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Liang S, Zhou Y, Chang Y, Li J, Zhang M, Gao P, Li Q, Yu H, Kawakami K, Ma J, Zhang R. A novel gene-trap line reveals the dynamic patterns and essential roles of cysteine and glycine-rich protein 3 in zebrafish heart development and regeneration. Cell Mol Life Sci 2024; 81:158. [PMID: 38556571 PMCID: PMC10982097 DOI: 10.1007/s00018-024-05189-0] [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: 10/03/2023] [Revised: 02/13/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
Mutations in cysteine and glycine-rich protein 3 (CSRP3)/muscle LIM protein (MLP), a key regulator of striated muscle function, have been linked to hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) in patients. However, the roles of CSRP3 in heart development and regeneration are not completely understood. In this study, we characterized a novel zebrafish gene-trap line, gSAIzGFFM218A, which harbors an insertion in the csrp3 genomic locus, heterozygous fish served as a csrp3 expression reporter line and homozygous fish served as a csrp3 mutant line. We discovered that csrp3 is specifically expressed in larval ventricular cardiomyocytes (CMs) and that csrp3 deficiency leads to excessive trabeculation, a common feature of CSRP3-related HCM and DCM. We further revealed that csrp3 expression increased in response to different cardiac injuries and was regulated by several signaling pathways vital for heart regeneration. Csrp3 deficiency impeded zebrafish heart regeneration by impairing CM dedifferentiation, hindering sarcomere reassembly, and reducing CM proliferation while aggravating apoptosis. Csrp3 overexpression promoted CM proliferation after injury and ameliorated the impairment of ventricle regeneration caused by pharmacological inhibition of multiple signaling pathways. Our study highlights the critical role of Csrp3 in both zebrafish heart development and regeneration, and provides a valuable animal model for further functional exploration that will shed light on the molecular pathogenesis of CSRP3-related human cardiac diseases.
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Affiliation(s)
- Shuzhang Liang
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yating Zhou
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yue Chang
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jiayi Li
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Min Zhang
- Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Peng Gao
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Qi Li
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Hong Yu
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan
| | - Jinmin Ma
- Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, China.
| | - Ruilin Zhang
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China.
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, 430071, China.
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
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Gholipour A, Zahedmehr A, Shakerian F, Irani S, Oveisee M, Mowla SJ, Malakootian M. Significance of microRNA-targeted ErbB signaling pathway genes in cardiomyocyte differentiation. Mol Cell Probes 2023; 69:101912. [PMID: 37019292 DOI: 10.1016/j.mcp.2023.101912] [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: 09/13/2022] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023]
Abstract
OBJECTIVE(S) Cardiomyocyte differentiation is a complex process that follows the progression of gene expression alterations. The ErbB signaling pathway is necessary for various stages of cardiac development. We aimed to identify potential microRNAs targeting the ErbB signaling pathway genes by in silico approaches. METHODS Small RNA-sequencing data were obtained from GSE108021 for cardiomyocyte differentiation. Differentially expressed miRNAs were acquired via the DESeq2 package. Signaling pathways and gene ontology processes for the identified miRNAs were determined and the targeted genes of those miRNAs affecting the ErbB signaling pathway were determined. RESULTS Results revealed highly differentially expressed miRNAs were common between the differentiation stages and they targeted the genes involved in the ErbB signaling pathway as follows: let-7g-5p targets both CDKN1A and NRAS, while let-7c-5p and let-7d-5p hit CDKN1A and NRAS exclusively. let-7 family members targeted MAPK8 and ABL2. GSK3B was targeted by miR-199a-5p and miR-214-3p, and ERBB4 was targeted by miR-199b-3p and miR-653-5p. miR-214-3p, miR-199b-3p, miR-1277-5p, miR-21-5p, and miR-21-3p targeted CBL, mTOR, Jun, JNKK, and GRB1, respectively. MAPK8 was targeted by miR-214-3p, and ABL2 was targeted by miR-125b-5p and miR-1277-5p, too. CONCLUSION We determined miRNAs and their target genes in the ErbB signaling pathway in cardiomyocyte development and consequently heart pathophysiology progression.
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Affiliation(s)
- Akram Gholipour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran; Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Zahedmehr
- Cardiovascular Intervention Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Farshad Shakerian
- Cardiovascular Intervention Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran; Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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The toxicity of 4-tert-butylphenol in early development of zebrafish: morphological abnormality, cardiotoxicity, and hypopigmentation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:45781-45795. [PMID: 36708478 DOI: 10.1007/s11356-023-25586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 01/23/2023] [Indexed: 01/29/2023]
Abstract
Endocrine disrupting effects of 4-tert-butylphenol (4-t-BP) are well described in literature. However, the evidence regarding developmental toxic effect of 4-t-BP is still vague. The present study used zebrafish as a model organism to investigate the toxic effect of 4-t-BP. The results showed that 4-t-BP exposure at 3, 6, and 12 μM induced developmental toxicity in zebrafish, such as reduced embryo hatchability and abnormality morphological. Flow cytometry analysis showed that 4-t-BP also induced intracellular ROS production. 4-t-BP induced changes in the expression of genes related to cardiac development and melanin synthesis, resulting in cardiotoxicity and hypopigmentation. 4-t-BP also caused oxidative stress, and initiated apoptosis through p53-bcl-2/bax-capase3 pathway. Integrative biomarker response analysis showed time- and dose-dependent effects of 4-t-BP on oxidative damage and developmental toxicity in zebrafish embryos. Overall, this study contributed to a comprehensive evaluation of the toxicity of 4-t-BP, and the findings provided new evidence for early warning of residues in aquatic environments.
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Zhao K, Yang Z. The second heart field: the first 20 years. Mamm Genome 2022:10.1007/s00335-022-09975-8. [PMID: 36550326 DOI: 10.1007/s00335-022-09975-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
In 2001, three independent groups reported the identification of a novel cluster of progenitor cells that contribute to heart development in mouse and chicken embryos. This population of progenitor cells was designated as the second heart field (SHF), and a new research direction in heart development was launched. Twenty years have since passed and a comprehensive understanding of the SHF has been achieved. This review provides retrospective insights in to the contribution, the signaling regulatory networks and the epithelial properties of the SHF. It also includes the spatiotemporal characteristics of SHF development and interactions between the SHF and other types of cells during heart development. Although considerable efforts will be required to investigate the cellular heterogeneity of the SHF, together with its intricate regulatory networks and undefined mechanisms, it is expected that the burgeoning new technology of single-cell sequencing and precise lineage tracing will advance the comprehension of SHF function and its molecular signals. The advances in SHF research will translate to clinical applications and to the treatment of congenital heart diseases, especially conotruncal defects, as well as to regenerative medicine.
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Affiliation(s)
- Ke Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing, 210093, China
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing, 210093, China.
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Akerberg AA, Trembley M, Butty V, Schwertner A, Zhao L, Beerens M, Liu X, Mahamdeh M, Yuan S, Boyer L, MacRae C, Nguyen C, Pu WT, Burns CE, Burns CG. RBPMS2 Is a Myocardial-Enriched Splicing Regulator Required for Cardiac Function. Circ Res 2022; 131:980-1000. [PMID: 36367103 PMCID: PMC9770155 DOI: 10.1161/circresaha.122.321728] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND RBPs (RNA-binding proteins) perform indispensable functions in the post-transcriptional regulation of gene expression. Numerous RBPs have been implicated in cardiac development or physiology based on gene knockout studies and the identification of pathogenic RBP gene mutations in monogenic heart disorders. The discovery and characterization of additional RBPs performing indispensable functions in the heart will advance basic and translational cardiovascular research. METHODS We performed a differential expression screen in zebrafish embryos to identify genes enriched in nkx2.5-positive cardiomyocytes or cardiopharyngeal progenitors compared to nkx2.5-negative cells from the same embryos. We investigated the myocardial-enriched gene RNA-binding protein with multiple splicing (variants) 2 [RBPMS2)] by generating and characterizing rbpms2 knockout zebrafish and human cardiomyocytes derived from RBPMS2-deficient induced pluripotent stem cells. RESULTS We identified 1848 genes enriched in the nkx2.5-positive population. Among the most highly enriched genes, most with well-established functions in the heart, we discovered the ohnologs rbpms2a and rbpms2b, which encode an evolutionarily conserved RBP. Rbpms2 localizes selectively to cardiomyocytes during zebrafish heart development and strong cardiomyocyte expression persists into adulthood. Rbpms2-deficient embryos suffer from early cardiac dysfunction characterized by reduced ejection fraction. The functional deficit is accompanied by myofibril disarray, altered calcium handling, and differential alternative splicing events in mutant cardiomyocytes. These phenotypes are also observed in RBPMS2-deficient human cardiomyocytes, indicative of conserved molecular and cellular function. RNA-sequencing and comparative analysis of genes mis-spliced in RBPMS2-deficient zebrafish and human cardiomyocytes uncovered a conserved network of 29 ortholog pairs that require RBPMS2 for alternative splicing regulation, including RBFOX2, SLC8A1, and MYBPC3. CONCLUSIONS Our study identifies RBPMS2 as a conserved regulator of alternative splicing, myofibrillar organization, and calcium handling in zebrafish and human cardiomyocytes.
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Affiliation(s)
- Alexander A. Akerberg
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.)
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Michael Trembley
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Vincent Butty
- BioMicroCenter, Department of Biology (V.B.), Massachusetts Institute of Technology, Cambridge‚ MA
- Department of Biology (V.B., L.B.), Massachusetts Institute of Technology, Cambridge‚ MA
| | - Asya Schwertner
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Long Zhao
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Manu Beerens
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (M.B., C.M.)
| | - Xujie Liu
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Mohammed Mahamdeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Shiaulou Yuan
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
| | - Laurie Boyer
- Department of Biology (V.B., L.B.), Massachusetts Institute of Technology, Cambridge‚ MA
- Department of Biological Engineering (L.B.), Massachusetts Institute of Technology, Cambridge‚ MA
| | - Calum MacRae
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA (M.B., C.M.)
| | - Christopher Nguyen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
- Cardiovascular Innovation Research Center, Heart Vascular & Thoracic Institute, Cleveland Clinic‚ Cleveland‚ OH (C.N.)
| | - William T. Pu
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
- Harvard Stem Cell Institute, Cambridge, MA (W.T.P., C.E.B.)
| | - Caroline E. Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.)
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
- Harvard Stem Cell Institute, Cambridge, MA (W.T.P., C.E.B.)
| | - C. Geoffrey Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children’s Hospital, Boston‚ MA (A.A.A., M.T., X.L., W.T.P., C.E.B., C.G.B.)
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown‚ MA (A.A.A., A.S., L.Z., M.M., S.Y., C.N., C.E.B., C.G.B.)
- Harvard Medical School, Boston, MA (A.A.A., M.T., A.S., L.Z., M.B., X.L., M.M., S.Y., C.M., C.N., W.T.P., C.E.B., C.G.B.)
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Kubra K, Gaddu GK, Liongue C, Heidary S, Ward AC, Dhillon AS, Basheer F. Phylogenetic and Expression Analysis of Fos Transcription Factors in Zebrafish. Int J Mol Sci 2022; 23:ijms231710098. [PMID: 36077499 PMCID: PMC9456341 DOI: 10.3390/ijms231710098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Members of the FOS protein family regulate gene expression responses to a multitude of extracellular signals and are dysregulated in several pathological states. Whilst mouse genetic models have provided key insights into the tissue-specific functions of these proteins in vivo, little is known about their roles during early vertebrate embryonic development. This study examined the potential of using zebrafish as a model for such studies and, more broadly, for investigating the mechanisms regulating the functions of Fos proteins in vivo. Through phylogenetic and sequence analysis, we identified six zebrafish FOS orthologues, fosaa, fosab, fosb, fosl1a, fosl1b, and fosl2, which show high conservation in key regulatory domains and post-translational modification sites compared to their equivalent human proteins. During embryogenesis, zebrafish fos genes exhibit both overlapping and distinct spatiotemporal patterns of expression in specific cell types and tissues. Most fos genes are also expressed in a variety of adult zebrafish tissues. As in humans, we also found that expression of zebrafish FOS orthologs is induced by oncogenic BRAF-ERK signalling in zebrafish melanomas. These findings suggest that zebrafish represent an alternate model to mice for investigating the regulation and functions of Fos proteins in vertebrate embryonic and adult tissues, and cancer.
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Affiliation(s)
- Khadizatul Kubra
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Gurveer K. Gaddu
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute of Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Somayyeh Heidary
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute of Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Amardeep S. Dhillon
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute of Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
- Olivia Newton-John Cancer Research Institute, Melbourne, VIC 3084, Australia
- School of Cancer Medicine, LaTrobe University, Melbourne, VIC 3086, Australia
- Correspondence: (A.S.D.); (F.B.)
| | - Faiza Basheer
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute of Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
- Correspondence: (A.S.D.); (F.B.)
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WhichTF is functionally important in your open chromatin data? PLoS Comput Biol 2022; 18:e1010378. [PMID: 36040971 PMCID: PMC9426921 DOI: 10.1371/journal.pcbi.1010378] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
We present WhichTF, a computational method to identify functionally important transcription factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF applies an ontology-guided functional approach to compute novel enrichment by integrating accessibility measurements, high-confidence pre-computed conservation-aware TF binding sites, and putative gene-regulatory models. Comparison with prior sheer abundance-based methods reveals the unique ability of WhichTF to identify context-specific TFs with functional relevance, including NF-κB family members in lymphocytes and GATA factors in cardiac cells. To distinguish the transcriptional regulatory landscape in closely related samples, we apply differential analysis and demonstrate its utility in lymphocyte, mesoderm developmental, and disease cells. We find suggestive, under-characterized TFs, such as RUNX3 in mesoderm development and GLI1 in systemic lupus erythematosus. We also find TFs known for stress response, suggesting routine experimental caveats that warrant careful consideration. WhichTF yields biological insight into known and novel molecular mechanisms of TF-mediated transcriptional regulation in diverse contexts, including human and mouse cell types, cell fate trajectories, and disease-associated cells. Transcription factors (TFs), a class of DNA binding proteins, regulate tissue- and cell-type-specific expression of genes. Identifying the critical TFs in a given cellular context leads to investigating molecular regulatory mechanisms in development, differentiation, and disease. Because there are more than 1,500 human TFs, experimental measurements of genome-wide occupancy across all TFs have been challenging. While computational approaches play pivotal roles, most existing methods rely on statistical enrichment, focusing either on sequence motif similarity recognized by TFs or the similarity of the genomic region of interest with the previously characterized TF occupancy profile. Here we propose WhichTF as an alternative, incorporating curated biomedical knowledge from ontology and integrating it with the high-confidence prediction of conserved TF binding sites in user-provided genomic regions of interest. We develop a new WhichTF score to rank TFs and demonstrate its applicability across human and mouse cell types, cellular differentiation trajectories, and disease-associated cells.
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8
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Sharpe M, González-Rosa JM, Wranitz F, Jeffrey S, Copenhaver K, Burns CG, Burns CE. Ruvbl2 Suppresses Cardiomyocyte Proliferation During Zebrafish Heart Development and Regeneration. Front Cell Dev Biol 2022; 10:800594. [PMID: 35178388 PMCID: PMC8844374 DOI: 10.3389/fcell.2022.800594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/06/2022] [Indexed: 11/22/2022] Open
Abstract
Cardiomyocyte proliferation is an important source of new myocardium during heart development and regeneration. Consequently, mutations in drivers of cardiomyocyte proliferation cause congenital heart disease, and infarcted human hearts scar because cardiomyocytes exit the cell cycle postnatally. To boost cardiomyocyte proliferation in either setting, critical regulators must be identified. Through an ENU screen in zebrafish, the liebeskummer (lik) mutant was isolated and described as having elevated cardiomyocyte numbers during embryogenesis. The lik mutation results in a three amino acid insertion into Ruvbl2, a highly conserved ATPase. Because both gain- and loss-of-function properties have been described for ruvbl2lik, it remains unclear whether Ruvbl2 positively or negatively regulates cardiomyocyte proliferation. Here, we demonstrate that Ruvbl2 is a suppressor of cardiomyocyte proliferation during zebrafish heart development and regeneration. First, we confirmed speculation that augmented cardiomyocyte numbers in ruvbl2lik/lik hearts arise by hyperproliferation. To characterize bona fide ruvbl2 null animals, we created a ruvbl2 locus deletion allele (ruvbl2Δ). Like ruvbl2lik/lik mutants, ruvbl2Δ/Δ and compound heterozygote ruvbl2lik/Δ animals display ventricular hyperplasia, demonstrating that lik is a loss of function allele and that ruvbl2 represses cardiomyocyte proliferation. This activity is autonomous because constitutive myocardial overexpression of Ruvbl2 is sufficient to suppress cardiomyocyte proliferation in control hearts and rescue the hyperproliferation observed in ruvbl2Δ/Δ mutant hearts. Lastly, heat-shock inducible overexpression of Ruvbl2 suppresses cardiomyocyte proliferation during heart regeneration and leads to scarring. Together, our data demonstrate that Ruvbl2 functions autonomously as a suppressor of cardiomyocyte proliferation during both zebrafish heart development and adult heart regeneration.
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Affiliation(s)
- Michka Sharpe
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA, United States.,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Juan Manuel González-Rosa
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA, United States.,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Felicia Wranitz
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Spencer Jeffrey
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Katherine Copenhaver
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA, United States.,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - C Geoffrey Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA, United States.,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Caroline E Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA, United States.,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States.,Harvard Medical School, Boston, MA, United States.,Harvard Stem Cell Institute, Cambridge, MA, United States
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9
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Abrial M, Basu S, Huang M, Butty V, Schwertner A, Jeffrey S, Jordan D, Burns CE, Burns CG. Latent TGFβ binding proteins 1 and 3 protect the larval zebrafish outflow tract from aneurysmal dilatation. Dis Model Mech 2022; 15:274139. [PMID: 35098309 PMCID: PMC8990920 DOI: 10.1242/dmm.046979] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
Abstract
Aortic root aneurysm is a common cause of morbidity and mortality in Loeys-Dietz and Marfan Syndromes, where perturbations in TGFβ signaling play a causal or contributory role, respectively. Despite the advantages of cross-species disease modeling, animal models of aortic root aneurysm are largely restricted to genetically engineered mice. Here, we report that zebrafish devoid of latent TGFβ binding protein (ltbp) 1 and 3 develop rapid and severe aneurysm of the outflow tract (OFT), the aortic root equivalent. Similar to syndromic aneurysm tissue, the distended OFTs display evidence for paradoxical hyperactivated TGFβ signaling. RNA-sequencing revealed significant overlap between the molecular signatures of disease tissue from mutant zebrafish and Marfan mice. Lastly, chemical inhibition of TGFβ signaling in wild-type animals phenocopied mutants but chemical activation did not, demonstrating that TGFβ signaling is protective against aneurysm. Human relevance is supported by recent studies implicating genetic lesions in LTBP3 and potentially LTBP1 as heritable causes of aortic root aneurysm. Ultimately, our data demonstrate that zebrafish can now be leveraged to interrogate thoracic aneurysmal disease and identify novel lead compounds through small molecule suppressor screens.
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Affiliation(s)
- Maryline Abrial
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Sandeep Basu
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Mengmeng Huang
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Vincent Butty
- Massachusetts Institute of Technology BioMicroCenter, Cambridge, MA 02139, USA
| | - Asya Schwertner
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Spencer Jeffrey
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Daniel Jordan
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Caroline E Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA.,Harvard Medical School, Boston, MA 02115, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - C Geoffrey Burns
- Division of Basic and Translational Cardiovascular Research, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA.,Harvard Medical School, Boston, MA 02115, USA
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10
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Zhang Q, Zheng Y, Ning M, Li T. KLRD1, FOSL2 and LILRB3 as potential biomarkers for plaques progression in acute myocardial infarction and stable coronary artery disease. BMC Cardiovasc Disord 2021; 21:344. [PMID: 34271875 PMCID: PMC8285847 DOI: 10.1186/s12872-021-01997-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/09/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Myocardial infarction (MI) contributes to high mortality and morbidity and can also accelerate atherosclerosis, thus inducing recurrent event due to status changing of coronary artery walls or plaques. The research aimed to investigate the differentially expressed genes (DEGs), which may be potential therapeutic targets for plaques progression in stable coronary artery disease (CAD) and ST-elevated MI (STEMI). METHODS Two human datasets (GSE56885 and GSE59867) were analyzed by GEO2R and enrichment analysis was applied through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. To explore the seed genes, the protein-protein interaction (PPI) network was constructed and seed genes, as well as top30 ranking neighbours were screened out. To validate these findings, one human dataset GSE120521 was analyzed. Linear regression analysis and ROC curve were also performed to determine which seed genes above mentioned could be independent factors for plaques progression. Mice MI model and ELISA of seed genes were applied and ROC curve was also performed for in vivo validation. RESULTS 169 DEGs and 573 DEGs were screened out in GSE56885 and GSE59867, respectively. Utilizing GO and KEGG analysis, these DEGs mainly enriched in immune system response and cytokines interaction. PPI network analysis was carried out and 19 seed genes were screened out. To validate these findings, GSE120521 was analyzed and three genes were demonstrated to be targets for plaques progression and stable CAD progression, including KLRD1, FOSL2 and LILRB3. KLRD1 and LILRB3 were demonstrated to be high-expressed at 1d after MI compared to SHAM group and FOSL2 expression was low-expressed at 1d and 1w. To investigate the diagnostic abilities of seed genes, ROC analysis was applied and the AUCs of KLRD1, FOSL2 and LILRB3, were 0.771, 0.938 and 0.972, respectively. CONCLUSION This study provided the screened seed genes, KLRD1, FOSL2 and LILRB3, as credible molecular biomarkers for plaques status changing in CAD progression and MI recurrence. Other seed genes, such as FOS, SOCS3 and MCL1, may also be potential targets for treatment due to their special clinical value in cardiovascular diseases.
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Affiliation(s)
- Qiang Zhang
- Cardiology, The Third Central Clinical College of Tianjin Medical University, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
- Cardiology, Nankai University Affiliated Third Center Hospital, Tianjin, 300170, China
- Cardiology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China
| | - Yue Zheng
- Cardiology, The Third Central Clinical College of Tianjin Medical University, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
- School of Medicine, Nankai University, Tianjin, 300071, China
- Cardiology, Nankai University Affiliated Third Center Hospital, Tianjin, 300170, China
- Cardiology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China
| | - Meng Ning
- Cardiology, The Third Central Clinical College of Tianjin Medical University, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China
- Cardiology, Nankai University Affiliated Third Center Hospital, Tianjin, 300170, China
- Cardiology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China
| | - Tong Li
- Cardiology, The Third Central Clinical College of Tianjin Medical University, No. 83, Jintang Road, Hedong District, Tianjin, 300170, China.
- Cardiology, Nankai University Affiliated Third Center Hospital, Tianjin, 300170, China.
- Cardiology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China.
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.
- Institute of Hepatobiliary Disease, Tianjin, China.
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11
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Smith KA, Uribe V. Getting to the Heart of Left-Right Asymmetry: Contributions from the Zebrafish Model. J Cardiovasc Dev Dis 2021; 8:64. [PMID: 34199828 PMCID: PMC8230053 DOI: 10.3390/jcdd8060064] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/28/2022] Open
Abstract
The heart is laterally asymmetric. Not only is it positioned on the left side of the body but the organ itself is asymmetric. This patterning occurs across scales: at the organism level, through left-right axis patterning; at the organ level, where the heart itself exhibits left-right asymmetry; at the cellular level, where gene expression, deposition of matrix and proteins and cell behaviour are asymmetric; and at the molecular level, with chirality of molecules. Defective left-right patterning has dire consequences on multiple organs; however, mortality and morbidity arising from disrupted laterality is usually attributed to complex cardiac defects, bringing into focus the particulars of left-right patterning of the heart. Laterality defects impact how the heart integrates and connects with neighbouring organs, but the anatomy of the heart is also affected because of its asymmetry. Genetic studies have demonstrated that cardiac asymmetry is influenced by left-right axis patterning and yet the heart also possesses intrinsic laterality, reinforcing the patterning of this organ. These inputs into cardiac patterning are established at the very onset of left-right patterning (formation of the left-right organiser) and continue through propagation of left-right signals across animal axes, asymmetric differentiation of the cardiac fields, lateralised tube formation and asymmetric looping morphogenesis. In this review, we will discuss how left-right asymmetry is established and how that influences subsequent asymmetric development of the early embryonic heart. In keeping with the theme of this issue, we will focus on advancements made through studies using the zebrafish model and describe how its use has contributed considerable knowledge to our understanding of the patterning of the heart.
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Affiliation(s)
- Kelly A. Smith
- Department of Physiology, The University of Melbourne, Parkville, VIC 3010, Australia;
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12
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Cavone L, McCann T, Drake LK, Aguzzi EA, Oprişoreanu AM, Pedersen E, Sandi S, Selvarajah J, Tsarouchas TM, Wehner D, Keatinge M, Mysiak KS, Henderson BEP, Dobie R, Henderson NC, Becker T, Becker CG. A unique macrophage subpopulation signals directly to progenitor cells to promote regenerative neurogenesis in the zebrafish spinal cord. Dev Cell 2021; 56:1617-1630.e6. [PMID: 34033756 DOI: 10.1016/j.devcel.2021.04.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 03/15/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022]
Abstract
Central nervous system injury re-initiates neurogenesis in anamniotes (amphibians and fishes), but not in mammals. Activation of the innate immune system promotes regenerative neurogenesis, but it is fundamentally unknown whether this is indirect through the activation of known developmental signaling pathways or whether immune cells directly signal to progenitor cells using mechanisms that are unique to regeneration. Using single-cell RNA-seq of progenitor cells and macrophages, as well as cell-type-specific manipulations, we provide evidence for a direct signaling axis from specific lesion-activated macrophages to spinal progenitor cells to promote regenerative neurogenesis in zebrafish. Mechanistically, TNFa from pro-regenerative macrophages induces Tnfrsf1a-mediated AP-1 activity in progenitors to increase regeneration-promoting expression of hdac1 and neurogenesis. This establishes the principle that macrophages directly communicate to spinal progenitor cells via non-developmental signals after injury, providing potential targets for future interventions in the regeneration-deficient spinal cord of mammals.
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Affiliation(s)
- Leonardo Cavone
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Tess McCann
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Louisa K Drake
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Erika A Aguzzi
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Ana-Maria Oprişoreanu
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Elisa Pedersen
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Soe Sandi
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Jathurshan Selvarajah
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Themistoklis M Tsarouchas
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Daniel Wehner
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK; Max Planck Institute for the Science of Light, Staudtstraße 2, Erlangen 91058, Germany; Max-Planck-Zentrum für Physik und Medizin, Staudtstraße 2, Erlangen 91058, Germany
| | - Marcus Keatinge
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Karolina S Mysiak
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Beth E P Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Thomas Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK.
| | - Catherina G Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK; Euan MacDonald Centre for Motor Neurone Disease Research University of Edinburgh, Edinburgh, UK.
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13
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Kemmler CL, Riemslagh FW, Moran HR, Mosimann C. From Stripes to a Beating Heart: Early Cardiac Development in Zebrafish. J Cardiovasc Dev Dis 2021; 8:17. [PMID: 33578943 PMCID: PMC7916704 DOI: 10.3390/jcdd8020017] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/18/2022] Open
Abstract
The heart is the first functional organ to form during vertebrate development. Congenital heart defects are the most common type of human birth defect, many originating as anomalies in early heart development. The zebrafish model provides an accessible vertebrate system to study early heart morphogenesis and to gain new insights into the mechanisms of congenital disease. Although composed of only two chambers compared with the four-chambered mammalian heart, the zebrafish heart integrates the core processes and cellular lineages central to cardiac development across vertebrates. The rapid, translucent development of zebrafish is amenable to in vivo imaging and genetic lineage tracing techniques, providing versatile tools to study heart field migration and myocardial progenitor addition and differentiation. Combining transgenic reporters with rapid genome engineering via CRISPR-Cas9 allows for functional testing of candidate genes associated with congenital heart defects and the discovery of molecular causes leading to observed phenotypes. Here, we summarize key insights gained through zebrafish studies into the early patterning of uncommitted lateral plate mesoderm into cardiac progenitors and their regulation. We review the central genetic mechanisms, available tools, and approaches for modeling congenital heart anomalies in the zebrafish as a representative vertebrate model.
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Affiliation(s)
| | | | | | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine and Children’s Hospital Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA; (C.L.K.); (F.W.R.); (H.R.M.)
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14
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Boezio GL, Bensimon-Brito A, Piesker J, Guenther S, Helker CS, Stainier DY. Endothelial TGF-β signaling instructs smooth muscle cell development in the cardiac outflow tract. eLife 2020; 9:57603. [PMID: 32990594 PMCID: PMC7524555 DOI: 10.7554/elife.57603] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/09/2020] [Indexed: 12/14/2022] Open
Abstract
The development of the cardiac outflow tract (OFT), which connects the heart to the great arteries, relies on a complex crosstalk between endothelial (ECs) and smooth muscle (SMCs) cells. Defects in OFT development can lead to severe malformations, including aortic aneurysms, which are frequently associated with impaired TGF-β signaling. To better understand the role of TGF-β signaling in OFT formation, we generated zebrafish lacking the TGF-β receptor Alk5 and found a strikingly specific dilation of the OFT: alk5-/- OFTs exhibit increased EC numbers as well as extracellular matrix (ECM) and SMC disorganization. Surprisingly, endothelial-specific alk5 overexpression in alk5-/- rescues the EC, ECM, and SMC defects. Transcriptomic analyses reveal downregulation of the ECM gene fibulin-5, which when overexpressed in ECs ameliorates OFT morphology and function. These findings reveal a new requirement for endothelial TGF-β signaling in OFT morphogenesis and suggest an important role for the endothelium in the etiology of aortic malformations.
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Affiliation(s)
- Giulia Lm Boezio
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Anabela Bensimon-Brito
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Janett Piesker
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Guenther
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Christian Sm Helker
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Yr Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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15
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The emerging roles of circular RNAs in regulating the fate of stem cells. Mol Cell Biochem 2020; 476:231-246. [PMID: 32918186 DOI: 10.1007/s11010-020-03900-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/02/2020] [Indexed: 01/23/2023]
Abstract
Circular RNAs(circRNAs) are a large family of RNAs shaping covalently closed ring-like molecules and have become a hotspot with thousands of newly published studies. Stem cells are undifferentiated cells and have great potential in medical treatment due to their self-renewal ability and differentiation capacity. Abundant researches have unveiled that circRNAs have unique expression profile during the differentiation of stem cells and could serve as promising biomarkers of these cells. There are key circRNAs relevant to the differentiation, proliferation, and apoptosis of stem cells with certain mechanisms such as sponging miRNAs, interacting with proteins, and interfering mRNA translation. Moreover, several circRNAs have joined in the interplay between stem cells and lymphocytes. Our review will shed lights on the emerging roles of circRNAs in regulating the fate of diverse stem cells.
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16
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Gao L, Jin HJ, Zhang D, Lin Q. Silencing circRNA_001937 may inhibit cutaneous squamous cell carcinoma proliferation and induce apoptosis by preventing the sponging of the miRNA‑597‑3p/FOSL2 pathway. Int J Mol Med 2020; 46:1653-1660. [PMID: 33000177 PMCID: PMC7521585 DOI: 10.3892/ijmm.2020.4723] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 12/30/2019] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are reported to be aberrantly expressed and perform different functions in numerous types of tumor; however, their expression levels in cutaneous squamous cell carcinoma (CSCC) remain largely unclear. Thus, the purpose of the present study was to investigate the function of circRNA_001937 in CSCC. Differential circRNA expression profiles of CSCC were analyzed using the Arraystar Human circRNAs chip and reverse transcription-quantitative PCR (RT-qPCR); and the effects of circRNA_001937 on cell behavior, in particular its regulation over the microRNA (miRNA)-597-3p/Fos-related antigen 2 (FOSL2) pathway, was investigated using a dual-luciferase reporter assay, and verified using RT-qPCR and western blotting. circRNA_001937 expression levels were significantly increased in CSCC tissues and cell lines compared with the corresponding adjacent tissues and control cells (P<0.05). The genetic silencing of circRNA_001937 with small interfering RNA significantly inhibited cell proliferation, and induced cell apoptosis (P<0.05). circRNA_001937 was observed to directly bind to miRNA-597-3p and serve as a sponge, which indirectly increased the expression levels of FOSL2, a miRNA-597-3p target gene. In conclusion, circRNA_001937 expression was increased in CSCC and silencing circRNA_001937 gene expression may inhibit CSCC progression by sponging the miRNA-597-3p/FOSL2 pathway.
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Affiliation(s)
- Ling Gao
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hong-Juan Jin
- Department of Plastic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Duo Zhang
- Department of Plastic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Quan Lin
- Department of Plastic Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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17
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Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury. PLoS One 2020; 15:e0232963. [PMID: 32730272 PMCID: PMC7392272 DOI: 10.1371/journal.pone.0232963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/24/2020] [Indexed: 12/25/2022] Open
Abstract
Mammalian cardiomyocytes exit the cell cycle shortly after birth. As a result, an occurrence of coronary occlusion-induced myocardial infarction often results in heart failure, postinfarction LV dilatation, or death, and represents one of the most significant public health morbidities worldwide. Interestingly however, the hearts of neonatal pigs have been shown to regenerate following an acute myocardial infarction (MI) occuring on postnatal day 1 (P1); a recovery period which is accompanied by an increased expression of markers for cell-cycle activity, and suggests that early postnatal myocardial regeneration may be driven in part by the MI-induced proliferation of pre-existing cardiomyocytes. In this study, we identified signaling pathways known to regulate the cell cycle, and determined of these, the pathways persistently upregulated in response to MI injury. We identified five pathways (mitogen associated protein kinase [MAPK], Hippo, cyclic [cAMP], Janus kinase/signal transducers and activators of transcription [JAK-STAT], and Ras) which were comprehensively upregulated in cardiac tissues collected on day 7 (P7) and/or P28 of the P1 injury hearts. Several of the initiating master regulators (e.g., CSF1/CSF1R, TGFB, and NPPA) and terminal effector molecules (e.g., ATF4, FOS, RELA/B, ITGB2, CCND1/2/3, PIM1, RAF1, MTOR, NKF1B) in these pathways were persistently upregulated at day 7 through day 28, suggesting there exists at least some degree of regenerative activity up to 4 weeks following MI at P1. Our observations provide a list of key regulators to be examined in future studies targeting cell-cycle activity as an avenue for myocardial regeneration.
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18
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Sidhwani P, Leerberg DM, Boezio GLM, Capasso TL, Yang H, Chi NC, Roman BL, Stainier DYR, Yelon D. Cardiac function modulates endocardial cell dynamics to shape the cardiac outflow tract. Development 2020; 147:dev185900. [PMID: 32439760 PMCID: PMC7328156 DOI: 10.1242/dev.185900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 04/27/2020] [Indexed: 01/06/2023]
Abstract
Physical forces are important participants in the cellular dynamics that shape developing organs. During heart formation, for example, contractility and blood flow generate biomechanical cues that influence patterns of cell behavior. Here, we address the interplay between function and form during the assembly of the cardiac outflow tract (OFT), a crucial connection between the heart and vasculature that develops while circulation is under way. In zebrafish, we find that the OFT expands via accrual of both endocardial and myocardial cells. However, when cardiac function is disrupted, OFT endocardial growth ceases, accompanied by reduced proliferation and reduced addition of cells from adjacent vessels. The flow-responsive TGFβ receptor Acvrl1 is required for addition of endocardial cells, but not for their proliferation, indicating distinct modes of function-dependent regulation for each of these essential cell behaviors. Together, our results indicate that cardiac function modulates OFT morphogenesis by triggering endocardial cell accumulation that induces OFT lumen expansion and shapes OFT dimensions. Moreover, these morphogenetic mechanisms provide new perspectives regarding the potential causes of cardiac birth defects.
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Affiliation(s)
- Pragya Sidhwani
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dena M Leerberg
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Giulia L M Boezio
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, 61231 Bad Nauheim, Germany
| | - Teresa L Capasso
- Department of Human Genetics, Graduate School of Public Health, and Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hongbo Yang
- Division of Cardiovascular Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neil C Chi
- Division of Cardiovascular Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Beth L Roman
- Department of Human Genetics, Graduate School of Public Health, and Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Didier Y R Stainier
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, 61231 Bad Nauheim, Germany
| | - Deborah Yelon
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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19
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MiR-195 enhances cardiomyogenic differentiation of the proepicardium/septum transversum by Smurf1 and Foxp1 modulation. Sci Rep 2020; 10:9334. [PMID: 32518241 PMCID: PMC7283354 DOI: 10.1038/s41598-020-66325-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular development is a complex developmental process in which multiple cell lineages are involved, namely the deployment of first and second heart fields. Beside the contribution of these cardiogenic fields, extracardiac inputs to the developing heart are provided by the migrating cardiac neural crest cells and the proepicardial derived cells. The proepicardium (PE) is a transitory cauliflower-like structure located between the cardiac and hepatic primordia. The PE is constituted by an internal mesenchymal component surrounded by an external epithelial lining. With development, cells derived from the proepicardium migrate to the neighboring embryonic heart and progressive cover the most external surface, leading to the formation of the embryonic epicardium. Experimental evidence in chicken have nicely demonstrated that epicardial derived cells can distinctly contribute to fibroblasts, endothelial and smooth muscle cells. Surprisingly, isolation of the developing PE anlage and ex vivo culturing spontaneously lead to differentiation into beating cardiomyocytes, a process that is enhanced by Bmp but halted by Fgf administration. In this study we provide a comprehensive characterization of the developmental expression profile of multiple microRNAs during epicardial development in chicken. Subsequently, we identified that miR-125, miR-146, miR-195 and miR-223 selectively enhance cardiomyogenesis both in the PE/ST explants as well as in the embryonic epicardium, a Smurf1- and Foxp1-driven process. In addition we identified three novel long non-coding RNAs with enhanced expression in the PE/ST, that are complementary regulated by Bmp and Fgf administration and well as by microRNAs that selectively promote cardiomyogenesis, supporting a pivotal role of these long non coding RNAs in microRNA-mediated cardiomyogenesis of the PE/ST cells.
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20
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Santos-Ledo A, Washer S, Dhanaseelan T, Eley L, Alqatani A, Chrystal PW, Papoutsi T, Henderson DJ, Chaudhry B. Alternative splicing of jnk1a in zebrafish determines first heart field ventricular cardiomyocyte numbers through modulation of hand2 expression. PLoS Genet 2020; 16:e1008782. [PMID: 32421721 PMCID: PMC7259801 DOI: 10.1371/journal.pgen.1008782] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/29/2020] [Accepted: 04/18/2020] [Indexed: 02/07/2023] Open
Abstract
The planar cell polarity pathway is required for heart development and whilst the functions of most pathway members are known, the roles of the jnk genes in cardiac morphogenesis remain unknown as mouse mutants exhibit functional redundancy, with early embryonic lethality of compound mutants. In this study zebrafish were used to overcome early embryonic lethality in mouse models and establish the requirement for Jnk in heart development. Whole mount in-situ hybridisation and RT-PCR demonstrated that evolutionarily conserved alternative spliced jnk1a and jnk1b transcripts were expressed in the early developing heart. Maternal zygotic null mutant zebrafish lines for jnk1a and jnk1b, generated using CRISPR-Cas9, revealed a requirement for jnk1a in formation of the proximal, first heart field (FHF)-derived portion of the cardiac ventricular chamber. Rescue of the jnk1a mutant cardiac phenotype was only possible by injection of the jnk1a EX7 Lg alternatively spliced transcript. Analysis of mutants indicated that there was a reduction in the size of the hand2 expression field in jnk1a mutants which led to a specific reduction in FHF ventricular cardiomyocytes within the anterior lateral plate mesoderm. Moreover, the jnk1a mutant ventricular defect could be rescued by injection of hand2 mRNA. This study reveals a novel and critical requirement for Jnk1 in heart development and highlights the importance of alternative splicing in vertebrate cardiac morphogenesis. Genetic pathways functioning through jnk1 may be important in human heart malformations with left ventricular hypoplasia.
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Affiliation(s)
- Adrian Santos-Ledo
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Sam Washer
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Tamil Dhanaseelan
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Lorraine Eley
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Ahlam Alqatani
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Paul W. Chrystal
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Tania Papoutsi
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Deborah J. Henderson
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
| | - Bill Chaudhry
- Biosciences Institute, Faculty of Medicine, International Centre for Life, Newcastle University, United Kingdom
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21
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Birnhuber A, Biasin V, Schnoegl D, Marsh LM, Kwapiszewska G. Transcription factor Fra-2 and its emerging role in matrix deposition, proliferation and inflammation in chronic lung diseases. Cell Signal 2019; 64:109408. [PMID: 31473307 DOI: 10.1016/j.cellsig.2019.109408] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Fos-related antigen-2 (Fra-2) belongs to the activator protein 1 (AP-1) family of transcription factors and is involved in a broad variety of cellular processes, such as proliferation or differentiation. Aberrant expression of Fra-2 or regulation can lead to severe growth defects or diverse pathologies. Elevated Fra-2 expression has been described in several chronic lung diseases, such as pulmonary fibrosis, chronic obstructive pulmonary disease and asthma. However, the pathomechanisms behind the Fra-2-induced pulmonary remodelling are still not fully elucidated. Fra-2 overexpressing mice were initially described as a model of systemic sclerosis associated organ fibrosis, with predominant alterations in the lung. High levels of Fra-2 expression give rise to profound inflammation with severe remodelling of the parenchyma and the vasculature, resulting in fibrosis and pulmonary hypertension, respectively, but also alters bronchial function. In this review we discuss the central role of Fra-2 connecting inflammation, cellular proliferation and extracellular matrix deposition underlying chronic lung diseases and what we can learn for future therapeutic options.
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Affiliation(s)
- A Birnhuber
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
| | - V Biasin
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
| | - D Schnoegl
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
| | - L M Marsh
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
| | - G Kwapiszewska
- Ludwig Boltzmann Institute for Lung Vascular Research, Graz, Austria; Otto Loewi Research Center, Medical University of Graz, Graz, Austria.
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22
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Ki S, Kwon SH, Eum J, Raslan AA, Kim KN, Hwang BJ, Kee Y. 3D light-sheet assay assessing novel valproate-associated cardiotoxicity and folic acid relief in zebrafish embryogenesis. CHEMOSPHERE 2019; 227:551-560. [PMID: 31004822 DOI: 10.1016/j.chemosphere.2019.04.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Precise in vivo toxicological assays to determine the cardiotoxicity of pharmaceuticals and their waste products are essential in order to evaluate their risks to humans and the environment following industrial release. In the present study, we aimed to develop the sensitive imaging-based cardiotoxicity assay and combined 3D light-sheet microscopy with a zebrafish model to identify hidden cardiovascular anomalies induced by valproic acid (VPA) exposure. The zebrafish model is advantageous for this assessment because its embryos remain transparent. The 3D spatial localization of fluorescence-labeled cardiac cells in and around the heart using light-sheet technology revealed dislocalization of the heart from the outflow tract in two-day-old zebrafish embryos treated with 50 μM and 100 μM VPA (P < 0.01) and those embryos exposed to 20 μM VPA presented hypoplastic distal ventricles (P < 0.01). These two observed phenotypes are second heart field-derived cardiac defects. Quantitative analysis of the light-sheet imaging demonstrated that folic acid (FA) supplementation significantly increased the numbers of endocardial and myocardial cells (P < 0.05) and the accretion of second heart field-derived cardiomyocytes to the arterial pole of the outflow tract. The heart rate increased in response to the cellular changes occurring in embryonic heart development (P < 0.05). The present study disclosed the cellular mechanism underlying the role of FA in spontaneous cellular changes in cardiogenesis and in VPA-associated cardiotoxicity. The 3D light-sheet assay may be the next-generation test to evaluate the risks of previously undetected pharmaceutical and environmental cardiotoxicities in both humans and animals.
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Affiliation(s)
- Seoyoung Ki
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
| | - Seung-Hae Kwon
- Korea Basic Science Institute Chuncheon Center, Chuncheon, South Korea
| | - Juneyong Eum
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
| | - Ahmed A Raslan
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
| | - Kil-Nam Kim
- Korea Basic Science Institute Chuncheon Center, Chuncheon, South Korea
| | - Byung Joon Hwang
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea.
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea.
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23
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van Duijvenboden K, de Bakker DEM, Man JCK, Janssen R, Günthel M, Hill MC, Hooijkaas IB, van der Made I, van der Kraak PH, Vink A, Creemers EE, Martin JF, Barnett P, Bakkers J, Christoffels VM. Conserved NPPB+ Border Zone Switches From MEF2- to AP-1-Driven Gene Program. Circulation 2019; 140:864-879. [PMID: 31259610 DOI: 10.1161/circulationaha.118.038944] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Surviving cells in the postinfarction border zone are subjected to intense fluctuations of their microenvironment. Recently, border zone cardiomyocytes have been specifically implicated in cardiac regeneration. Here, we defined their unique transcriptional and regulatory properties, and comprehensively validated new molecular markers, including Nppb, encoding B-type natriuretic peptide, after infarction. METHODS Transgenic reporter mice were used to identify the Nppb-positive border zone after myocardial infarction. Transcriptome analysis of remote, border, and infarct zones and of purified cardiomyocyte nuclei was performed using RNA-sequencing. Top candidate genes displaying border zone spatial specificity were histologically validated in ischemic human hearts. Mice in which Nppb was deleted by genome editing were subjected to myocardial infarction. Chromatin accessibility landscapes of border zone and control cardiomyocyte nuclei were assessed by using assay for transposase-accessible chromatin using sequencing. RESULTS We identified the border zone as a spatially confined region transcriptionally distinct from the remote myocardium. The transcriptional response of the border zone was much stronger than that of the remote ventricular wall, involving acute downregulation of mitochondrial oxidative phosphorylation, fatty acid metabolism, calcium handling, and sarcomere function, and the activation of a stress-response program. Analysis of infarcted human hearts revealed that the transcriptionally discrete border zone is conserved in humans, and led to the identification of novel conserved border zone markers including NPPB, ANKRD1, DES, UCHL1, JUN, and FOXP1. Homozygous Nppb mutant mice developed acute and lethal heart failure after myocardial infarction, indicating that B-type natriuretic peptide is required to preserve postinfarct heart function. Assay for transposase-accessible chromatin using sequencing revealed thousands of cardiomyocyte lineage-specific MEF2-occupied regulatory elements that lost accessibility in the border zone. Putative injury-responsive enhancers that gained accessibility were highly associated with AP-1 (activator protein 1) binding sites. Nuclear c-Jun, a component of AP-1, was observed specifically in border zone cardiomyocytes. CONCLUSIONS Cardiomyocytes in a discrete zone bordering the infarct switch from a MEF2-driven homeostatic lineage-specific to an AP-1-driven injury-induced gene expression program. This program is conserved between mouse and human, and includes Nppb expression, which is required to prevent acute heart failure after infarction.
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Affiliation(s)
- Karel van Duijvenboden
- Departments of Medical Biology, Amsterdam Cardiovascular Sciences (K.v.D., J.C.K.M., R.J., M.G., I.B.H., P.B., V.M.C.), Academic Medical Center, Amsterdam, The Netherlands
| | - Dennis E M de Bakker
- Hubrecht Institute (D.E.M.d.B., J.B.), University Medical Centre Utrecht, The Netherlands
| | - Joyce C K Man
- Departments of Medical Biology, Amsterdam Cardiovascular Sciences (K.v.D., J.C.K.M., R.J., M.G., I.B.H., P.B., V.M.C.), Academic Medical Center, Amsterdam, The Netherlands
| | - Rob Janssen
- Departments of Medical Biology, Amsterdam Cardiovascular Sciences (K.v.D., J.C.K.M., R.J., M.G., I.B.H., P.B., V.M.C.), Academic Medical Center, Amsterdam, The Netherlands
| | - Marie Günthel
- Departments of Medical Biology, Amsterdam Cardiovascular Sciences (K.v.D., J.C.K.M., R.J., M.G., I.B.H., P.B., V.M.C.), Academic Medical Center, Amsterdam, The Netherlands
| | - Matthew C Hill
- Program in Developmental Biology (M.C.H., J.F.M.), Baylor College of Medicine, Houston, TX
| | - Ingeborg B Hooijkaas
- Departments of Medical Biology, Amsterdam Cardiovascular Sciences (K.v.D., J.C.K.M., R.J., M.G., I.B.H., P.B., V.M.C.), Academic Medical Center, Amsterdam, The Netherlands
| | - Ingeborg van der Made
- Experimental Cardiology (I.v.d.M., E.E.C.), Academic Medical Center, Amsterdam, The Netherlands
| | - Petra H van der Kraak
- Department of Pathology (P.H.v.d.K., A.V.), University Medical Centre Utrecht, The Netherlands
| | - Aryan Vink
- Department of Pathology (P.H.v.d.K., A.V.), University Medical Centre Utrecht, The Netherlands
| | - Esther E Creemers
- Experimental Cardiology (I.v.d.M., E.E.C.), Academic Medical Center, Amsterdam, The Netherlands
| | - James F Martin
- Program in Developmental Biology (M.C.H., J.F.M.), Baylor College of Medicine, Houston, TX.,Department of Molecular Physiology and Biophysics (J.F.M.), Baylor College of Medicine, Houston, TX
| | - Phil Barnett
- Departments of Medical Biology, Amsterdam Cardiovascular Sciences (K.v.D., J.C.K.M., R.J., M.G., I.B.H., P.B., V.M.C.), Academic Medical Center, Amsterdam, The Netherlands
| | - Jeroen Bakkers
- Hubrecht Institute (D.E.M.d.B., J.B.), University Medical Centre Utrecht, The Netherlands
| | - Vincent M Christoffels
- Departments of Medical Biology, Amsterdam Cardiovascular Sciences (K.v.D., J.C.K.M., R.J., M.G., I.B.H., P.B., V.M.C.), Academic Medical Center, Amsterdam, The Netherlands
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24
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Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers. Cell Stem Cell 2019; 25:69-86.e5. [PMID: 31080136 DOI: 10.1016/j.stem.2019.03.022] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/07/2018] [Accepted: 03/25/2019] [Indexed: 11/21/2022]
Abstract
The cardiogenic transcription factors (TFs) Mef2c, Gata4, and Tbx5 can directly reprogram fibroblasts to induced cardiac-like myocytes (iCLMs), presenting a potential source of cells for cardiac repair. While activity of these TFs is enhanced by Hand2 and Akt1, their genomic targets and interactions during reprogramming are not well studied. We performed genome-wide analyses of cardiogenic TF binding and enhancer profiling during cardiac reprogramming. We found that these TFs synergistically activate enhancers highlighted by Mef2c binding sites and that Hand2 and Akt1 coordinately recruit other TFs to enhancer elements. Intriguingly, these enhancer landscapes collectively resemble patterns of enhancer activation during embryonic cardiogenesis. We further constructed a cardiac reprogramming gene regulatory network and found repression of EGFR signaling pathway genes. Consistently, chemical inhibition of EGFR signaling augmented reprogramming. Thus, by defining epigenetic landscapes these findings reveal synergistic transcriptional activation across a broad landscape of cardiac enhancers and key signaling pathways that govern iCLM reprogramming.
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25
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Zimmer AM, Pan YK, Chandrapalan T, Kwong RWM, Perry SF. Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing? ACTA ACUST UNITED AC 2019; 222:222/7/jeb175737. [PMID: 30948498 DOI: 10.1242/jeb.175737] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss-of-function technologies, such as morpholino- and RNAi-mediated gene knockdown, and TALEN- and CRISPR/Cas9-mediated gene knockout, are widely used to investigate gene function and its physiological significance. Here, we provide a general overview of the various knockdown and knockout technologies commonly used in comparative physiology and discuss the merits and drawbacks of these technologies with a particular focus on research conducted in zebrafish. Despite their widespread use, there is an ongoing debate surrounding the use of knockdown versus knockout approaches and their potential off-target effects. This debate is primarily fueled by the observations that, in some studies, knockout mutants exhibit phenotypes different from those observed in response to knockdown using morpholinos or RNAi. We discuss the current debate and focus on the discrepancies between knockdown and knockout phenotypes, providing literature and primary data to show that the different phenotypes are not necessarily a direct result of the off-target effects of the knockdown agents used. Nevertheless, given the recent evidence of some knockdown phenotypes being recapitulated in knockout mutants lacking the morpholino or RNAi target, we stress that results of knockdown experiments need to be interpreted with caution. We ultimately argue that knockdown experiments should not be discontinued if proper control experiments are performed, and that with careful interpretation, knockdown approaches remain useful to complement the limitations of knockout studies (e.g. lethality of knockout and compensatory responses).
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Affiliation(s)
- Alex M Zimmer
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Yihang K Pan
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | | | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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26
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Ren W, Yang L, Deng T, Wu C, Li Y, Wu J, Huang Z, Du F, Guo L. Calcitonin gene‑related peptide regulates FOSL2 expression and cell proliferation of BMSCs via mmu_circRNA_003795. Mol Med Rep 2019; 19:3732-3742. [PMID: 30896827 PMCID: PMC6472134 DOI: 10.3892/mmr.2019.10038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/07/2019] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs that may have important regulatory potency in various biological processes. However, the role of circRNAs and their potential functions in bone marrow mesenchymal stem cells of mice (BMSCs) are still ambiguous. The current study aims to examine the expression of circRNAs and to investigate their effects on FOS like 2 AP-1 transcription factor subunit (FOSL2) expression following stimulation of BMSCs with calcitonin gene-related peptide (CGRP). RNA generated from BMSCs stimulated with or without CGRP was used in a microarray to detect expression of circRNAs. There were 58 significantly differentially expressed circRNAs following CGRP treatment, with 44 circRNAs downregulated and 14 upregulated. Bioinformatics analysis and regulatory networks were used to identify the potential interactions between circRNAs and microRNAs (miRs). mmu_circRNA_003795 was significantly increased in the CGRP-stimulated BMSCs compared with the blank control. Silencing of mmu_circRNA_003795, significantly increased the expression of mmu_miR-504-3p, whereas FOSL2 expression and cell proliferation were decreased. Furthermore, silencing of mmu_mir-504-3p using an miR inhibitor led to increased FOSL2 expression. Additionally, silencing of mmu_circRNA_003795 using small interfering RNA induced marked alterations in the cell cycle of BMSCs. The results demonstrated that mmu_circRNA_003795 can indirectly regulate FOSL2 expression via sponging of miR-504-3p, resulting in alterations in BMSC proliferation.
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Affiliation(s)
- Wen Ren
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Lan Yang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Tian Deng
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Caijuan Wu
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Yuanjing Li
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Jingwen Wu
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Zhu Huang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Faliang Du
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Lvhua Guo
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
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27
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Gibb N, Lazic S, Yuan X, Deshwar AR, Leslie M, Wilson MD, Scott IC. Hey2 regulates the size of the cardiac progenitor pool during vertebrate heart development. Development 2018; 145:dev.167510. [PMID: 30355727 DOI: 10.1242/dev.167510] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/13/2018] [Indexed: 01/04/2023]
Abstract
A key event in heart development is the timely addition of cardiac progenitor cells, defects in which can lead to congenital heart defects. However, how the balance and proportion of progenitor proliferation versus addition to the heart is regulated remains poorly understood. Here, we demonstrate that Hey2 functions to regulate the dynamics of cardiac progenitor addition to the zebrafish heart. We found that the previously noted increase in myocardial cell number found in the absence of Hey2 function was due to a pronounced expansion in the size of the cardiac progenitor pool. Expression analysis and lineage tracing of hey2-expressing cells showed that hey2 is active in cardiac progenitors. Hey2 acted to limit proliferation of cardiac progenitors, prior to heart tube formation. Use of a transplantation approach demonstrated a likely cell-autonomous (in cardiac progenitors) function for Hey2. Taken together, our data suggest a previously unappreciated role for Hey2 in controlling the proliferative capacity of cardiac progenitors, affecting the subsequent contribution of late-differentiating cardiac progenitors to the developing vertebrate heart.
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Affiliation(s)
- Natalie Gibb
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Savo Lazic
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Xuefei Yuan
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Ashish R Deshwar
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Meaghan Leslie
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Michael D Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Ian C Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada .,Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada.,Ted Rogers Centre for Heart Research, Toronto, Ontario M5G 1M1, Canada.,Heart and Stroke Richard Lewar Centres of Excellence in Cardiovascular Research, Toronto, Ontario M5S 3H2, Canada
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28
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sox9b is required in cardiomyocytes for cardiac morphogenesis and function. Sci Rep 2018; 8:13906. [PMID: 30224706 PMCID: PMC6141582 DOI: 10.1038/s41598-018-32125-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 09/03/2018] [Indexed: 12/18/2022] Open
Abstract
The high mobility group transcription factor SOX9 is expressed in stem cells, progenitor cells, and differentiated cell-types in developing and mature organs. Exposure to a variety of toxicants including dioxin, di(2-ethylhexyl) phthalate, 6:2 chlorinated polyfluorinated ether sulfonate, and chlorpyrifos results in the downregulation of tetrapod Sox9 and/or zebrafish sox9b. Disruption of Sox9/sox9b function through environmental exposures or genetic mutations produce a wide range of phenotypes and adversely affect organ development and health. We generated a dominant-negative sox9b (dnsox9b) to inhibit sox9b target gene expression and used the Gal4/UAS system to drive dnsox9b specifically in cardiomyocytes. Cardiomyocyte-specific inhibition of sox9b function resulted in a decrease in ventricular cardiomyocytes, an increase in atrial cardiomyocytes, hypoplastic endothelial cushions, and impaired epicardial development, ultimately culminating in heart failure. Cardiomyocyte-specific dnsox9b expression significantly reduced end diastolic volume, which corresponded with a decrease in stroke volume, ejection fraction, and cardiac output. Further analysis of isolated cardiac tissue by RT-qPCR revealed cardiomyocyte-specific inhibition of sox9b function significantly decreased the expression of the critical cardiac development genes nkx2.5, nkx2.7, and myl7, as well as c-fos, an immediate early gene necessary for cardiomyocyte progenitor differentiation. Together our studies indicate sox9b transcriptional regulation is necessary for cardiomyocyte development and function.
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29
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González-Rosa JM, Sharpe M, Field D, Soonpaa MH, Field LJ, Burns CE, Burns CG. Myocardial Polyploidization Creates a Barrier to Heart Regeneration in Zebrafish. Dev Cell 2018; 44:433-446.e7. [PMID: 29486195 PMCID: PMC5830170 DOI: 10.1016/j.devcel.2018.01.021] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/11/2017] [Accepted: 01/26/2018] [Indexed: 01/07/2023]
Abstract
Correlative evidence suggests that polyploidization of heart muscle, which occurs naturally in post-natal mammals, creates a barrier to heart regeneration. Here, we move beyond a correlation by demonstrating that experimental polyploidization of zebrafish cardiomyocytes is sufficient to suppress their proliferative potential during regeneration. Initially, we determined that zebrafish myocardium becomes susceptible to polyploidization upon transient cytokinesis inhibition mediated by dominant-negative Ect2. Using a transgenic strategy, we generated adult animals containing mosaic hearts composed of differentially labeled diploid and polyploid-enriched cardiomyocyte populations. Diploid cardiomyocytes outcompeted their polyploid neighbors in producing regenerated heart muscle. Moreover, hearts composed of equivalent proportions of diploid and polyploid cardiomyocytes failed to regenerate altogether, demonstrating that a critical percentage of diploid cardiomyocytes is required to achieve heart regeneration. Our data identify cardiomyocyte polyploidization as a barrier to heart regeneration and suggest that mobilizing rare diploid cardiomyocytes in the human heart will improve its regenerative capacity.
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Affiliation(s)
- Juan Manuel González-Rosa
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Michka Sharpe
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Dorothy Field
- The Krannert Institute of Cardiology, the Wells Center for Pediatric Research, and Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark H Soonpaa
- The Krannert Institute of Cardiology, the Wells Center for Pediatric Research, and Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Loren J Field
- The Krannert Institute of Cardiology, the Wells Center for Pediatric Research, and Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Caroline E Burns
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - C Geoffrey Burns
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA.
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30
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Colombo S, de Sena-Tomás C, George V, Werdich AA, Kapur S, MacRae CA, Targoff KL. Nkx genes establish second heart field cardiomyocyte progenitors at the arterial pole and pattern the venous pole through Isl1 repression. Development 2018; 145:dev.161497. [PMID: 29361575 DOI: 10.1242/dev.161497] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/04/2017] [Indexed: 12/28/2022]
Abstract
NKX2-5 is the most commonly mutated gene associated with human congenital heart defects (CHDs), with a predilection for cardiac pole abnormalities. This homeodomain transcription factor is a central regulator of cardiac development and is expressed in both the first and second heart fields (FHF and SHF). We have previously revealed essential functions of nkx2.5 and nkx2.7, two Nkx2-5 homologs expressed in zebrafish cardiomyocytes, in maintaining ventricular identity. However, the differential roles of these genes in the specific subpopulations of the anterior (aSHF) and posterior (pSHF) SHFs have yet to be fully defined. Here, we show that Nkx genes regulate aSHF and pSHF progenitors through independent mechanisms. We demonstrate that Nkx genes restrict proliferation of aSHF progenitors in the outflow tract, delimit the number of pSHF progenitors at the venous pole and pattern the sinoatrial node acting through Isl1 repression. Moreover, optical mapping highlights the requirement for Nkx gene dose in establishing electrophysiological chamber identity and in integrating the physiological connectivity of FHF and SHF cardiomyocytes. Ultimately, our results may shed light on the discrete errors responsible for NKX2-5-dependent human CHDs of the cardiac outflow and inflow tracts.
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Affiliation(s)
- Sophie Colombo
- Division of Cardiology, Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Carmen de Sena-Tomás
- Division of Cardiology, Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Vanessa George
- Division of Cardiology, Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Andreas A Werdich
- Brigham and Women's Hospital/Harvard Medical School, Cardiovascular Division, 75 Francis Street, Thorn 11, Boston, MA 02115, USA
| | - Sunil Kapur
- Brigham and Women's Hospital/Harvard Medical School, Cardiovascular Division, 75 Francis Street, Thorn 11, Boston, MA 02115, USA
| | - Calum A MacRae
- Brigham and Women's Hospital/Harvard Medical School, Cardiovascular Division, 75 Francis Street, Thorn 11, Boston, MA 02115, USA
| | - Kimara L Targoff
- Division of Cardiology, Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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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: 50] [Impact Index Per Article: 8.3] [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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32
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Disruption of the hydrogen bonding network determines the pH-induced non-fluorescent state of the fluorescent protein ZsYellow by protonation of Glu221. Biochem Biophys Res Commun 2017; 493:562-567. [DOI: 10.1016/j.bbrc.2017.08.152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 08/30/2017] [Indexed: 11/18/2022]
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33
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Liu Q, Jiang C, Xu J, Zhao MT, Van Bortle K, Cheng X, Wang G, Chang HY, Wu JC, Snyder MP. Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs. Circ Res 2017; 121:376-391. [PMID: 28663367 DOI: 10.1161/circresaha.116.310456] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 06/21/2017] [Accepted: 06/28/2017] [Indexed: 01/13/2023]
Abstract
RATIONALE Recent advances have improved our ability to generate cardiomyocytes from human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs). However, our understanding of the transcriptional regulatory networks underlying early stages (ie, from mesoderm to cardiac mesoderm) of cardiomyocyte differentiation remains limited. OBJECTIVE To characterize transcriptome and chromatin accessibility during early cardiomyocyte differentiation from hiPSCs and hESCs. METHODS AND RESULTS We profiled the temporal changes in transcriptome and chromatin accessibility at genome-wide levels during cardiomyocyte differentiation derived from 2 hiPSC lines and 2 hESC lines at 4 stages: pluripotent stem cells, mesoderm, cardiac mesoderm, and differentiated cardiomyocytes. Overall, RNA sequencing analysis revealed that transcriptomes during early cardiomyocyte differentiation were highly concordant between hiPSCs and hESCs, and clustering of 4 cell lines within each time point demonstrated that changes in genome-wide chromatin accessibility were similar across hiPSC and hESC cell lines. Weighted gene co-expression network analysis (WGCNA) identified several modules that were strongly correlated with different stages of cardiomyocyte differentiation. Several novel genes were identified with high weighted connectivity within modules and exhibited coexpression patterns with other genes, including noncoding RNA LINC01124 and uncharacterized RNA AK127400 in the module related to the mesoderm stage; E-box-binding homeobox 1 (ZEB1) in the module correlated with postcardiac mesoderm. We further demonstrated that ZEB1 is required for early cardiomyocyte differentiation. In addition, based on integrative analysis of both WGCNA and transcription factor motif enrichment analysis, we determined numerous transcription factors likely to play important roles at different stages during cardiomyocyte differentiation, such as T and eomesodermin (EOMES; mesoderm), lymphoid enhancer-binding factor 1 (LEF1) and mesoderm posterior BHLH transcription factor 1 (MESP1; from mesoderm to cardiac mesoderm), meis homeobox 1 (MEIS1) and GATA-binding protein 4 (GATA4) (postcardiac mesoderm), JUN and FOS families, and MEIS2 (cardiomyocyte). CONCLUSIONS Both hiPSCs and hESCs share similar transcriptional regulatory mechanisms underlying early cardiac differentiation, and our results have revealed transcriptional regulatory networks and new factors (eg, ZEB1) controlling early stages of cardiomyocyte differentiation.
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Affiliation(s)
- Qing Liu
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Chao Jiang
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Jin Xu
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Ming-Tao Zhao
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Kevin Van Bortle
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Xun Cheng
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Guangwen Wang
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Howard Y Chang
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Joseph C Wu
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Michael P Snyder
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA.
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