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Zinski J, Chung H, Joshi P, Warrick F, Berg BD, Glova G, McGrail M, Balciunas D, Friedberg I, Mullins M. EpicTope: narrating protein sequence features to identify non-disruptive epitope tagging sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583232. [PMID: 38559275 PMCID: PMC10979891 DOI: 10.1101/2024.03.03.583232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Epitope tagging is an invaluable technique enabling the identification, tracking, and purification of proteins in vivo. We developed a tool, EpicTope, to facilitate this method by identifying amino acid positions suitable for epitope insertion. Our method uses a scoring function that considers multiple protein sequence and structural features to determine locations least disruptive to the protein's function. We validated our approach on the zebrafish Smad5 protein, showing that multiple predicted internally tagged Smad5 proteins rescue zebrafish smad5 mutant embryos, while the N- and C-terminal tagged variants do not, also as predicted. We further show that the internally tagged Smad5 proteins are accessible to antibodies in wholemount zebrafish embryo immunohistochemistry and by western blot. Our work demonstrates that EpicTope is an accessible and effective tool for designing epitope tag insertion sites. EpicTope is available under a GPL-3 license from: https://github.com/FriedbergLab/Epictope.
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Affiliation(s)
- Joseph Zinski
- Department of Cell and Development Biology, University of Pennsylvania Perelman School of Medicine
| | - Henri Chung
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University
- Program in Bioinformatics and Computational Biology, Iowa State University
| | - Parnal Joshi
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University
- Program in Bioinformatics and Computational Biology, Iowa State University
| | - Finn Warrick
- Department of Cell and Development Biology, University of Pennsylvania Perelman School of Medicine
| | | | - Greg Glova
- Department of Cell and Development Biology, University of Pennsylvania Perelman School of Medicine
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University
| | - Darius Balciunas
- Department of Biology, Temple University
- Institute of Biotechnology, Life Sciences Center, Vilnius University
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University
| | - Mary Mullins
- Department of Cell and Development Biology, University of Pennsylvania Perelman School of Medicine
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Long X, Wei J, Fang Q, Yuan X, Du J. Single-cell RNA sequencing reveals the transcriptional heterogeneity of Tbx18-positive cardiac cells during heart development. Funct Integr Genomics 2024; 24:18. [PMID: 38265516 DOI: 10.1007/s10142-024-01290-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The T-box family transcription factor 18 (Tbx18) has been found to play a critical role in regulating the development of the mammalian heart during the primary stages of embryonic development while the cellular heterogeneity and landscape of Tbx18-positive (Tbx18+) cardiac cells remain incompletely characterized. Here, we analyzed prior published single-cell RNA sequencing (scRNA-seq) mouse heart data to explore the heterogeneity of Tbx18+ cardiac cell subpopulations and provide a comprehensive transcriptional landscape of Tbx18+ cardiac cells during their development. Bioinformatic analysis methods were utilized to identify the heterogeneity between cell groups. Based on the gene expression characteristics, Tbx18+ cardiac cells can be classified into a minimum of two distinct cell populations, namely fibroblast-like cells and cardiomyocytes. In terms of temporal heterogeneity, these cells exhibit three developmental stages, namely the MEM stage, ML_P0 stage, and P stage Tbx18+ cardiac cells. Furthermore, Tbx18+ cardiac cells encompass several cell types, including cardiac progenitor-like cells, cardiomyocytes, and epicardial/stromal cells, as determined by specific transcriptional regulatory networks. The scRNA-seq results revealed the involvement of extracellular matrix (ECM) signals and epicardial epithelial-to-mesenchymal transition (EMT) in the development of Tbx18+ cardiac cells. The utilization of a lineage-tracing model served to validate the crucial function of Tbx18 in the differentiation of cardiac cells. Consequently, these findings offer a comprehensive depiction of the cellular heterogeneity within Tbx18+ cardiac cells.
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Affiliation(s)
- Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Jiangjun Wei
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Qinghua Fang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
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Luna-Zurita L, Flores-Garza BG, Grivas D, Siguero-Álvarez M, de la Pompa JL. Cooperative Response to Endocardial Notch Reveals Interaction With Hippo Pathway. Circ Res 2023; 133:1022-1039. [PMID: 37961886 PMCID: PMC10699509 DOI: 10.1161/circresaha.123.323474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND The endocardium is a crucial signaling center for cardiac valve development and maturation. Genetic analysis has identified several human endocardial genes whose inactivation leads to bicuspid aortic valve formation and calcific aortic valve disease, but knowledge is very limited about the role played in valve development and disease by noncoding endocardial regulatory regions and upstream factors. METHODS We manipulated Notch signaling in mouse embryonic endocardial cells by short-term and long-term coculture with OP9 stromal cells expressing Notch ligands and inhibition of Notch activity. We examined the transcriptional profile and chromatin accessibility landscape for each condition, integrated transcriptomic, transcription factor occupancy, chromatin accessibility, and proteomic datasets. We generated in vitro and in vivo models with CRISPR-Cas9-edited deletions of various noncoding regulatory elements and validated their regulatory potential. RESULTS We identified primary and secondary transcriptional responses to Notch ligands in the mouse embryonic endocardium, and a NOTCH-dependent transcriptional signature in valve development and disease. By defining the changes in the chromatin accessibility landscape and integrating with the landscape in developing mouse endocardium and adult human valves, we identify potential noncoding regulatory elements, validated selected candidates, propose interacting cofactors, and define the timeframe of their regulatory activity. Additionally, we found cooperative transcriptional repression with Hippo pathway by inhibiting nuclear Yap (Yes-associated protein) activity in the endocardium during cardiac valve development. CONCLUSIONS Sequential Notch-dependent transcriptional regulation in the embryonic endocardium involves multiple factors. Notch activates certain noncoding elements through these factors and simultaneously suppresses elements that could hinder cardiac valve development and homeostasis. Biorxviv: https://www.biorxiv.org/content/10.1101/2023.03.23.533882v1.full.
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Affiliation(s)
- Luis Luna-Zurita
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
- Ciber CV, Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
| | - Brenda Giselle Flores-Garza
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
- Ciber CV, Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
| | - Dimitrios Grivas
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
- Ciber CV, Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
- Developmental Biology, Centre for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Greece (D.G.)
| | - Marcos Siguero-Álvarez
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
- Ciber CV, Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
| | - José Luis de la Pompa
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
- Ciber CV, Madrid, Spain (L.L.-Z., B.G.F.-G., D.G., M.S.-A., J.L.d.l.P.)
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Sarwar S, Shabana, Tahir A, Liaqat Z, Naseer S, Seme RS, Mehmood S, Shahid SU, Hasnain S. Study of variants associated with ventricular septal defects (VSDs) highlights the unique genetic structure of the Pakistani population. Ital J Pediatr 2022; 48:124. [PMID: 35870951 PMCID: PMC9308904 DOI: 10.1186/s13052-022-01323-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Background Ventricular septal defects (VSDs) are one of the leading causes of death due to cardiac anomalies during the first months of life. The prevalence of VSD in neonates is reported up to 4%. Despite the remarkable progress in medication, treatment and surgical procedure for VSDs, the genetic etiology of VSDs is still in infancy because of the complex genetic and environmental interactions. Methods Three hundred fifty subjects (200 VSD children and 150 healthy controls) were recruited from different pediatric cardiac units. Pediatric clinical and demographic data were collected. A total of six variants, rs1017 (ISL1), rs7240256 (NFATc1), rs36208048 (VEGF), variant of HEY2, rs11067075 (TBX5) and rs1801133 (MTHFR) genes were genotyped by tetra-ARMS PCR and PCR–RFLP methods. Results The results showed that in cases, the rs1017 (g.16138A > T) variant in the ISL1 gene has an allele frequency of 0.42 and 0.58 respectively for the T and A alleles, and 0.75 and 0.25 respectively in the controls. The frequencies of the AA, TA and TT genotypes were, 52%, 11% and 37% in cases versus 21%, 8% and 71% respectively in the controls. For the NFATc1 variant rs7240256, minor allele frequency (MAF) was 0.43 in cases while 0.23 in controls. For the variant in the VEGF gene, genotype frequencies were 0% (A), 32% (CA) and 68% (CC) in cases and 0.0%, 33% and 67% respectively in controls. The allele frequency of C and A were 0.84 and 0.16 in cases and 0.83 and 0.17 respectively in controls. The TBX5 polymorphism rs11067075 (g.51682G > T) had an allelic frequency of 0.44 and 0.56 respectively for T and G alleles in cases, versus 0.26 and 0.74 in the controls. We did not detect the presence of the HEY2 gene variant (g.126117350A > C) in our pediatric cohort. For the rs1801133 (g.14783C > T) variant in the MTHFR gene, the genotype frequencies were 25% (CC), 62% (CT) and 13% (TT) in cases, versus 88%, 10% and 2% in controls. The ISL1, NFATc1, TBX5 and MTHFR variants were found to be in association with VSD in the Pakistani pediatric cohort whilst the VEGF and HEY2 variants were completely absent in our cohort. Conclusion We propose that a wider programme of genetic screening of the Pakistani population for genetic markers in heart development genes would be helpful in reducing the risk of VSDs.
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Okada D, Okamoto Y, Io T, Oka M, Kobayashi D, Ito S, Yamada R, Ishii K, Ono K. Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans. Biomolecules 2022; 12:biom12060859. [PMID: 35740984 PMCID: PMC9221511 DOI: 10.3390/biom12060859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. Here, we analyzed transcriptome data in mouse, rat, and human atria, ventricles, and sinoatrial nodes (SA) obtained from different platforms and compared them by calculating specificity measure (SPM) values in consideration of species differences. Among the three heart regions, the species differences in SA were the greatest, and we searched for genes that determined the essential characteristics of SA, which was SHOX2 in our criteria. The SPM value of SHOX2 was prominently high across species. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. This study identified the importance of SHOX2 as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies.
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Affiliation(s)
- Daigo Okada
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Shogoinkawahara-cho, Kyoto 606-8507, Japan; (D.O.); (R.Y.)
| | - Yosuke Okamoto
- Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan; (D.K.); (S.I.); (K.O.)
- Correspondence:
| | - Toshiro Io
- Research Department, Ono Pharmaceutical Co., Ltd., Kyutaromachi, Osaka 618-8585, Japan; (T.I.); (M.O.)
| | - Miho Oka
- Research Department, Ono Pharmaceutical Co., Ltd., Kyutaromachi, Osaka 618-8585, Japan; (T.I.); (M.O.)
| | - Daiki Kobayashi
- Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan; (D.K.); (S.I.); (K.O.)
| | - Suzuka Ito
- Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan; (D.K.); (S.I.); (K.O.)
| | - Ryo Yamada
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Shogoinkawahara-cho, Kyoto 606-8507, Japan; (D.O.); (R.Y.)
| | - Kuniaki Ishii
- Department of Pharmacology, Faculty of medicine, Yamagata University, Iida-Nishi, Yamagata 990-9585, Japan;
| | - Kyoichi Ono
- Department of Cell Physiology, Akita Graduate School of Medicine, Hondo, Akita 010-8543, Japan; (D.K.); (S.I.); (K.O.)
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Desmin deficiency affects the microenvironment of the cardiac side population and Sca1+ stem cell population of the adult heart and impairs their cardiomyogenic commitment. Cell Tissue Res 2022; 389:309-326. [DOI: 10.1007/s00441-022-03643-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/20/2022] [Indexed: 11/02/2022]
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Prummel KD, Crowell HL, Nieuwenhuize S, Brombacher EC, Daetwyler S, Soneson C, Kresoja-Rakic J, Kocere A, Ronner M, Ernst A, Labbaf Z, Clouthier DE, Firulli AB, Sánchez-Iranzo H, Naganathan SR, O'Rourke R, Raz E, Mercader N, Burger A, Felley-Bosco E, Huisken J, Robinson MD, Mosimann C. Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma. Nat Commun 2022; 13:1677. [PMID: 35354817 PMCID: PMC8967825 DOI: 10.1038/s41467-022-29311-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/04/2022] [Indexed: 01/27/2023] Open
Abstract
The mesothelium lines body cavities and surrounds internal organs, widely contributing to homeostasis and regeneration. Mesothelium disruptions cause visceral anomalies and mesothelioma tumors. Nonetheless, the embryonic emergence of mesothelia remains incompletely understood. Here, we track mesothelial origins in the lateral plate mesoderm (LPM) using zebrafish. Single-cell transcriptomics uncovers a post-gastrulation gene expression signature centered on hand2 in distinct LPM progenitor cells. We map mesothelial progenitors to lateral-most, hand2-expressing LPM and confirm conservation in mouse. Time-lapse imaging of zebrafish hand2 reporter embryos captures mesothelium formation including pericardium, visceral, and parietal peritoneum. We find primordial germ cells migrate with the forming mesothelium as ventral migration boundary. Functionally, hand2 loss disrupts mesothelium formation with reduced progenitor cells and perturbed migration. In mouse and human mesothelioma, we document expression of LPM-associated transcription factors including Hand2, suggesting re-initiation of a developmental program. Our data connects mesothelium development to Hand2, expanding our understanding of mesothelial pathologies.
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Affiliation(s)
- Karin D Prummel
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zürich, Switzerland
| | - Susan Nieuwenhuize
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Eline C Brombacher
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephan Daetwyler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, United States
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Charlotte Soneson
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zürich, Switzerland
| | - Jelena Kresoja-Rakic
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zurich, Zürich, Switzerland
| | - Agnese Kocere
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Manuel Ronner
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zurich, Zürich, Switzerland
| | | | - Zahra Labbaf
- Institute for Cell Biology, ZMBE, Muenster, Germany
| | - David E Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Anthony B Firulli
- Herman B Wells Center for Pediatric Research, Departments of Pediatrics, Anatomy and Medical and Molecular Genetics, Indiana Medical School, Indianapolis, IN, USA
| | - Héctor Sánchez-Iranzo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Madrid, Spain
- Institute of Biological and Chemical System - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Sundar R Naganathan
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Rebecca O'Rourke
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Erez Raz
- Institute for Cell Biology, ZMBE, Muenster, Germany
| | - Nadia Mercader
- Institute of Anatomy, University of Bern, Bern, Switzerland
- Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Madrid, Spain
| | - Alexa Burger
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, University Hospital Zurich, Zürich, Switzerland
| | - Jan Huisken
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Morgridge Institute for Research, Madison, WI, USA
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zürich, Switzerland
| | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA.
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Venegas-Zamora L, Bravo-Acuña F, Sigcho F, Gomez W, Bustamante-Salazar J, Pedrozo Z, Parra V. New Molecular and Organelle Alterations Linked to Down Syndrome Heart Disease. Front Genet 2022; 12:792231. [PMID: 35126461 PMCID: PMC8808411 DOI: 10.3389/fgene.2021.792231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
Down syndrome (DS) is a genetic disorder caused by a trisomy of the human chromosome 21 (Hsa21). Overexpression of Hsa21 genes that encode proteins and non-coding RNAs (ncRNAs) can disrupt several cellular functions and biological processes, especially in the heart. Congenital heart defects (CHDs) are present in 45–50% of individuals with DS. Here, we describe the genetic background of this condition (Hsa21 and non-Hsa21 genes), including the role of ncRNAs, and the relevance of these new players in the study of the pathophysiology of DS heart diseases. Additionally, we discuss several distinct pathways in cardiomyocytes which help maintain a functional heart, but that might trigger hypertrophy and oxidative stress when altered. Moreover, we highlight the importance of investigating how mitochondrial and lysosomal dysfunction could eventually contribute to understanding impaired heart function and development in subjects with the Hsa21 trisomy. Altogether, this review focuses on the newest insights about the gene expression, molecular pathways, and organelle alterations involved in the cardiac phenotype of DS.
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Affiliation(s)
- Leslye Venegas-Zamora
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco Bravo-Acuña
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco Sigcho
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Wileidy Gomez
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - José Bustamante-Salazar
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Zully Pedrozo
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Programa de Fisiología y Biofísica, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Red para El Estudio de Enfermedades Cardiopulmonares de Alta Letalidad (REECPAL), Universidad de Chile, Santiago, Chile
- *Correspondence: Zully Pedrozo, ; Valentina Parra,
| | - Valentina Parra
- Advanced Center of Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas y Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Red para El Estudio de Enfermedades Cardiopulmonares de Alta Letalidad (REECPAL), Universidad de Chile, Santiago, Chile
- *Correspondence: Zully Pedrozo, ; Valentina Parra,
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Luo H, Zhang Y, Deng Y, Li L, Sheng Z, Yu Y, Lin Y, Chen X, Feng P. Nxhl Controls Angiogenesis by Targeting VE-PTP Through Interaction With Nucleolin. Front Cell Dev Biol 2021; 9:728821. [PMID: 34733844 PMCID: PMC8558974 DOI: 10.3389/fcell.2021.728821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
Precise regulation of angiogenesis is required for organ development, wound repair, and tumor progression. Here, we identified a novel gene, nxhl (New XingHuo light), that is conserved in vertebrates and that plays a crucial role in vascular integrity and angiogenesis. Bioinformatic analysis uncovered its essential roles in development based on co-expression with several key developmental genes. Knockdown of nxhl in zebrafish causes global and pericardial edema, loss of blood circulation, and vascular defects characterized by both reduced vascularization in intersegmental vessels and decreased sprouting in the caudal vein plexus. The nxhl gene also affects human endothelial cell behavior in vitro. We found that nxhl functions in part by targeting VE-PTP through interaction with NCL (nucleolin). Loss of ptprb (a VE-PTP ortholo) in zebrafish resulted in defects similar to nxhl knockdown. Moreover, nxhl deficiency attenuates tumor invasion and proteins (including VE-PTP and NCL) associated with angiogenesis and EMT. These findings illustrate that nxhl can regulate angiogenesis via a novel nxhl-NCL-VE-PTP axis, providing a new therapeutic target for modulating vascular formation and function, especially for cancer treatment.
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Affiliation(s)
- Honglin Luo
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China.,Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Yongde Zhang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yanfei Deng
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lequn Li
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Zhaoan Sheng
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yanling Yu
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yong Lin
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiaohan Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Pengfei Feng
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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10
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Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Front Genet 2021; 12:642975. [PMID: 33777110 PMCID: PMC7987942 DOI: 10.3389/fgene.2021.642975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bound by lineage-determining transcription factors and signaling effectors, enhancers play essential roles in controlling spatiotemporal gene expression profiles during development, homeostasis and disease. Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target genes. Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has helped inform our understanding of cardiac development and disease.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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11
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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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12
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She P, Zhang H, Peng X, Sun J, Gao B, Zhou Y, Zhu X, Hu X, Lai KS, Wong J, Zhou B, Wang L, Zhong TP. The Gridlock transcriptional repressor impedes vertebrate heart regeneration by restricting expression of lysine methyltransferase. Development 2020; 147:147/18/dev190678. [PMID: 32988975 PMCID: PMC7541343 DOI: 10.1242/dev.190678] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/03/2020] [Indexed: 12/19/2022]
Abstract
Teleost zebrafish and neonatal mammalian hearts exhibit the remarkable capacity to regenerate through dedifferentiation and proliferation of pre-existing cardiomyocytes (CMs). Although many mitogenic signals that stimulate zebrafish heart regeneration have been identified, transcriptional programs that restrain injury-induced CM renewal are incompletely understood. Here, we report that mutations in gridlock (grl; also known as hey2), encoding a Hairy-related basic helix-loop-helix transcriptional repressor, enhance CM proliferation and reduce fibrosis following damage. In contrast, myocardial grl induction blunts CM dedifferentiation and regenerative responses to heart injury. RNA sequencing analyses uncover Smyd2 lysine methyltransferase (KMT) as a key transcriptional target repressed by Grl. Reduction in Grl protein levels triggered by injury induces smyd2 expression at the wound myocardium, enhancing CM proliferation. We show that Smyd2 functions as a methyltransferase and modulates the Stat3 methylation and phosphorylation activity. Inhibition of the KMT activity of Smyd2 reduces phosphorylated Stat3 at cardiac wounds, suppressing the elevated CM proliferation in injured grl mutant hearts. Our findings establish an injury-specific transcriptional repression program in governing CM renewal during heart regeneration, providing a potential strategy whereby silencing Grl repression at local regions might empower regeneration capacity to the injured mammalian heart. Highlighted Article: Novel mechanisms of the Grl-Smyd2 network govern vertebrate CM renewal and heart regeneration, which might be relevant in developing strategies for regeneration interventions in humans.
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Affiliation(s)
- Peilu She
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.,Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Huifang Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xiangwen Peng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Jianjian Sun
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Bangjun Gao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yating Zhou
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xuejiao Zhu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xueli Hu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Kaa Seng Lai
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Bin Zhou
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Linhui Wang
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, 200003, China
| | - Tao P Zhong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
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13
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Cunningham CM, Bellipanni G, Habas R, Balciunas D. Deletion of morpholino binding sites (DeMOBS) to assess specificity of morphant phenotypes. Sci Rep 2020; 10:15366. [PMID: 32958829 PMCID: PMC7506532 DOI: 10.1038/s41598-020-71708-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/13/2020] [Indexed: 01/05/2023] Open
Abstract
Two complimentary approaches are widely used to study gene function in zebrafish: induction of genetic mutations, usually using targeted nucleases such as CRISPR/Cas9, and suppression of gene expression, typically using Morpholino oligomers. Neither method is perfect. Morpholinos (MOs) sometimes produce off-target or toxicity-related effects that can be mistaken for true phenotypes. Conversely, genetic mutants can be subject to compensation, or may fail to yield a null phenotype due to leakiness (e.g. use of cryptic splice sites or downstream AUGs). When discrepancy between mutant and morpholino-induced (morphant) phenotypes is observed, experimental validation of such phenotypes becomes very labor intensive. We have developed a simple genetic method to differentiate between genuine morphant phenotypes and those produced due to off-target effects. We speculated that indels within 5' untranslated regions would be unlikely to have a significant negative effect on gene expression. Mutations induced within a MO target site would result in a Morpholino-refractive allele thus suppressing true MO phenotypes whilst non-specific phenotypes would remain. We tested this hypothesis on one gene with an exclusively zygotic function, tbx5a, and one gene with strong maternal effect, ctnnb2. We found that indels within the Morpholino binding site are indeed able to suppress both zygotic and maternal morphant phenotypes. We also observed that the ability of such indels to suppress morpholino phenotypes does depend on the size and the location of the deletion. Nonetheless, mutating the morpholino binding sites in both maternal and zygotic genes can ascertain the specificity of morphant phenotypes.
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Affiliation(s)
| | - Gianfranco Bellipanni
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Raymond Habas
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Darius Balciunas
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA.
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14
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van Walree ES, Dombrowsky G, Jansen IE, Mirkov MU, Zwart R, Ilgun A, Guo D, Clur SAB, Amin AS, Savage JE, van der Wal AC, Waisfisz Q, Maugeri A, Wilsdon A, Bu'Lock FA, Hurles ME, Dittrich S, Berger F, Audain Martinez E, Christoffels VM, Hitz MP, Milewicz DM, Posthuma D, Meijers-Heijboer H, Postma AV, Mathijssen IB. Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms. Genet Med 2020; 23:103-110. [PMID: 32820247 PMCID: PMC8804301 DOI: 10.1038/s41436-020-00939-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
Purpose In this study we aimed to establish the genetic cause of a myriad of cardiovascular defects prevalent in individuals from a genetically isolated population, who were found to share a common ancestor in 1728. Methods Trio genome sequencing was carried out in an index patient with critical congenital heart disease (CHD), family members had either exome or Sanger sequencing. To confirm enrichment, we performed a gene-based association test and meta-analysis in two independent validation cohorts: one with 2685 CHD cases versus 4370 controls, and the other 326 cases with familial thoracic aortic aneurysms (FTAA) and dissections versus 570 ancestry-matched controls. Functional consequences of identified variants were evaluated using expression studies. Results We identified a loss-of-function variant in the Notch target transcription factor-encoding gene HEY2. The homozygous state (n=3) causes life-threatening congenital heart defects, while 80% of heterozygous carriers (n=20) had cardiovascular defects, mainly CHD and FTAA of the ascending aorta. We confirm enrichment of rare risk variants in HEY2 functional domains after meta-analysis (meta-SKAT p=0.018). Furthermore, we show that several identified variants lead to dysregulation of repression by HEY2. Conclusion A homozygous germline loss-of-function variant in HEY2 leads to critical CHD. The majority of heterozygotes show a myriad of cardiovascular defects.
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Affiliation(s)
- Eva S van Walree
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands. .,Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands.
| | - Gregor Dombrowsky
- Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel, Kiel, Germany
| | - Iris E Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Maša Umićević Mirkov
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - Rob Zwart
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Aho Ilgun
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Dongchuan Guo
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sally-Ann B Clur
- Department of Pediatric Cardiology, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ahmed S Amin
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - Allard C van der Wal
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Medisch Centrum, Amsterdam, The Netherlands
| | - Alessandra Maugeri
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Medisch Centrum, Amsterdam, The Netherlands
| | - Anna Wilsdon
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Frances A Bu'Lock
- East Midlands Congenital Heart Centre and University of Leicester, Glenfield Hospital, Leicester, United Kingdom
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sven Dittrich
- Department of Pediatric Cardiology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Felix Berger
- German Heart Center Berlin, Department of Congenital Heart Disease, Pediatric Cardiology, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Enrique Audain Martinez
- Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel, Kiel, Germany
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc-Philip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, Universitätsklinikum Schleswig-Holstein Kiel, Kiel, Germany
| | - Dianna M Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Daniëlle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Medisch Centrum, Amsterdam, The Netherlands
| | - Alex V Postma
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Inge B Mathijssen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
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15
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Holowiecki A, Linstrum K, Ravisankar P, Chetal K, Salomonis N, Waxman JS. Pbx4 limits heart size and fosters arch artery formation by partitioning second heart field progenitors and restricting proliferation. Development 2020; 147:dev185652. [PMID: 32094112 PMCID: PMC7063670 DOI: 10.1242/dev.185652] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
Vertebrate heart development requires the integration of temporally distinct differentiating progenitors. However, few signals are understood that restrict the size of the later-differentiating outflow tract (OFT). We show that improper specification and proliferation of second heart field (SHF) progenitors in zebrafish lazarus (lzr) mutants, which lack the transcription factor Pbx4, produces enlarged hearts owing to an increase in ventricular and smooth muscle cells. Specifically, Pbx4 initially promotes the partitioning of the SHF into anterior progenitors, which contribute to the OFT, and adjacent endothelial cell progenitors, which contribute to posterior pharyngeal arches. Subsequently, Pbx4 limits SHF progenitor (SHFP) proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed previously unappreciated distinct differentiation states and progenitor subpopulations that normally reside within the SHF and arterial pole of the heart. Specifically, the transcriptional profiles of Pbx4-deficient nkx2.5+ SHFPs are less distinct and display characteristics of normally discrete proliferative progenitor and anterior, differentiated cardiomyocyte populations. Therefore, our data indicate that the generation of proper OFT size and arch arteries requires Pbx-dependent stratification of unique differentiation states to facilitate both homeotic-like transformations and limit progenitor production within the SHF.
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Affiliation(s)
- Andrew Holowiecki
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Kelsey Linstrum
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Molecular Genetics Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Padmapriyadarshini Ravisankar
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Kashish Chetal
- Bioinformatics Division, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Bioinformatics Division, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joshua S Waxman
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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16
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Lee SH, Hadipour-Lakmehsari S, Murthy HR, Gibb N, Miyake T, Teng ACT, Cosme J, Yu JC, Moon M, Lim S, Wong V, Liu P, Billia F, Fernandez-Gonzalez R, Stagljar I, Sharma P, Kislinger T, Scott IC, Gramolini AO. REEP5 depletion causes sarco-endoplasmic reticulum vacuolization and cardiac functional defects. Nat Commun 2020; 11:965. [PMID: 32075961 PMCID: PMC7031342 DOI: 10.1038/s41467-019-14143-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
The sarco-endoplasmic reticulum (SR/ER) plays an important role in the development and progression of many heart diseases. However, many aspects of its structural organization remain largely unknown, particularly in cells with a highly differentiated SR/ER network. Here, we report a cardiac enriched, SR/ER membrane protein, REEP5 that is centrally involved in regulating SR/ER organization and cellular stress responses in cardiac myocytes. In vitro REEP5 depletion in mouse cardiac myocytes results in SR/ER membrane destabilization and luminal vacuolization along with decreased myocyte contractility and disrupted Ca2+ cycling. Further, in vivo CRISPR/Cas9-mediated REEP5 loss-of-function zebrafish mutants show sensitized cardiac dysfunction upon short-term verapamil treatment. Additionally, in vivo adeno-associated viral (AAV9)-induced REEP5 depletion in the mouse demonstrates cardiac dysfunction. These results demonstrate the critical role of REEP5 in SR/ER organization and function as well as normal heart function and development.
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Affiliation(s)
- Shin-Haw Lee
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON, M5G1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
| | - Sina Hadipour-Lakmehsari
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON, M5G1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
| | - Harsha R Murthy
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G1X8, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
| | - Natalie Gibb
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G1X8, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
| | - Tetsuaki Miyake
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
- Department of Biology, Faculty of Science, York University, Toronto, ON, M3J1P3, Canada
| | - Allen C T Teng
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON, M5G1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
| | - Jake Cosme
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON, M5G1M1, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
| | - Jessica C Yu
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON, M5G1M1, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S3G9, Canada
| | - Mark Moon
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
- Ottawa Heart Institute, Ottawa, ON, K1Y4W7, Canada
| | - SangHyun Lim
- Donnelly Centre, University of Toronto, Toronto, ON, M5S1M8, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto Canada, Toronto, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, ON, M5S1M8, Canada
| | - Peter Liu
- Ottawa Heart Institute, Ottawa, ON, K1Y4W7, Canada
| | - Filio Billia
- Toronto General Research Institute, University Health Network, Toronto, ON, M5G2C4, Canada
| | - Rodrigo Fernandez-Gonzalez
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON, M5G1M1, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S3G9, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, M5S1M8, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto Canada, Toronto, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Canada
- Mediterranean Institute for Life Sciences, Split, Croatia
| | - Parveen Sharma
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
- Institute of Translational Medicine, University of Liverpool, Liverpool, L693BX, UK
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, Toronto, ON, M5G1L7, Canada
| | - Ian C Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G1X8, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada
| | - Anthony O Gramolini
- Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research, Toronto, ON, M5G1M1, Canada.
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1M8, Canada.
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17
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Li J, Li HY, Gu SY, Zi HX, Jiang L, Du JL. One-step generation of zebrafish carrying a conditional knockout-knockin visible switch via CRISPR/Cas9-mediated intron targeting. SCIENCE CHINA. LIFE SCIENCES 2020; 63:59-67. [PMID: 31872378 DOI: 10.1007/s11427-019-1607-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 12/16/2019] [Indexed: 01/05/2023]
Abstract
The zebrafish has become a popular vertebrate animal model in biomedical research. However, it is still challenging to make conditional gene knockout (CKO) models in zebrafish due to the low efficiency of homologous recombination (HR). Here we report an efficient non-HR-based method for generating zebrafish carrying a CKO and knockin (KI) switch (zCKOIS) coupled with dual-color fluorescent reporters. Using this strategy, we generated hey2zKOIS which served as a hey2 KI reporter with EGFP expression. Upon Cre induction in targeted cells, the hey2zCKOIS was switched to a non-functional CKO allele hey2zCKOIS-invassociated with TagRFP expression, enabling visualization of the CKO alleles. Thus, simplification of the design, and the visibility and combination of both CKO and KI alleles make our zCKOIS strategy an applicable CKO approach for zebrafish.
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Affiliation(s)
- Jia Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Hong-Yu Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan-Ye Gu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Hua-Xing Zi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Jiu-Lin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 200031, China.
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18
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Yuan X, Song M, Devine P, Bruneau BG, Scott IC, Wilson MD. Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development. Nat Commun 2018; 9:4977. [PMID: 30478328 PMCID: PMC6255839 DOI: 10.1038/s41467-018-07451-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
During the phylotypic period, embryos from different genera show similar gene expression patterns, implying common regulatory mechanisms. Here we set out to identify enhancers involved in the initial events of cardiogenesis, which occurs during the phylotypic period. We isolate early cardiac progenitor cells from zebrafish embryos and characterize 3838 open chromatin regions specific to this cell population. Of these regions, 162 overlap with conserved non-coding elements (CNEs) that also map to open chromatin regions in human. Most of the zebrafish conserved open chromatin elements tested drive gene expression in the developing heart. Despite modest sequence identity, human orthologous open chromatin regions recapitulate the spatial temporal expression patterns of the zebrafish sequence, potentially providing a basis for phylotypic gene expression patterns. Genome-wide, we discover 5598 zebrafish-human conserved open chromatin regions, suggesting that a diverse repertoire of ancient enhancers is established prior to organogenesis and the phylotypic period. During early embryogenesis, critical cardiac specification events occur. Here the authors isolate cardiac progenitor cells from early zebrafish embryos and characterize accessible chromatin regions specific to this cell population, finding that many of these regions overlap with conserved non-coding elements that are ortholgous to accessible chromatin regions in human.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mengyi Song
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Patrick Devine
- Gladstone Institutes, San Francisco, CA, 94158, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA, 94143-0511, USA
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, 94158, USA.,Department of Pediatrics and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ian C Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Michael D Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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