic aetiology in fetuses with multi-system CHAs is high. Clinicians must consider the clinical utility of offering PES in selected isolated cardiac lesions.
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Affiliation(s)
- K Reilly
- Centre for Public Health, Queens University Belfast, Belfast, UK
| | - S Sonner
- Centre for Public Health, Queens University Belfast, Belfast, UK
| | - N McCay
- Department of Paediatric Cardiology, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - D L Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Victoria, Australia
| | - F Casey
- Department of Paediatric Cardiology, Royal Belfast Hospital for Sick Children, Belfast, UK
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - A N Seale
- Department of Paediatric Cardiology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Cardiovascular Science, University of Birmingham, Birmingham, UK
| | - C J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - A Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong, China
| | - T H T Lai
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong, China
| | - B H Y Chung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - K E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M I Srebniak
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - E Dempsey
- South West Thames Regional Genetics Service, London, UK
- School of Biological and Molecular Sciences, St George's University of London, London, UK
| | - S Drury
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - J Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Columbia University Medical Center, New York, New York, USA
| | - R Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Columbia University Medical Center, New York, New York, USA
| | - M D Kilby
- Fetal Medicine Center, Birmingham Women's & Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - L S Chitty
- Great Ormond Street NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - F Mone
- Centre for Public Health, Queens University Belfast, Belfast, UK
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3
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Nunes Santos L, Sousa Costa ÂM, Nikolov M, Carvalho JE, Coelho Sampaio A, Stockdale FE, Wang GF, Andrade Castillo H, Bortoletto Grizante M, Dudczig S, Vasconcelos M, Rosenthal N, Jusuf PR, Nim HT, de Oliveira P, Guimarães de Freitas Matos T, Nikovits W, Tambones IL, Figueira ACM, Schubert M, Ramialison M, Xavier-Neto J. Unraveling the evolutionary origin of the complex Nuclear Receptor Element (cNRE), a cis-regulatory module required for preferential expression in the atrial chamber. Commun Biol 2024; 7:371. [PMID: 38575811 PMCID: PMC10995137 DOI: 10.1038/s42003-024-05972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
Cardiac function requires appropriate proteins in each chamber. Atria requires slow myosin to act as reservoirs, while ventricles demand fast myosin for swift pumping. Myosins are thus under chamber-biased cis-regulation, with myosin gene expression imbalances leading to congenital heart dysfunction. To identify regulatory inputs leading to cardiac chamber-biased expression, we computationally and molecularly dissected the quail Slow Myosin Heavy Chain III (SMyHC III) promoter that drives preferential expression to the atria. We show that SMyHC III gene states are orchestrated by a complex Nuclear Receptor Element (cNRE) of 32 base pairs. Using transgenesis in zebrafish and mice, we demonstrate that preferential atrial expression is achieved by a combinatorial regulatory input composed of atrial activation motifs and ventricular repression motifs. Using comparative genomics, we show that the cNRE might have emerged from an endogenous viral element through infection of an ancestral host germline, revealing an evolutionary pathway to cardiac chamber-specific expression.
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Affiliation(s)
- Luana Nunes Santos
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- Australian Regenerative Medicine Institute, Monash University, VIC Australia - Systems Biology Institute, Melbourne, Australia
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Ângela Maria Sousa Costa
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Martin Nikolov
- Australian Regenerative Medicine Institute, Monash University, VIC Australia - Systems Biology Institute, Melbourne, Australia
| | - João E Carvalho
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Allysson Coelho Sampaio
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
- Faculdade Santa Marcelina - São Paulo, São Paulo, SP, Brazil
| | | | - Gang Feng Wang
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Hozana Andrade Castillo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- Australian Regenerative Medicine Institute, Monash University, VIC Australia - Systems Biology Institute, Melbourne, Australia
| | - Mariana Bortoletto Grizante
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Stefanie Dudczig
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Michelle Vasconcelos
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Nadia Rosenthal
- The Jackson Laboratory, Bar Harbor, Maine, USA
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Hieu T Nim
- Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Paulo de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | | | | | - Izabella Luisa Tambones
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, VIC Australia - Systems Biology Institute, Melbourne, Australia.
- Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - José Xavier-Neto
- Department of Morphology, Federal University of Ceará (UFC), Ceará, CE, Brazil.
- Health Scientist-in-Chief of Ceará State, Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico, Ceará, CE, Brazil.
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Zambrano-Carrasco J, Zou J, Wang W, Sun X, Li J, Su H. Emerging Roles of Cullin-RING Ubiquitin Ligases in Cardiac Development. Cells 2024; 13:235. [PMID: 38334627 PMCID: PMC10854628 DOI: 10.3390/cells13030235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Heart development is a spatiotemporally regulated process that extends from the embryonic phase to postnatal stages. Disruption of this highly orchestrated process can lead to congenital heart disease or predispose the heart to cardiomyopathy or heart failure. Consequently, gaining an in-depth understanding of the molecular mechanisms governing cardiac development holds considerable promise for the development of innovative therapies for various cardiac ailments. While significant progress in uncovering novel transcriptional and epigenetic regulators of heart development has been made, the exploration of post-translational mechanisms that influence this process has lagged. Culling-RING E3 ubiquitin ligases (CRLs), the largest family of ubiquitin ligases, control the ubiquitination and degradation of ~20% of intracellular proteins. Emerging evidence has uncovered the critical roles of CRLs in the regulation of a wide range of cellular, physiological, and pathological processes. In this review, we summarize current findings on the versatile regulation of cardiac morphogenesis and maturation by CRLs and present future perspectives to advance our comprehensive understanding of how CRLs govern cardiac developmental processes.
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Affiliation(s)
- Josue Zambrano-Carrasco
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
| | - Jianqiu Zou
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
| | - Wenjuan Wang
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Jie Li
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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5
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Yamaguchi N, Chang EW, Lin Z, Shekhar A, Bu L, Khodadadi-Jamayran A, Tsirigos A, Cen Y, Phoon CKL, Moskowitz IP, Park DS. An Anterior Second Heart Field Enhancer Regulates the Gene Regulatory Network of the Cardiac Outflow Tract. Circulation 2023; 148:1705-1722. [PMID: 37772400 PMCID: PMC10905423 DOI: 10.1161/circulationaha.123.065700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Conotruncal defects due to developmental abnormalities of the outflow tract (OFT) are an important cause of cyanotic congenital heart disease. Dysregulation of transcriptional programs tuned by NKX2-5 (NK2 homeobox 5), GATA6 (GATA binding protein 6), and TBX1 (T-box transcription factor 1) have been implicated in abnormal OFT morphogenesis. However, there remains no consensus on how these transcriptional programs function in a unified gene regulatory network within the OFT. METHODS We generated mice harboring a 226-nucleotide deletion of a highly conserved cardiac enhancer containing 2 GATA-binding sites located ≈9.4 kb upstream of the transcription start site of Nkx2-5 (Nkx2-5∆enh) using CRISPR-Cas9 gene editing and assessed phenotypes. Cardiac defects in Nkx2-5∆enh/∆enh mice were structurally characterized using histology and scanning electron microscopy, and physiologically assessed using electrocardiography, echocardiography, and optical mapping. Transcriptome analyses were performed using RNA sequencing and single-cell RNA sequencing data sets. Endogenous GATA6 interaction with and activity on the NKX2-5 enhancer was studied using chromatin immunoprecipitation sequencing and transposase-accessible chromatin sequencing in human induced pluripotent stem cell-derived cardiomyocytes. RESULTS Nkx2-5∆enh/∆enh mice recapitulated cyanotic conotruncal defects seen in patients with NKX2-5, GATA6, and TBX1 mutations. Nkx2-5∆enh/∆enh mice also exhibited defects in right Purkinje fiber network formation, resulting in right bundle-branch block. Enhancer deletion reduced embryonic Nkx2-5 expression selectively in the right ventricle and OFT of mutant hearts, indicating that enhancer activity is localized to the anterior second heart field. Transcriptional profiling of the mutant OFT revealed downregulation of important genes involved in OFT rotation and septation, such as Tbx1, Pitx2, and Sema3c. Endogenous GATA6 interacted with the highly conserved enhancer in human induced pluripotent stem cell-derived cardiomyocytes and in wild-type mouse hearts. We found critical dose dependency of cardiac enhancer accessibility on GATA6 gene dosage in human induced pluripotent stem cell-derived cardiomyocytes. CONCLUSIONS Our results using human and mouse models reveal an essential gene regulatory network of the OFT that requires an anterior second heart field enhancer to link GATA6 with NKX2-5-dependent rotation and septation gene programs.
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Affiliation(s)
- Naoko Yamaguchi
- The Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, 435 East 30th Street, Science Building 723, New York, NY, 10016, USA
| | - Ernest W. Chang
- The Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, 435 East 30th Street, Science Building 723, New York, NY, 10016, USA
| | - Ziyan Lin
- NYU Applied Bioinformatics Labs, New York University Grossman School of Medicine, 227 East 30th Street, TRB, New York, NY,10016, USA
| | - Akshay Shekhar
- Regeneron Pharmaceuticals, Inc. Biotechnology, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, USA
| | - Lei Bu
- The Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, 435 East 30th Street, Science Building 723, New York, NY, 10016, USA
| | - Alireza Khodadadi-Jamayran
- NYU Applied Bioinformatics Labs, New York University Grossman School of Medicine, 227 East 30th Street, TRB, New York, NY,10016, USA
| | - Aristotelis Tsirigos
- NYU Applied Bioinformatics Labs, New York University Grossman School of Medicine, 227 East 30th Street, TRB, New York, NY,10016, USA
| | - Yiyun Cen
- The Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, 435 East 30th Street, Science Building 723, New York, NY, 10016, USA
| | - Colin K. L. Phoon
- Division of Pediatric Cardiology, Hassenfeld Children’s Hospital at NYU Langone, New York University Grossman School of Medicine, Fink Children’s Center, 160 East 32nd Street, 2nd floor/L-3, New York, NY, 10016, USA
| | - Ivan P. Moskowitz
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, 900 East 57th Street, KCBD Room 5102, Chicago, IL, 60637, USA
| | - David S. Park
- The Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, 435 East 30th Street, Science Building 723, New York, NY, 10016, USA
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Lovato TL, Blotz B, Bileckyj C, Johnston CA, Cripps RM. Modeling a variant of unknown significance in the Drosophila ortholog of the human cardiogenic gene NKX2.5. Dis Model Mech 2023; 16:dmm050059. [PMID: 37691628 PMCID: PMC10548113 DOI: 10.1242/dmm.050059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 09/05/2023] [Indexed: 09/12/2023] Open
Abstract
Sequencing of human genome samples has unearthed genetic variants for which functional testing is necessary to validate their clinical significance. We used the Drosophila system to analyze a variant of unknown significance in the human congenital heart disease gene NKX2.5 (also known as NKX2-5). We generated an R321N allele of the NKX2.5 ortholog tinman (tin) to model a human K158N variant and tested its function in vitro and in vivo. The R321N Tin isoform bound poorly to DNA in vitro and was deficient in activating a Tin-dependent enhancer in tissue culture. Mutant Tin also showed a significantly reduced interaction with a Drosophila T-box cardiac factor named Dorsocross1. We generated a tinR321N allele using CRISPR/Cas9, for which homozygotes were viable and had normal heart specification, but showed defects in the differentiation of the adult heart that were exacerbated by further loss of tin function. We propose that the human K158N variant is pathogenic through causing a deficiency in DNA binding and a reduced ability to interact with a cardiac co-factor, and that cardiac defects might arise later in development or adult life.
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Affiliation(s)
- TyAnna L. Lovato
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Brenna Blotz
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Cayleen Bileckyj
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | | | - Richard M. Cripps
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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7
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Lovato TL, Blotz B, Bileckyj C, Johnston CA, Cripps RM. Using Drosophila to model a variant of unknown significance in the human cardiogenic gene Nkx2.5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546937. [PMID: 37425758 PMCID: PMC10327092 DOI: 10.1101/2023.06.28.546937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Sequencing of human genome samples has unearthed genetic variants for which functional testing is necessary to validate their clinical significance. We used the Drosophila system to analyze a variant of unknown significance in the human congenital heart disease gene, Nkx2 . 5 . We generated an R321N allele of the Nkx2 . 5 ortholog tinman ( tin ) to model a human K158N variant and tested its function in vitro and in vivo. The R321N Tin isoform bound poorly to DNA in vitro and was deficient in activating a Tin-dependent enhancer in tissue culture. Mutant Tin also showed a significantly reduced interaction with a Drosophila Tbox cardiac factor named Dorsocross1. We generated a tin R321N allele using CRISPR/Cas9, for which homozygotes were viable and had normal heart specification, but showed defects in the differentiation of the adult heart that were exacerbated by further loss of tin function. We conclude that the human K158N mutation is likely pathogenic through causing both a deficiency in DNA binding and a reduced ability to interact with a cardiac cofactor, and that cardiac defects might arise later in development or adult life.
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8
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Temporary and permanent control of partially specified Boolean networks. Biosystems 2023; 223:104795. [PMID: 36377120 DOI: 10.1016/j.biosystems.2022.104795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 01/11/2023]
Abstract
Boolean networks (BNs) are a well-accepted modelling formalism in computational systems biology. Nevertheless, modellers often cannot identify only a single BN that matches the biological reality. The typical reasons for this is insufficient knowledge or a lack of experimental data. Formally, this uncertainty can be expressed using partially specified Boolean networks (PSBNs), which encode the wide range of network candidates into a single structure. In this paper, we target the control of PSBNs. The goal of BN control is to find perturbations which guarantee stabilisation of the system in the desired state. Specifically, we consider variable perturbations (gene knock-out and over-expression) with three types of application time-window: one-step, temporary, and permanent. While the control of fully specified BNs is a thoroughly explored topic, control of PSBNs introduces additional challenges that we address in this paper. In particular, the unspecified components of the model cause a significant amount of additional state space explosion. To address this issue, we propose a fully symbolic methodology that can represent the numerous system variants in a compact form. In fully specified models, the efficiency of a perturbation is characterised by the count of perturbed variables (the perturbation size). However, in the case of a PSBN, a perturbation might work only for a subset of concrete BN models. To that end, we introduce and quantify perturbation robustness. This metric characterises how efficient the given perturbation is with respect to the model uncertainty. Finally, we evaluate the novel control methods using non-trivial real-world PSBN models. We inspect the method's scalability and efficiency with respect to the size of the state space and the number of unspecified components. We also compare the robustness metrics for all three perturbation types. Our experiments support the hypothesis that one-step perturbations are significantly less robust than temporary and permanent ones.
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Deciphering Transcriptional Networks during Human Cardiac Development. Cells 2022; 11:cells11233915. [PMID: 36497174 PMCID: PMC9739390 DOI: 10.3390/cells11233915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Human heart development is governed by transcription factor (TF) networks controlling dynamic and temporal gene expression alterations. Therefore, to comprehensively characterize these transcriptional regulations, day-to-day transcriptomic profiles were generated throughout the directed cardiac differentiation, starting from three distinct human- induced pluripotent stem cell lines from healthy donors (32 days). We applied an expression-based correlation score to the chronological expression profiles of the TF genes, and clustered them into 12 sequential gene expression waves. We then identified a regulatory network of more than 23,000 activation and inhibition links between 216 TFs. Within this network, we observed previously unknown inferred transcriptional activations linking IRX3 and IRX5 TFs to three master cardiac TFs: GATA4, NKX2-5 and TBX5. Luciferase and co-immunoprecipitation assays demonstrated that these five TFs could (1) activate each other's expression; (2) interact physically as multiprotein complexes; and (3) together, finely regulate the expression of SCN5A, encoding the major cardiac sodium channel. Altogether, these results unveiled thousands of interactions between TFs, generating multiple robust hypotheses governing human cardiac development.
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10
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Mansfield C, Zhao MT, Basu M. Translational potential of hiPSCs in predictive modeling of heart development and disease. Birth Defects Res 2022; 114:926-947. [PMID: 35261209 PMCID: PMC9458775 DOI: 10.1002/bdr2.1999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/21/2022] [Indexed: 11/11/2022]
Abstract
Congenital heart disease (CHD) represents a major class of birth defects worldwide and is associated with cardiac malformations that often require surgical intervention immediately after birth. Despite the intense efforts from multicentric genome/exome sequencing studies that have identified several genetic variants, the etiology of CHD remains diverse and often unknown. Genetically modified animal models with candidate gene deficiencies continue to provide novel molecular insights that are responsible for fetal cardiac development. However, the past decade has seen remarkable advances in the field of human induced pluripotent stem cell (hiPSC)-based disease modeling approaches to better understand the development of CHD and discover novel preventative therapies. The iPSCs are derived from reprogramming of differentiated somatic cells to an embryonic-like pluripotent state via overexpression of key transcription factors. In this review, we describe how differentiation of hiPSCs to specialized cardiac cellular identities facilitates our understanding of the development and pathogenesis of CHD subtypes. We summarize the molecular and functional characterization of hiPSC-derived differentiated cells in support of normal cardiogenesis, those that go awry in CHD and other heart diseases. We illustrate how stem cell-based disease modeling enables scientists to dissect the molecular mechanisms of cell-cell interactions underlying CHD. We highlight the current state of hiPSC-based studies that are in the verge of translating into clinical trials. We also address limitations including hiPSC-model reproducibility and scalability and differentiation methods leading to cellular heterogeneity. Last, we provide future perspective on exploiting the potential of hiPSC technology as a predictive model for patient-specific CHD, screening pharmaceuticals, and provide a source for cell-based personalized medicine. In combination with existing clinical and animal model studies, data obtained from hiPSCs will yield further understanding of oligogenic, gene-environment interaction, pathophysiology, and management for CHD and other genetic cardiac disorders.
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Affiliation(s)
- Corrin Mansfield
- Center for Cardiovascular Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Ming-Tao Zhao
- Center for Cardiovascular Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Madhumita Basu
- Center for Cardiovascular Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
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11
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Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nat Neurosci 2022; 25:1049-1058. [PMID: 35915179 PMCID: PMC9343253 DOI: 10.1038/s41593-022-01123-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022]
Abstract
Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.
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12
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Nim HT, Dang L, Thiyagarajah H, Bakopoulos D, See M, Charitakis N, Sibbritt T, Eichenlaub MP, Archer SK, Fossat N, Burke RE, Tam PPL, Warr CG, Johnson TK, Ramialison M. A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease. Genome Biol 2021; 22:335. [PMID: 34906219 PMCID: PMC8672579 DOI: 10.1186/s13059-021-02539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. RESULTS We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. CONCLUSIONS Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
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Affiliation(s)
- Hieu T. Nim
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
| | - Louis Dang
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Harshini Thiyagarajah
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Daniel Bakopoulos
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Michael See
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Natalie Charitakis
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Tennille Sibbritt
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Michael P. Eichenlaub
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Stuart K. Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Nicolas Fossat
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
- Present address: Copenhagen Hepatitis C Program, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Present address: Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Richard E. Burke
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Patrick P. L. Tam
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Coral G. Warr
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
- School of Molecular Sciences, La Trobe University, Bundoora, Victoria 3083 Australia
| | - Travis K. Johnson
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
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13
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Ma X, Li W. Amisulbrom causes cardiovascular toxicity in zebrafish (Danio rerio). CHEMOSPHERE 2021; 283:131236. [PMID: 34182637 DOI: 10.1016/j.chemosphere.2021.131236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Amisulbrom (AML), a sulfonamide fungicide used to control oomycete diseases, is regarded as a threat to aquatic species. The objective of this study was to evaluate the potential effects of AML on fish using a zebrafish model. Zebrafish embryos were exposed to 0.0075 μM, 0.075 μM, and 0.75 μM AML. AML-treated zebrafish embryos exhibited severe developmental defects, including pericardial edema, blood-clot clustering, increased hatching rates, decreased heart rates, and abnormal hemoglobin distributions. Compared with controls, key marker genes associated with cardiovascular development (i.e., nkx2.5, myh6, myh7, myl7, alas2, hbbe1, hbbe2, and gata1a) were abnormally expressed in response to AML treatment, suggesting that AML might specifically affect cardiovascular development. These results provide a valuable reference for the effects of AML on zebrafish embryos and may help to further clarify the potential risks posed by AML to aquatic ecosystems.
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Affiliation(s)
- Xueying Ma
- Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Xiamen Marine and Gene Drugs, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, PR China
| | - Wenhua Li
- Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Xiamen Marine and Gene Drugs, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, PR China.
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14
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Mohenska M, Tan NM, Tokolyi A, Furtado MB, Costa MW, Perry AJ, Hatwell-Humble J, van Duijvenboden K, Nim HT, Ji YMM, Charitakis N, Bienroth D, Bolk F, Vivien C, Knaupp AS, Powell DR, Elliott DA, Porrello ER, Nilsson SK, Del Monte-Nieto G, Rosenthal NA, Rossello FJ, Polo JM, Ramialison M. 3D-cardiomics: A spatial transcriptional atlas of the mammalian heart. J Mol Cell Cardiol 2021; 163:20-32. [PMID: 34624332 DOI: 10.1016/j.yjmcc.2021.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022]
Abstract
Understanding the spatial gene expression and regulation in the heart is key to uncovering its developmental and physiological processes, during homeostasis and disease. Numerous techniques exist to gain gene expression and regulation information in organs such as the heart, but few utilize intuitive true-to-life three-dimensional representations to analyze and visualise results. Here we combined transcriptomics with 3D-modelling to interrogate spatial gene expression in the mammalian heart. For this, we microdissected and sequenced transcriptome-wide 18 anatomical sections of the adult mouse heart. Our study has unveiled known and novel genes that display complex spatial expression in the heart sub-compartments. We have also created 3D-cardiomics, an interface for spatial transcriptome analysis and visualization that allows the easy exploration of these data in a 3D model of the heart. 3D-cardiomics is accessible from http://3d-cardiomics.erc.monash.edu/.
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Affiliation(s)
- Monika Mohenska
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Nathalia M Tan
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Alex Tokolyi
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Milena B Furtado
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; The Jackson Laboratory, Bar Harbor, ME, USA
| | - Mauro W Costa
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; The Jackson Laboratory, Bar Harbor, ME, USA
| | - Andrew J Perry
- Monash Bioinformatics Platform, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Jessica Hatwell-Humble
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; Biomedical Manufacturing, CSIRO Manufacturing, Bag 10, Clayton South, Australia
| | | | - Hieu T Nim
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; Faculty of Information Technology, Monash University, Clayton, Victoria, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Systems Biology Institute Australia, Clayton, Victoria, Australia
| | - Yuan M M Ji
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Natalie Charitakis
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Denis Bienroth
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia
| | - Francesca Bolk
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne 3052, VIC, Australia
| | - Celine Vivien
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia
| | - Anja S Knaupp
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - David A Elliott
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Enzo R Porrello
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne 3052, VIC, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne 3010, VIC, Australia
| | - Susan K Nilsson
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; Biomedical Manufacturing, CSIRO Manufacturing, Bag 10, Clayton South, Australia
| | - Gonzalo Del Monte-Nieto
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Nadia A Rosenthal
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; The Jackson Laboratory, Bar Harbor, ME, USA; National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, Victoria, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia.
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, Victoria, Australia; The Jackson Laboratory, Bar Harbor, ME, USA; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne 3052, VIC, Australia; Systems Biology Institute Australia, Clayton, Victoria, Australia.
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15
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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: 3.0] [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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16
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Xu M, Yao J, Shi Y, Yi H, Zhao W, Lin X, Yang Z. The SRCAP chromatin remodeling complex promotes oxidative metabolism during prenatal heart development. Development 2021; 148:237772. [PMID: 33913477 DOI: 10.1242/dev.199026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Mammalian heart development relies on cardiomyocyte mitochondrial maturation and metabolism. Embryonic cardiomyocytes make a metabolic shift from anaerobic glycolysis to oxidative metabolism by mid-gestation. VHL-HIF signaling favors anaerobic glycolysis but this process subsides by E14.5. Meanwhile, oxidative metabolism becomes activated but its regulation is largely elusive. Here, we first pinpointed a crucial temporal window for mitochondrial maturation and metabolic shift, and uncovered the pivotal role of the SRCAP chromatin remodeling complex in these processes in mouse. Disruption of this complex massively suppressed the transcription of key genes required for the tricarboxylic acid cycle, fatty acid β-oxidation and ubiquinone biosynthesis, and destroyed respirasome stability. Furthermore, we found that the SRCAP complex functioned through H2A.Z deposition to activate transcription of metabolic genes. These findings have unveiled the important physiological functions of the SRCAP complex in regulating mitochondrial maturation and promoting oxidative metabolism during heart development, and shed new light on the transcriptional regulation of ubiquinone biosynthesis.
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Affiliation(s)
- Mingjie Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Jie Yao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Yingchao Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Huijuan Yi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing 210093, China.,MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210093, China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210093, China
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17
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Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Front Genet 2021; 12:642975. [PMID: 33777110 PMCID: PMC7987942 DOI: 10.3389/fgene.2021.642975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bound by lineage-determining transcription factors and signaling effectors, enhancers play essential roles in controlling spatiotemporal gene expression profiles during development, homeostasis and disease. Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target genes. Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has helped inform our understanding of cardiac development and disease.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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18
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Nachtigall PG, Bovolenta LA, Patton JG, Fromm B, Lemke N, Pinhal D. A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks. BMC Genomics 2021; 22:153. [PMID: 33663371 PMCID: PMC7931589 DOI: 10.1186/s12864-021-07441-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/12/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND During vertebrate evolution, the heart has undergone remarkable changes that lead to morphophysiological differences in the fully formed heart of these species, such as chamber septation, heart rate frequency, blood pressure, and cardiac output volume. Despite these differences, the heart developmental process is guided by a core gene set conserved across vertebrates. Nonetheless, the regulatory mechanisms controlling the expression of genes involved in heart development and maintenance are largely uncharted. MicroRNAs (miRNAs) have been described as important regulatory elements in several biological processes, including heart biology. These small RNA molecules are broadly conserved in sequence and genomic context in metazoans. Mutations may occur in miRNAs and/or genes that contribute to the establishment of distinct repertoires of miRNA-target interactions, thereby favoring the differential control of gene expression and, consequently, the origin of novel phenotypes. In fact, several studies showed that miRNAs are integrated into genetic regulatory networks (GRNs) governing specific developmental programs and diseases. However, studies integrating miRNAs in vertebrate heart GRNs under an evolutionary perspective are still scarce. RESULTS We comprehensively examined and compared the heart miRNome of 20 species representatives of the five major vertebrate groups. We found 54 miRNA families with conserved expression and a variable number of miRNA families with group-specific expression in fishes, amphibians, reptiles, birds, and mammals. We also detected that conserved miRNAs present higher expression levels and a higher number of targets, whereas the group-specific miRNAs present lower expression levels and few targets. CONCLUSIONS Both the conserved and group-specific miRNAs can be considered modulators orchestrating the core and peripheral genes of heart GRNs of vertebrates, which can be related to the morphophysiological differences and similarities existing in the heart of distinct vertebrate groups. We propose a hypothesis to explain evolutionary differences in the putative functional roles of miRNAs in the heart GRNs analyzed. Furthermore, we present new insights into the molecular mechanisms that could be helping modulate the diversity of morphophysiology in the heart organ of vertebrate species.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório Especial de Toxinologia Aplicada (LETA), CeTICS, Instituto Butantan, São Paulo, Brazil. .,Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil.
| | - Luiz A Bovolenta
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute (MBW), Stockholm University, Stockholm, Sweden
| | - Ney Lemke
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
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19
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Varshney A, Chahal G, Santos L, Stolper J, Hallab JC, Nim HT, Nikolov M, Yip A, Ramialison M. Human Cardiac Transcription Factor Networks. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11597-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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20
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Shim WJ, Sinniah E, Xu J, Vitrinel B, Alexanian M, Andreoletti G, Shen S, Sun Y, Balderson B, Boix C, Peng G, Jing N, Wang Y, Kellis M, Tam PPL, Smith A, Piper M, Christiaen L, Nguyen Q, Bodén M, Palpant NJ. Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity. Cell Syst 2020; 11:625-639.e13. [PMID: 33278344 PMCID: PMC7781436 DOI: 10.1016/j.cels.2020.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
Determining genes that orchestrate cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes a genome-wide metric based on the gene-repressive trimethylation of histone H3 at lysine 27 (H3K27me3) across hundreds of diverse cell types to identify genetic regulators of cell differentiation. We introduce a computational method, TRIAGE, which uses discordance between gene-repressive tendency and expression to identify genetic drivers of cell identity. We apply TRIAGE to millions of genome-wide single-cell transcriptomes, diverse omics platforms, and eukaryotic cells and tissue types. Using a wide range of data, we validate the performance of TRIAGE in identifying cell-type-specific regulatory factors across diverse species including human, mouse, boar, bird, fish, and tunicate. Using CRISPR gene editing, we use TRIAGE to experimentally validate RNF220 as a regulator of Ciona cardiopharyngeal development and SIX3 as required for differentiation of endoderm in human pluripotent stem cells. A record of this paper’s transparent peer review process is included in the Supplemental Information. Perturbing genes controlling cell decisions have major implications in development or disease. However, identifying key regulatory genes from the thousands expressed in a cell is challenging. TRIAGE is a computational method that distills patterns of epigenetic repression across diverse cell types to infer regulatory genes using input gene expression data from any cell type. Demonstrating its utility, we combine single-cell RNA-seq and TRIAGE to identify and experimentally confirm novel regulators of heart development in evolutionarily distant species.
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Affiliation(s)
- Woo Jun Shim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jun Xu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Burcu Vitrinel
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Michael Alexanian
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA
| | - Gaia Andreoletti
- Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Brad Balderson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Carles Boix
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Guangdun Peng
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences and Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Naihe Jing
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences and Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuliang Wang
- Paul G. Allen School of Computer Science and Engineering and Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Patrick P L Tam
- The University of Sydney, Children's Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, Westmead, NSW 2145, Australia
| | - Aaron Smith
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia; Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
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21
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Xia J, Meng Z, Ruan H, Yin W, Xu Y, Zhang T. Heart Development and Regeneration in Non-mammalian Model Organisms. Front Cell Dev Biol 2020; 8:595488. [PMID: 33251221 PMCID: PMC7673453 DOI: 10.3389/fcell.2020.595488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular disease is a serious threat to human health and a leading cause of mortality worldwide. Recent years have witnessed exciting progress in the understanding of heart formation and development, enabling cardiac biologists to make significant advance in the field of therapeutic heart regeneration. Most of our understanding of heart development and regeneration, including the genes and signaling pathways, are driven by pioneering works in non-mammalian model organisms, such as fruit fly, fish, frog, and chicken. Compared to mammalian animal models, non-mammalian model organisms have special advantages in high-throughput applications such as disease modeling, drug discovery, and cardiotoxicity screening. Genetically engineered animals of cardiovascular diseases provide valuable tools to investigate the molecular and cellular mechanisms of pathogenesis and to evaluate therapeutic strategies. A large number of congenital heart diseases (CHDs) non-mammalian models have been established and tested for the genes and signaling pathways involved in the diseases. Here, we reviewed the mechanisms of heart development and regeneration revealed by these models, highlighting the advantages of non-mammalian models as tools for cardiac research. The knowledge from these animal models will facilitate therapeutic discoveries and ultimately serve to accelerate translational medicine.
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Affiliation(s)
- Jianhong Xia
- GMU-GIBH Joint School of Life Sciences, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Zhongxuan Meng
- GMU-GIBH Joint School of Life Sciences, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hongyue Ruan
- GMU-GIBH Joint School of Life Sciences, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wenguang Yin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yiming Xu
- School of Basic Medical Sciences, The Sixth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Tiejun Zhang
- GMU-GIBH Joint School of Life Sciences, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, China
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22
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Zhang Y, Wang F, Wu F, Wang Y, Wang X, Gui Y, Li Q. Tnni1b-ECR183-d2, an 87 bp cardiac enhancer of zebrafish. PeerJ 2020; 8:e10289. [PMID: 33194440 PMCID: PMC7648457 DOI: 10.7717/peerj.10289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Background Several heart malformations are associated with mutations in the regulatory regions of cardiac genes. Troponin I type 1b (tnni1b) is important for the formation of the atrioventricular canal in zebrafish hearts; however, the regulation of tnni1b is poorly understand. We aimed to identify a small but functional enhancer that is distal to tnni1b. Methods Evolutionary Conserved Region (ECR) Browser was used to analyze the 219 kb zebrafish and human genomes covering the tnni1b gene as well as the 100 kb regions upstream and downstream of tnni1b. Putative transcription factor binding sites (TFBSs) were analyzed using JASPAR and PROMO, and the enhancer activity was identified using zebrafish embryos and the luciferase reporter assay. A correlation analysis between the enhancer and transcription factors (TFs) was performed via TF overexpression and TFBS mutation experiments and the electrophoretic mobility shift assay (EMSA). To analyze the conservation between zebrafish and human enhancers, human DNA fragments were functionally verified. Images were captured and analyzed by fluorescence microscopy or confocal microscopy. Results Combined with comparative analysis and functional validation, we identified a 183 bp ECR (termed tnni1b-ECR183) that was located approximately 84 kb upstream of tnni1b that had the heart-specific enhancer activity in zebrafish. TFBS analysis and the enhancer activity detection assay data showed that the 87 bp core region (termed tnni1b-ECR183-d2) was capable of driving specific GFP expression near the atrioventricular junction and increased luciferase expression in HEK293 and HL1 cell lines. The GFP pattern in zebrafish embryos was similar to the expression profiles of tnni1b. A correlation analysis showed that the enhancer activity of tnni1b-ECR183-d2 was increased when NKX2.5 (p = 0.0006) or JUN (p < 0.0001) was overexpressed and was decreased when the TFBSs of NKX2.5 (p < 0.0001) or JUN (p = 0.0018) were mutated. In addition, DNA-protein interactions were not observed between these TFs and tnni1b-ECR183-d2 in the EMSA experiment. The conservation analysis showed that tnni1b-ECR183-h179 (aligned from tnni1b-ECR183) drove GFP expression in the heart and skeletal muscles and increased the luciferase expression after NKX2.5 (p < 0.0001), JUN (p < 0.0001) or ETS1 (p < 0.0001) was overexpressed. Interestingly, the truncated fragment tnni1b-ECR183-h84 mainly drove GFP expression in the skeletal muscles of zebrafish and the enhancer activity decreased when NKX2.5 (p = 0.0028), ETS1 (p = 0.0001) or GATA4 (p < 0.0001) was overexpressed. Conclusions An 87 bp cardiac-specific enhancer located 84 kb upstream of tnni1b in zebrafish was positively correlated with NKX2.5 or JUN. The zebrafish and human enhancers in this study target different tissues. The GFP expression mediated by tnni1b-ECR183-d2 is a valuable tool for marking the domain around the atrioventricular junction.
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Affiliation(s)
- Yawen Zhang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Feng Wang
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Fang Wu
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China.,Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Youhua Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xu Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yonghao Gui
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Qiang Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
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23
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Alexanian M, Ounzain S. Long Noncoding RNAs in Cardiac Development. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a037374. [PMID: 31932317 DOI: 10.1101/cshperspect.a037374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The exquisite transcriptional control of developmental gene programs is critical for hardwiring the complex expression patterns that govern cell-fate determination and differentiation during heart development. During the past several years, studies have illuminated our understanding of a complex noncoding transcriptional landscape, primarily associated with long noncoding RNAs (lncRNAs), that is implicated in these developmental processes and has begun to reveal key functions of these transcripts. In this review, we discuss the expanding roles for lncRNAs in the earliest points of cardiac development and through differentiation and maturation of multiple cell types within the adult heart. We go on to outline the diverse mechanisms by which cardiovascular lncRNAs orchestrate these transcriptional programs, explore the challenges linked to the study of lncRNAs in developmental phenotypes, and summarize the implications for these molecules in human cardiovascular disorders.
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Affiliation(s)
| | - Samir Ounzain
- HAYA Therapeutics SA, Lausanne, Vaud 1066, Switzerland
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24
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Abstract
PURPOSE OF REVIEW Emerging single-cell RNA sequencing technologies hold great promises to boost our understanding of the heterogeneity and molecular regulation of diverse cell phenotypes during organ development. In this review, we aimed at summarizing recent advances in employing single-cell transcriptomic analysis to depict the landscape of embryonic heart development, in particular, focusing on cardiac progenitor (CP) differentiation. RECENT FINDINGS Recent studies unbiasedly cataloged and characterized cardiac cell types in the spatial and temporal resolution during early heart development. Pseudo-time analysis revealed a temporal continuum of the differentiation progress from embryonic day (E) 6.5 to E9.5, implicating early cardiac lineage restriction during mouse gastrulation. First and second heart field (FHF and SHF) CPs adopted different differentiation strategies and underwent distinct transcriptional regulation. Collectively, the comprehensive molecular atlases yield a rich resource for identification of the key cardiac regulators and signaling molecules within the key cardiac gene regulatory network (GRN) governing cardiac cell fate determinations. This review offers insights into the exquisite process and its regulation of CP differentiation at single-cell resolution. As single-cell technologies continuously grow and evolve, computational integration of multimodal single-cell data with well-designed experimental validation promises to further delineate molecular basis in deploying cardiac progenitors of distinct sources with anatomical information.
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25
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Ni J, Wang H, Wei X, Shen K, Sha Y, Dong Y, Shu Y, Wan X, Cheng J, Wang F, Liu Y. Isoniazid causes heart looping disorder in zebrafish embryos by the induction of oxidative stress. BMC Pharmacol Toxicol 2020; 21:22. [PMID: 32178728 PMCID: PMC7076990 DOI: 10.1186/s40360-020-0399-2] [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: 09/07/2019] [Accepted: 02/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background The cardiotoxicity of isoniazid on zebrafish embryos and its underlying mechanism is unclear. Methods Here, we exposed zebrafish embryos at 4 h post-fertilization to different levels of isoniazid and recorded the morphology and number of malformed and dead embryos under the microscope. Results The high concentration of isoniazid group showed more malformed and dead embryos than the low concentration of isoniazid group and control group. The morphology of the heart and its alteration were visualized using transgenic zebrafish (cmlc2: GFP) and confirmed by in situ hybridization. The negative effects of isoniazid on the developing heart were characterized by lower heart rate and more heart looping disorders. Mechanistically, PCR showed decreased expression of heart-specific transcription factors when exposed to isoniazid. Oxidative stress was induced by isoniazid in cardiomyocytes, mediated by decreased activities of catalase and superoxide dismutase, which were rescued by scavengers of reactive oxygen species. Conclusion In conclusion, this study demonstrated that isoniazid led to heart looping disturbance by the downregulation of cardiac-specific transcription factors and induction of cardiomyocyte apoptosis.
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Affiliation(s)
- Jie Ni
- Department of Emergency, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu Province, China
| | - Hongye Wang
- The First Clinical Medical School, Nanjing Medical University, Nanjing, China
| | - Xiyi Wei
- The First Clinical Medical School, Nanjing Medical University, Nanjing, China.,Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kangjie Shen
- The First Clinical Medical School, Nanjing Medical University, Nanjing, China
| | - Yeqin Sha
- The First Clinical Medical School, Nanjing Medical University, Nanjing, China
| | - Yuxiang Dong
- The First Clinical Medical School, Nanjing Medical University, Nanjing, China
| | - Yimei Shu
- The First Clinical Medical School, Nanjing Medical University, Nanjing, China
| | - Xiaojie Wan
- Clinical School of Imaging, Nanjing Medical University, Nanjing, China
| | - Jingwen Cheng
- The Medical School of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Fang Wang
- Department of Emergency, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing, 210008, Jiangsu Province, China.
| | - Yihai Liu
- Department of Cardiology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, China.
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26
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Ruan H, Liao Y, Ren Z, Mao L, Yao F, Yu P, Ye Y, Zhang Z, Li S, Xu H, Liu J, Diao L, Zhou B, Han L, Wang L. Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment. BMC Biol 2019; 17:89. [PMID: 31722692 PMCID: PMC6854813 DOI: 10.1186/s12915-019-0709-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Cardiac differentiation from human pluripotent stem cells provides a unique opportunity to study human heart development in vitro and offers a potential cell source for cardiac regeneration. Compared to the large body of studies investigating cardiac maturation and cardiomyocyte subtype-specific induction, molecular events underlying cardiac lineage commitment from pluripotent stem cells at early stage remain poorly characterized. RESULTS In order to uncover key molecular events and regulators controlling cardiac lineage commitment from a pluripotent state during differentiation, we performed single-cell RNA-Seq sequencing and obtained high-quality data for 6879 cells collected from 6 stages during cardiac differentiation from human embryonic stem cells and identified multiple cell subpopulations with distinct molecular features. Through constructing developmental trajectory of cardiac differentiation and putative ligand-receptor interactions, we revealed crosstalk between cardiac progenitor cells and endoderm cells, which could potentially provide a cellular microenvironment supporting cardiac lineage commitment at day 5. In addition, computational analyses of single-cell RNA-Seq data unveiled ETS1 (ETS Proto-Oncogene 1) activation as an important downstream event induced by crosstalk between cardiac progenitor cells and endoderm cells. Consistent with the findings from single-cell analysis, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) against ETS1 revealed genomic occupancy of ETS1 at cardiac structural genes at day 9 and day 14, whereas ETS1 depletion dramatically compromised cardiac differentiation. CONCLUSION Together, our study not only characterized the molecular features of different cell types and identified ETS1 as a crucial factor induced by cell-cell crosstalk contributing to cardiac lineage commitment from a pluripotent state, but may also have important implications for understanding human heart development at early embryonic stage, as well as directed manipulation of cardiac differentiation in regenerative medicine.
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Affiliation(s)
- Hang Ruan
- 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
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin St, MSB6.166, Houston, TX, 77030, USA
| | - Yingnan Liao
- 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
| | - Zongna Ren
- 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
| | - Lin Mao
- 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
| | - Fang Yao
- 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
| | - Peng Yu
- 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
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin St, MSB6.166, Houston, TX, 77030, USA
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin St, MSB6.166, Houston, TX, 77030, USA
| | - Shengli Li
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin St, MSB6.166, Houston, TX, 77030, USA
| | - Hanshi Xu
- 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
| | - Jiewei Liu
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin St, MSB6.166, Houston, TX, 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - 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
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin St, MSB6.166, Houston, TX, 77030, USA.
| | - 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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27
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Forte E, Furtado MB, Rosenthal N. The interstitium in cardiac repair: role of the immune-stromal cell interplay. Nat Rev Cardiol 2019; 15:601-616. [PMID: 30181596 DOI: 10.1038/s41569-018-0077-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cardiac regeneration, that is, restoration of the original structure and function in a damaged heart, differs from tissue repair, in which collagen deposition and scar formation often lead to functional impairment. In both scenarios, the early-onset inflammatory response is essential to clear damaged cardiac cells and initiate organ repair, but the quality and extent of the immune response vary. Immune cells embedded in the damaged heart tissue sense and modulate inflammation through a dynamic interplay with stromal cells in the cardiac interstitium, which either leads to recapitulation of cardiac morphology by rebuilding functional scaffolds to support muscle regrowth in regenerative organisms or fails to resolve the inflammatory response and produces fibrotic scar tissue in adult mammals. Current investigation into the mechanistic basis of homeostasis and restoration of cardiac function has increasingly shifted focus away from stem cell-mediated cardiac repair towards a dynamic interplay of cells composing the less-studied interstitial compartment of the heart, offering unexpected insights into the immunoregulatory functions of cardiac interstitial components and the complex network of cell interactions that must be considered for clinical intervention in heart diseases.
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Affiliation(s)
| | | | - Nadia Rosenthal
- The Jackson Laboratory, Bar Harbor, ME, USA. .,National Heart and Lung Institute, Imperial College London, Faculty of Medicine, Imperial Centre for Translational and Experimental Medicine, London, UK.
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28
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Liu Y, Lu P, Wang Y, Morrow BE, Zhou B, Zheng D. Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis. J Am Heart Assoc 2019; 8:e012941. [PMID: 31322043 PMCID: PMC6761639 DOI: 10.1161/jaha.119.012941] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Background Heart tube looping to form a 4-chambered heart is a critical stage of embryonic heart development, but the gene drivers and their regulatory targets have not been extensively characterized at the cell-type level. Methods and Results To study the interaction of signaling pathways, transcription factors (TFs), and genetic networks in the process, we constructed gene co-expression networks and identified gene modules highly activated in individual cardiomyocytes at multiple anatomical regions and developmental stages using previously published single-cell RNA-seq data. Function analyses of the modules uncovered major pathways important for spatiotemporal cardiomyocyte differentiation. Interestingly, about half of the pathways were highly active in cardiomyocytes at the outflow tract (OFT) and atrioventricular canal, including well-known pathways for cardiac development and many newly identified ones. We predicted that these OFT-atrioventricular canal pathways were regulated by a large number of TFs actively expressed at the OFT-atrioventricular canal cardiomyocytes, with the prediction supported by motif enrichment analysis, including 10 TFs that have not been previously associated with cardiac development (eg, Etv5, Rbpms, and Baz2b). Furthermore, we found that TF targets in the OFT-atrioventricular canal modules were most significantly enriched with genes associated with mouse heart developmental abnormalities and human congenital heart defects, in comparison with TF targets in other modules, consistent with the critical developmental roles of OFT. Conclusions By analyzing gene co-expression at single cardiomyocytes, our systematic study has uncovered many known and additional new important TFs and their regulated molecular signaling pathways that are spatiotemporally active during heart looping.
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Affiliation(s)
- Yang Liu
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Pengfei Lu
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Yidong Wang
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
| | - Bernice E. Morrow
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of Ob/Gyn and PediatricsAlbert Einstein College of MedicineBronxNY
| | - Bin Zhou
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of Ob/Gyn and PediatricsAlbert Einstein College of MedicineBronxNY
- Department of MedicineAlbert Einstein College of MedicineBronxNY
| | - Deyou Zheng
- Department of GeneticsAlbert Einstein College of MedicineBronxNY
- Department of NeurologyAlbert Einstein College of MedicineBronxNY
- Department of NeuroscienceAlbert Einstein College of MedicineBronxNY
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29
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Nguyen AH, Marsh P, Schmiess-Heine L, Burke PJ, Lee A, Lee J, Cao H. Cardiac tissue engineering: state-of-the-art methods and outlook. J Biol Eng 2019; 13:57. [PMID: 31297148 PMCID: PMC6599291 DOI: 10.1186/s13036-019-0185-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/03/2019] [Indexed: 12/17/2022] Open
Abstract
The purpose of this review is to assess the state-of-the-art fabrication methods, advances in genome editing, and the use of machine learning to shape the prospective growth in cardiac tissue engineering. Those interdisciplinary emerging innovations would move forward basic research in this field and their clinical applications. The long-entrenched challenges in this field could be addressed by novel 3-dimensional (3D) scaffold substrates for cardiomyocyte (CM) growth and maturation. Stem cell-based therapy through genome editing techniques can repair gene mutation, control better maturation of CMs or even reveal its molecular clock. Finally, machine learning and precision control for improvements of the construct fabrication process and optimization in tissue-specific clonal selections with an outlook of cardiac tissue engineering are also presented.
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Affiliation(s)
- Anh H. Nguyen
- Electrical and Computer Engineering Department, University of Alberta, Edmonton, Alberta Canada
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
| | - Paul Marsh
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
| | - Lauren Schmiess-Heine
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
| | - Peter J. Burke
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
- Biomedical Engineering Department, University of California Irvine, Irvine, CA USA
- Chemical Engineering and Materials Science Department, University of California Irvine, Irvine, CA USA
| | - Abraham Lee
- Biomedical Engineering Department, University of California Irvine, Irvine, CA USA
- Mechanical and Aerospace Engineering Department, University of California Irvine, Irvine, CA USA
| | - Juhyun Lee
- Bioengineering Department, University of Texas at Arlington, Arlington, TX USA
| | - Hung Cao
- Electrical Engineering and Computer Science Department, University of California Irvine, Irvine, CA USA
- Biomedical Engineering Department, University of California Irvine, Irvine, CA USA
- Henry Samueli School of Engineering, University of California, Irvine, USA
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30
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Xiong H, Luo Y, Yue Y, Zhang J, Ai S, Li X, Wang X, Zhang YL, Wei Y, Li HH, Hu X, Li C, He A. Single-Cell Transcriptomics Reveals Chemotaxis-Mediated Intraorgan Crosstalk During Cardiogenesis. Circ Res 2019; 125:398-410. [PMID: 31221018 DOI: 10.1161/circresaha.119.315243] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RATIONALE We hypothesized that the differentiation processes of cardiac progenitor cell (CP) from first and second heart fields (FHF and SHF) may undergo the unique instructive gene regulatory networks or signaling pathways, and the precise SHF progression is contingent on the FHF signaling developmental cues. OBJECTIVE We investigated how the intraorgan communications control sequential building of discrete anatomic regions of the heart at single-cell resolution. METHODS AND RESULTS By single-cell transcriptomic analysis of Nkx2-5 (NK2 homeobox 5) and Isl1 (ISL LIM homeobox 1) lineages at embryonic day 7.75, embryonic day 8.25, embryonic day 8.75, and embryonic day 9.25, we present a panoramic view of distinct CP differentiation hierarchies. Computational identifications of FHF- and SHF-CP descendants revealed that SHF differentiation toward cardiomyocytes underwent numerous step-like transitions, whereas earlier FHF progressed toward cardiomyocytes in a wave-like manner. Importantly, single-cell pairing analysis demonstrated that SHF-CPs were attracted to and expanded FHF-populated heart tube region through interlineage communications mediated by the chemotactic guidance (MIF [macrophage migration inhibitory factor]-CXCR2 [C-X-C motif chemokine receptor 2]). This finding was verified by pharmacological blockade of this chemotaxis in embryos manifesting limited SHF cell migration and contribution to the growth of the outflow tract and right ventricle but undetectable effects on the left ventricle or heart tube initiation. Genetic loss-of-function assay of Cxcr2 showed that the expression domain of CXCR4 was expanded predominantly at SHF. Furthermore, double knockout of Cxcr2/Cxcr4 exhibited defective SHF development, corroborating the redundant function. Mechanistically, NKX2-5 directly bound the Cxcr2 and Cxcr4 genomic loci and activated their transcription in SHF. CONCLUSIONS Collectively, we propose a model in which the chemotaxis-mediated intraorgan crosstalk spatiotemporally guides the successive process of positioning SHF-CP and promoting primary heart expansion and patterning upon FHF-derived heart tube initiation.
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Affiliation(s)
- Haiqing Xiong
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China.,Peking-Tsinghua Center for Life Sciences (H.X., Y.L., A.H.), Peking University, China.,Academy for Advanced Interdisciplinary Studies (H.X., Y.L.), Peking University, China
| | - Yingjie Luo
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China.,Peking-Tsinghua Center for Life Sciences (H.X., Y.L., A.H.), Peking University, China.,Academy for Advanced Interdisciplinary Studies (H.X., Y.L.), Peking University, China
| | - Yanzhu Yue
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Jiejie Zhang
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Shanshan Ai
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Xin Li
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Xuelian Wang
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Yun-Long Zhang
- Department of Cardiology, Institute of Cardiovascular Diseases, First Affiliated Hospital of Dalian Medical University, China (Y.-L.Z., H.-H.L.)
| | - Yusheng Wei
- School of Life Sciences (Y.W., C.L.), Peking University, China
| | - Hui-Hua Li
- Department of Cardiology, Institute of Cardiovascular Diseases, First Affiliated Hospital of Dalian Medical University, China (Y.-L.Z., H.-H.L.)
| | - Xinli Hu
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China
| | - Cheng Li
- School of Life Sciences (Y.W., C.L.), Peking University, China.,Center for Statistical Science, Center for Bioinformatics (C.L.), Peking University, China
| | - Aibin He
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine (H.X., Y.L., Y.Y., J.Z., S.A., X.L., X.W., X.H., A.H.), Peking University, China.,Peking-Tsinghua Center for Life Sciences (H.X., Y.L., A.H.), Peking University, China
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31
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Poelmann RE, Gittenberger-de Groot AC. Development and evolution of the metazoan heart. Dev Dyn 2019; 248:634-656. [PMID: 31063648 PMCID: PMC6767493 DOI: 10.1002/dvdy.45] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
The mechanisms of the evolution and development of the heart in metazoans are highlighted, starting with the evolutionary origin of the contractile cell, supposedly the precursor of cardiomyocytes. The last eukaryotic common ancestor is likely a combination of several cellular organisms containing their specific metabolic pathways and genetic signaling networks. During evolution, these tool kits diversified. Shared parts of these conserved tool kits act in the development and functioning of pumping hearts and open or closed circulations in such diverse species as arthropods, mollusks, and chordates. The genetic tool kits became more complex by gene duplications, addition of epigenetic modifications, influence of environmental factors, incorporation of viral genomes, cardiac changes necessitated by air‐breathing, and many others. We evaluate mechanisms involved in mollusks in the formation of three separate hearts and in arthropods in the formation of a tubular heart. A tubular heart is also present in embryonic stages of chordates, providing the septated four‐chambered heart, in birds and mammals passing through stages with first and second heart fields. The four‐chambered heart permits the formation of high‐pressure systemic and low‐pressure pulmonary circulation in birds and mammals, allowing for high metabolic rates and maintenance of body temperature. Crocodiles also have a (nearly) separated circulation, but their resting temperature conforms with the environment. We argue that endothermic ancestors lost the capacity to elevate their body temperature during evolution, resulting in ectothermic modern crocodilians. Finally, a clinically relevant paragraph reviews the occurrence of congenital cardiac malformations in humans as derailments of signaling pathways during embryonic development. The cardiac regulatory toolkit contains many factors including epigenetic, genetic, viral, hemodynamic, and environmental factors, but also transcriptional activators, repressors, duplicated genes, redundancies and dose‐dependancies. Numerous toolkits regulate mechanisms including cell‐cell interactions, EMT, mitosis patterns, cell migration and differentiation and left/right sidedness involved in the development of endocardial cushions, looping, septum complexes, pharyngeal arch arteries, chamber and valve formation and conduction system. Evolutionary development of the yolk sac circulation likely preceded the advent of endothermy in amniotes. Parallel evolutionary traits regulate the development of contractile pumps in various taxa often in conjunction with the gut, lungs and excretory organs.
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Affiliation(s)
- Robert E Poelmann
- Institute of Biology, Department of Animal Sciences and Health, Leiden University, Leiden, The Netherlands.,Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
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32
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Sánchez-Iranzo H, Galardi-Castilla M, Minguillón C, Sanz-Morejón A, González-Rosa JM, Felker A, Ernst A, Guzmán-Martínez G, Mosimann C, Mercader N. Tbx5a lineage tracing shows cardiomyocyte plasticity during zebrafish heart regeneration. Nat Commun 2018; 9:428. [PMID: 29382818 PMCID: PMC5789846 DOI: 10.1038/s41467-017-02650-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 12/15/2017] [Indexed: 12/30/2022] Open
Abstract
During development, mesodermal progenitors from the first heart field (FHF) form a primitive cardiac tube, to which progenitors from the second heart field (SHF) are added. The contribution of FHF and SHF progenitors to the adult zebrafish heart has not been studied to date. Here we find, using genetic tbx5a lineage tracing tools, that the ventricular myocardium in the adult zebrafish is mainly derived from tbx5a+ cells, with a small contribution from tbx5a- SHF progenitors. Notably, ablation of ventricular tbx5a+-derived cardiomyocytes in the embryo is compensated by expansion of SHF-derived cells. In the adult, tbx5a expression is restricted to the trabeculae and excluded from the outer cortical layer. tbx5a-lineage tracing revealed that trabecular cardiomyocytes can switch their fate and differentiate into cortical myocardium during adult heart regeneration. We conclude that a high degree of cardiomyocyte cell fate plasticity contributes to efficient regeneration.
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Affiliation(s)
- Héctor Sánchez-Iranzo
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - María Galardi-Castilla
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Carolina Minguillón
- CSIC-Institut de Biologia Molecular de Barcelona Parc Científic de Barcelona C/ Baldiri i Reixac, 10 08028, Barcelona, Spain
- Barcelonabeta Brain Research Center, Pasqual Maragall Foundation, 08005, Barcelona, Spain
| | - Andrés Sanz-Morejón
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Institute of Anatomy, University of Bern, 3000, Bern 9, Switzerland
| | - Juan Manuel González-Rosa
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Anastasia Felker
- Institute of Molecular Life Sciences, University of Zürich, 8057, Zürich, Switzerland
| | - Alexander Ernst
- Institute of Anatomy, University of Bern, 3000, Bern 9, Switzerland
| | | | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, 8057, Zürich, Switzerland
| | - Nadia Mercader
- Development of the Epicardium and Its Role during Regeneration Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Melchor Fernández Almagro 3, 28029, Madrid, Spain.
- Institute of Anatomy, University of Bern, 3000, Bern 9, Switzerland.
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33
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Platelet-derived growth factor-C and -D in the cardiovascular system and diseases. Mol Aspects Med 2017; 62:12-21. [PMID: 28965749 DOI: 10.1016/j.mam.2017.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022]
Abstract
The cardiovascular system is among the first organs formed during development and is pivotal for the formation and function of the rest of the organs and tissues. Therefore, the function and homeostasis of the cardiovascular system are finely regulated by many important molecules. Extensive studies have shown that platelet-derived growth factors (PDGFs) and their receptors are critical regulators of the cardiovascular system. Even though PDGF-C and PDGF-D are relatively new members of the PDGF family, their critical roles in the cardiovascular system as angiogenic and survival factors have been amply demonstrated. Understanding the functions of PDGF-C and PDGF-D and the signaling pathways involved may provide novel insights into both basic biomedical research and new therapeutic possibilities for the treatment of cardiovascular diseases.
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34
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Desjardins CA, Naya FJ. Antagonistic regulation of cell-cycle and differentiation gene programs in neonatal cardiomyocytes by homologous MEF2 transcription factors. J Biol Chem 2017; 292:10613-10629. [PMID: 28473466 DOI: 10.1074/jbc.m117.776153] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/03/2017] [Indexed: 12/30/2022] Open
Abstract
Cardiomyocytes acquire their primary specialized function (contraction) before exiting the cell cycle. In this regard, proliferation and differentiation must be precisely coordinated for proper cardiac morphogenesis. Here, we have investigated the complex transcriptional mechanisms employed by cardiomyocytes to coordinate antagonistic cell-cycle and differentiation gene programs through the molecular dissection of the core cardiac transcription factor, MEF2. Knockdown of individual MEF2 proteins, MEF2A, -C, and -D, in primary neonatal cardiomyocytes resulted in radically distinct and opposite effects on cellular homeostasis and gene regulation. MEF2A and MEF2D were absolutely required for cardiomyocyte survival, whereas MEF2C, despite its major role in cardiac morphogenesis and direct reprogramming, was dispensable for this process. Inhibition of MEF2A or -D also resulted in the activation of cell-cycle genes and down-regulation of markers of terminal differentiation. In striking contrast, the regulation of cell-cycle and differentiation gene programs by MEF2C was antagonistic to that of MEF2A and -D. Computational analysis of regulatory regions from MEF2 isoform-dependent gene sets identified the Notch and Hedgehog signaling pathways as key determinants in coordinating MEF2 isoform-specific control of antagonistic gene programs. These results reveal that mammalian MEF2 family members have distinct transcriptional functions in cardiomyocytes and suggest that these differences are critical for proper development and maturation of the heart. Analysis of MEF2 isoform-specific function in neonatal cardiomyocytes has yielded insight into an unexpected transcriptional regulatory mechanism by which these specialized cells utilize homologous members of a core cardiac transcription factor to coordinate cell-cycle and differentiation gene programs.
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Affiliation(s)
- Cody A Desjardins
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Francisco J Naya
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
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35
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Ramialison M, Waardenberg AJ, Schonrock N, Doan T, de Jong D, Bouveret R, Harvey RP. Analysis of steric effects in DamID profiling of transcription factor target genes. Genomics 2017; 109:75-82. [DOI: 10.1016/j.ygeno.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/19/2017] [Accepted: 01/29/2017] [Indexed: 01/08/2023]
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36
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Waardenberg AJ, Homan B, Mohamed S, Harvey RP, Bouveret R. Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. Open Biol 2016; 6:rsob.160183. [PMID: 27683156 PMCID: PMC5043580 DOI: 10.1098/rsob.160183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/05/2016] [Indexed: 01/14/2023] Open
Abstract
The ability to accurately predict the DNA targets and interacting cofactors of transcriptional regulators from genome-wide data can significantly advance our understanding of gene regulatory networks. NKX2-5 is a homeodomain transcription factor that sits high in the cardiac gene regulatory network and is essential for normal heart development. We previously identified genomic targets for NKX2-5 in mouse HL-1 atrial cardiomyocytes using DNA-adenine methyltransferase identification (DamID). Here, we apply machine learning algorithms and propose a knowledge-based feature selection method for predicting NKX2-5 protein : protein interactions based on motif grammar in genome-wide DNA-binding data. We assessed model performance using leave-one-out cross-validation and a completely independent DamID experiment performed with replicates. In addition to identifying previously described NKX2-5-interacting proteins, including GATA, HAND and TBX family members, a number of novel interactors were identified, with direct protein : protein interactions between NKX2-5 and retinoid X receptor (RXR), paired-related homeobox (PRRX) and Ikaros zinc fingers (IKZF) validated using the yeast two-hybrid assay. We also found that the interaction of RXRα with NKX2-5 mutations found in congenital heart disease (Q187H, R189G and R190H) was altered. These findings highlight an intuitive approach to accessing protein-protein interaction information of transcription factors in DNA-binding experiments.
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Affiliation(s)
- Ashley J Waardenberg
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia Children's Medical Research Institute, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Bernou Homan
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Stephanie Mohamed
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia St Vincent's Clinical School, University of Sydney, Westmead, New South Wales 2145, Australia School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Romaric Bouveret
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia St Vincent's Clinical School, University of Sydney, Westmead, New South Wales 2145, Australia
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37
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Rowton M, Moskowitz IP. Many ways to break a heart. eLife 2015; 4. [PMID: 26305497 PMCID: PMC4548206 DOI: 10.7554/elife.10040] [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] [Indexed: 11/13/2022] Open
Abstract
A mutant transcription factor that has been linked to congenital heart disease has wider effects than previously thought.
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Affiliation(s)
- Megan Rowton
- Departments of Pediatrics, Pathology and Human Genetics, University of Chicago, Chicago, United States
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology and Human Genetics, University of Chicago, Chicago, United States
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38
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Abstract
The mammalian heart is a highly specialized organ, comprised of many different cell types arising from distinct embryonic progenitor populations during cardiogenesis. Three precursor populations have been identified to contribute to different myocytic and nonmyocytic cell lineages of the heart: cardiogenic mesoderm cells (CMC), the proepicardium (PE), and cardiac neural crest cells (CNCCs). This review will focus on molecular cues necessary for proper induction, expansion, and lineage-specific differentiation of these progenitor populations during cardiac development in vivo. Moreover, we will briefly discuss how the knowledge gained on embryonic heart progenitor biology can be used to develop novel therapeutic strategies for the management of congenital heart disease as well as for improvement of cardiac function in ischemic heart disease.
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