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Chang Z, Xu Y, Dong X, Gao Y, Wang C. Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro. Bioinformatics 2024; 40:btae466. [PMID: 39024032 PMCID: PMC11288411 DOI: 10.1093/bioinformatics/btae466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/05/2024] [Accepted: 07/17/2024] [Indexed: 07/20/2024] Open
Abstract
MOTIVATION The burgeoning generation of single-cell or spatial multiomic data allows for the characterization of gene regulation networks (GRNs) at an unprecedented resolution. However, the accurate reconstruction of GRNs from sparse and noisy single-cell or spatial multiomic data remains challenging. RESULTS Here, we present SCRIPro, a comprehensive computational framework that robustly infers GRNs for both single-cell and spatial multi-omics data. SCRIPro first improves sample coverage through a density clustering approach based on multiomic and spatial similarities. Additionally, SCRIPro scans transcriptional regulator (TR) importance by performing chromatin reconstruction and in silico deletion analyses using a comprehensive reference covering 1,292 human and 994 mouse TRs. Finally, SCRIPro combines TR-target importance scores derived from multiomic data with TR-target expression levels to ensure precise GRN reconstruction. We benchmarked SCRIPro on various datasets, including single-cell multiomic data from human B-cell lymphoma, mouse hair follicle development, Stereo-seq of mouse embryos, and Spatial-ATAC-RNA from mouse brain. SCRIPro outperforms existing motif-based methods and accurately reconstructs cell type-specific, stage-specific, and region-specific GRNs. Overall, SCRIPro emerges as a streamlined and fast method capable of reconstructing TR activities and GRNs for both single-cell and spatial multi-omic data. AVAILABILITY SCRIPro is available at https://github.com/wanglabtongji/SCRIPro. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhanhe Chang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunfan Xu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Yawei Gao
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
- National Key Laboratory of Autonomous Intelligent Unmanned Systems, Tongji University, Shanghai 200120, China
- Frontier Science Center for Intelligent Autonomous Systems, Tongji University, Shanghai 200120, China
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Piñeiro-Sabarís R, MacGrogan D, de la Pompa JL. Intricate MIB1-NOTCH-GATA6 Interactions in Cardiac Valvular and Septal Development. J Cardiovasc Dev Dis 2024; 11:223. [PMID: 39057643 PMCID: PMC11277162 DOI: 10.3390/jcdd11070223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/02/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Genome-wide association studies and experimental mouse models implicate the MIB1 and GATA6 genes in congenital heart disease (CHD). Their close physical proximity and conserved synteny suggest that these two genes might be involved in analogous cardiac developmental processes. Heterozygous Gata6 loss-of-function mutations alone or humanized Mib1 mutations in a NOTCH1-sensitized genetic background cause bicuspid aortic valve (BAV) and a membranous ventricular septal defect (VSD), consistent with MIB1 and NOTCH1 functioning in the same pathway. To determine if MIB1-NOTCH and GATA6 interact in valvular and septal development, we generated compound heterozygote mice carrying different Mib1 missense (Mib1K735R and Mib1V943F) or nonsense (Mib1R530X) mutations with the Gata6STOP/+ heterozygous null mutation. Combining Mib1R530X/+ or Mib1K735R/+ with Gata6STOP/+ does not affect Gata6STOP/+ single mutant phenotypes. In contrast, combining Mib1V943F/+ with Gata6STOP/+ decreases the incidence of BAV and VSD by 50%, suggesting a suppressive effect of Mib1V943F/+ on Gata6STOP/+. Transcriptomic and functional analyses revealed that while the EMT pathway term is depleted in the Gata6STOP/+ mutant, introducing the Mib1V943F variant robustly enriches this term, consistent with the Mib1V943F/+ phenotypic suppression of Gata6STOP/+. Interestingly, combined Notch1 and Gata6 insufficiency led to a nearly fully penetrant VSD but did not affect the BAV phenotype, underscoring the complex functional relationship between MIB1, NOTCH, and GATA6 in valvular and septal development.
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Affiliation(s)
- Rebeca Piñeiro-Sabarís
- Intercellular Signaling in Cardiovascular Development & Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain;
- Ciber de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Donal MacGrogan
- Intercellular Signaling in Cardiovascular Development & Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain;
- Ciber de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - José Luis de la Pompa
- Intercellular Signaling in Cardiovascular Development & Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain;
- Ciber de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Melchor Fernández Almagro 3, 28029 Madrid, Spain
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Udugampolage NS, Frolova S, Taurino J, Pini A, Martelli F, Voellenkle C. Coding and Non-Coding Transcriptomic Landscape of Aortic Complications in Marfan Syndrome. Int J Mol Sci 2024; 25:7367. [PMID: 39000474 PMCID: PMC11242319 DOI: 10.3390/ijms25137367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Marfan syndrome (MFS) is a rare congenital disorder of the connective tissue, leading to thoracic aortic aneurysms (TAA) and dissection, among other complications. Currently, the most efficient strategy to prevent life-threatening dissection is preventive surgery. Periodic imaging applying complex techniques is required to monitor TAA progression and to guide the timing of surgical intervention. Thus, there is an acute demand for non-invasive biomarkers for diagnosis and prognosis, as well as for innovative therapeutic targets of MFS. Unraveling the intricate pathomolecular mechanisms underlying the syndrome is vital to address these needs. High-throughput platforms are particularly well-suited for this purpose, as they enable the integration of different datasets, such as transcriptomic and epigenetic profiles. In this narrative review, we summarize relevant studies investigating changes in both the coding and non-coding transcriptome and epigenome in MFS-induced TAA. The collective findings highlight the implicated pathways, such as TGF-β signaling, extracellular matrix structure, inflammation, and mitochondrial dysfunction. Potential candidates as biomarkers, such as miR-200c, as well as therapeutic targets emerged, like Tfam, associated with mitochondrial respiration, or miR-632, stimulating endothelial-to-mesenchymal transition. While these discoveries are promising, rigorous and extensive validation in large patient cohorts is indispensable to confirm their clinical relevance and therapeutic potential.
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Affiliation(s)
| | - Svetlana Frolova
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, 20097 Milan, Italy; (S.F.); (C.V.)
- Department of Biosciences, University of Milan, 20122 Milan, Italy
| | - Jacopo Taurino
- Cardiovascular-Genetic Center, IRCCS Policlinico San Donato, 20097 Milan, Italy; (N.S.U.); (J.T.); (A.P.)
| | - Alessandro Pini
- Cardiovascular-Genetic Center, IRCCS Policlinico San Donato, 20097 Milan, Italy; (N.S.U.); (J.T.); (A.P.)
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, 20097 Milan, Italy; (S.F.); (C.V.)
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, 20097 Milan, Italy; (S.F.); (C.V.)
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Neagu AN, Whitham D, Bruno P, Arshad A, Seymour L, Morrissiey H, Hukovic AI, Darie CC. Onco-Breastomics: An Eco-Evo-Devo Holistic Approach. Int J Mol Sci 2024; 25:1628. [PMID: 38338903 PMCID: PMC10855488 DOI: 10.3390/ijms25031628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Known as a diverse collection of neoplastic diseases, breast cancer (BC) can be hyperbolically characterized as a dynamic pseudo-organ, a living organism able to build a complex, open, hierarchically organized, self-sustainable, and self-renewable tumor system, a population, a species, a local community, a biocenosis, or an evolving dynamical ecosystem (i.e., immune or metabolic ecosystem) that emphasizes both developmental continuity and spatio-temporal change. Moreover, a cancer cell community, also known as an oncobiota, has been described as non-sexually reproducing species, as well as a migratory or invasive species that expresses intelligent behavior, or an endangered or parasite species that fights to survive, to optimize its features inside the host's ecosystem, or that is able to exploit or to disrupt its host circadian cycle for improving the own proliferation and spreading. BC tumorigenesis has also been compared with the early embryo and placenta development that may suggest new strategies for research and therapy. Furthermore, BC has also been characterized as an environmental disease or as an ecological disorder. Many mechanisms of cancer progression have been explained by principles of ecology, developmental biology, and evolutionary paradigms. Many authors have discussed ecological, developmental, and evolutionary strategies for more successful anti-cancer therapies, or for understanding the ecological, developmental, and evolutionary bases of BC exploitable vulnerabilities. Herein, we used the integrated framework of three well known ecological theories: the Bronfenbrenner's theory of human development, the Vannote's River Continuum Concept (RCC), and the Ecological Evolutionary Developmental Biology (Eco-Evo-Devo) theory, to explain and understand several eco-evo-devo-based principles that govern BC progression. Multi-omics fields, taken together as onco-breastomics, offer better opportunities to integrate, analyze, and interpret large amounts of complex heterogeneous data, such as various and big-omics data obtained by multiple investigative modalities, for understanding the eco-evo-devo-based principles that drive BC progression and treatment. These integrative eco-evo-devo theories can help clinicians better diagnose and treat BC, for example, by using non-invasive biomarkers in liquid-biopsies that have emerged from integrated omics-based data that accurately reflect the biomolecular landscape of the primary tumor in order to avoid mutilating preventive surgery, like bilateral mastectomy. From the perspective of preventive, personalized, and participatory medicine, these hypotheses may help patients to think about this disease as a process governed by natural rules, to understand the possible causes of the disease, and to gain control on their own health.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iași, Carol I bvd. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Aneeta Arshad
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Logan Seymour
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Angiolina I. Hukovic
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
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Yasuhara J, Manivannan SN, Majumdar U, Gordon DM, Lawrence PJ, Aljuhani M, Myers K, Stiver C, Bigelow AM, Galantowicz M, Yamagishi H, McBride KL, White P, Garg V. Novel pathogenic GATA6 variant associated with congenital heart disease, diabetes mellitus and necrotizing enterocolitis. Pediatr Res 2024; 95:146-155. [PMID: 37700164 DOI: 10.1038/s41390-023-02811-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/11/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND Pathogenic GATA6 variants have been associated with congenital heart disease (CHD) and a spectrum of extracardiac abnormalities, including pancreatic agenesis, congenital diaphragmatic hernia, and developmental delay. However, the comprehensive genotype-phenotype correlation of pathogenic GATA6 variation in humans remains to be fully understood. METHODS Exome sequencing was performed in a family where four members had CHD. In vitro functional analysis of the GATA6 variant was performed using immunofluorescence, western blot, and dual-luciferase reporter assay. RESULTS A novel, heterozygous missense variant in GATA6 (c.1403 G > A; p.Cys468Tyr) segregated with affected members in a family with CHD, including three with persistent truncus arteriosus. In addition, one member had childhood onset diabetes mellitus (DM), and another had necrotizing enterocolitis (NEC) with intestinal perforation. The p.Cys468Tyr variant was located in the c-terminal zinc finger domain encoded by exon 4. The mutant protein demonstrated an abnormal nuclear localization pattern with protein aggregation and decreased transcriptional activity. CONCLUSIONS We report a novel, familial GATA6 likely pathogenic variant associated with CHD, DM, and NEC with intestinal perforation. These findings expand the phenotypic spectrum of pathologic GATA6 variation to include intestinal abnormalities. IMPACT Exome sequencing identified a novel heterozygous GATA6 variant (p.Cys468Tyr) that segregated in a family with CHD including persistent truncus arteriosus, atrial septal defects and bicuspid aortic valve. Additionally, affected members displayed extracardiac findings including childhood-onset diabetes mellitus, and uniquely, necrotizing enterocolitis with intestinal perforation in the first four days of life. In vitro functional assays demonstrated that GATA6 p.Cys468Tyr variant leads to cellular localization defects and decreased transactivation activity. This work supports the importance of GATA6 as a causative gene for CHD and expands the phenotypic spectrum of pathogenic GATA6 variation, highlighting neonatal intestinal perforation as a novel extracardiac phenotype.
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Affiliation(s)
- Jun Yasuhara
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sathiya N Manivannan
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
| | - Uddalak Majumdar
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
| | - David M Gordon
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Patrick J Lawrence
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Mona Aljuhani
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
| | - Katherine Myers
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
| | - Corey Stiver
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Amee M Bigelow
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Mark Galantowicz
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
| | - Hiroyuki Yamagishi
- Division of Pediatric Cardiology, Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kim L McBride
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Peter White
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Vidu Garg
- Center for Cardiovascular Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA.
- The Heart Center, Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
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Gill E, Bamforth SD. Molecular Pathways and Animal Models of Truncus Arteriosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:853-865. [PMID: 38884754 DOI: 10.1007/978-3-031-44087-8_52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
In normal cardiovascular development in birds and mammals, the outflow tract of the heart is divided into two distinct channels to separate the oxygenated systemic blood flow from the deoxygenated pulmonary circulation. When the process of outflow tract septation fails, a single common outflow vessel persists resulting in a serious clinical condition known as persistent truncus arteriosus or common arterial trunk. In this chapter, we will review molecular pathways and the cells that are known to play a role in the formation and development of the outflow tract and how genetic manipulation of these pathways in animal models can result in common arterial trunk.
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Affiliation(s)
- Eleanor Gill
- Newcastle University Biosciences Institute, Newcastle, UK
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7
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Yamagishi H. Human Genetics of Truncus Arteriosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:841-852. [PMID: 38884753 DOI: 10.1007/978-3-031-44087-8_51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Integrated human genetics and molecular/developmental biology studies have revealed that truncus arteriosus is highly associated with 22q11.2 deletion syndrome. Other congenital malformation syndromes and variants in genes encoding TBX, GATA, and NKX transcription factors and some signaling proteins have also been reported as its etiology.
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Affiliation(s)
- Hiroyuki Yamagishi
- Division of Pediatric Cardiology, Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan.
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Bao C, Tourdot RW, Brunette GJ, Stewart C, Sun L, Baba H, Watanabe M, Agoston AT, Jajoo K, Davison JM, Nason KS, Getz G, Wang KK, Imamura Y, Odze R, Bass AJ, Stachler MD, Zhang CZ. Genomic signatures of past and present chromosomal instability in Barrett's esophagus and early esophageal adenocarcinoma. Nat Commun 2023; 14:6203. [PMID: 37794034 PMCID: PMC10550953 DOI: 10.1038/s41467-023-41805-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.
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Affiliation(s)
- Chunyang Bao
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Richard W Tourdot
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Gregory J Brunette
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Chip Stewart
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Lili Sun
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 2 Chome-40-1 Kurokami, Chuo Ward, Kumamoto, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Agoston T Agoston
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kunal Jajoo
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Jon M Davison
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Katie S Nason
- Department of Surgery, Baystate Medical Center, University of Massachusetts Medical School, 759 Chestnut St, Springfield, MA, 01107, USA
| | - Gad Getz
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Robert Odze
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Department of Pathology and Lab Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | - Matthew D Stachler
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Department of Pathology, University of California, San Francisco. 513 Parnassus Ave, San Francisco, CA, 94143, USA.
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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Hedaya OM, Venkata Subbaiah KC, Jiang F, Xie LH, Wu J, Khor ES, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. Nat Commun 2023; 14:6166. [PMID: 37789015 PMCID: PMC10547706 DOI: 10.1038/s41467-023-41799-1] [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: 10/17/2022] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we data-mined human and mouse heart ribosome profiling analyses and identified a double-stranded RNA (dsRNA) structure within the GATA4 uORF that cooperates with the start codon to augment uORF translation and inhibits mORF translation. A trans-acting RNA helicase DDX3X inhibits the GATA4 uORF-dsRNA activity and modulates the translational balance of uORF and mORF. Antisense oligonucleotides (ASOs) that disrupt this dsRNA structure promote mORF translation, while ASOs that base-pair immediately downstream (i.e., forming a bimolecular double-stranded region) of either the uORF or mORF start codon enhance uORF or mORF translation, respectively. Human cardiomyocytes and mice treated with a uORF-enhancing ASO showed reduced cardiac GATA4 protein levels and increased resistance to cardiomyocyte hypertrophy. We further show the broad utility of uORF-dsRNA- or mORF-targeting ASO to regulate mORF translation for other mRNAs. This work demonstrates that the uORF-dsRNA element regulates the translation of multiple mRNAs as a generalizable translational control mechanism. Moreover, we develop a valuable strategy to alter protein expression and cellular phenotypes by targeting or generating dsRNA downstream of a uORF or mORF start codon.
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Affiliation(s)
- Omar M Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Kadiam C Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Li Huitong Xie
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Eng-Soon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Chris Proschel
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, 14642, USA.
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10
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Mahadevan A, Tipler A, Jones H. Shared developmental pathways of the placenta and fetal heart. Placenta 2023; 141:35-42. [PMID: 36604258 DOI: 10.1016/j.placenta.2022.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
Congenital heart defects (CHD) remain the most common class of birth defect worldwide, affecting 1 in every 110 live births. A host of clinical and morphological indicators of placental dysfunction are observed in pregnancies complicated by fetal CHD and, with the recent emergence of single-cell sequencing capabilities, the molecular and physiological associations between the embryonic heart and developing placenta are increasingly evident. In CHD pregnancies, a hostile intrauterine environment may negatively influence and alter fetal development. Placental maldevelopment and dysfunction creates this hostile in-utero environment and may manifest in the development of various subtypes of CHD, with downstream perfusion and flow-related alterations leading to yet further disruption in placental structure and function. The adverse in-utero environment of CHD-complicated pregnancies is well studied, however the specific etiological role that the placenta plays in CHD development remains unclear. Many mouse and rat models have been used to characterize the relationship between CHD and placental dysfunction, but these paradigms present substantial limitations in the assessment of both the heart and placenta. Improvements in non-invasive placental assessment can mitigate these limitations and drive human-specific investigation in relation to fetal and placental development. Here, we review the clinical, structural, and molecular relationships between CHD and placental dysfunction, the CHD subtype-dependence of these changes, and the future of Placenta-Heart axis modeling and investigation.
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Affiliation(s)
- Aditya Mahadevan
- Physiology and Aging, University of Florida College of Medicine, USA; Center for Research in Perinatal Outcomes, University of Florida, USA
| | - Alyssa Tipler
- Physiology and Aging, University of Florida College of Medicine, USA; Center for Research in Perinatal Outcomes, University of Florida, USA
| | - Helen Jones
- Physiology and Aging, University of Florida College of Medicine, USA; Center for Research in Perinatal Outcomes, University of Florida, USA.
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11
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Zhu X, Hao J, Zhang H, Chi M, Wang Y, Huang J, Xu R, Xincai Z, Xin B, Sun X, Zhang J, Zhou S, Cheng D, Yuan T, Ding J, Zheng S, Guo C, Yang Q. Oncometabolite D-2-hydroxyglutarate-dependent metabolic reprogramming induces skeletal muscle atrophy during cancer cachexia. Commun Biol 2023; 6:977. [PMID: 37741882 PMCID: PMC10518016 DOI: 10.1038/s42003-023-05366-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023] Open
Abstract
Cancer cachexia is characterized by weight loss and skeletal muscle wasting. Based on the up-regulation of catabolism and down-regulation of anabolism, here we showed genetic mutation-mediated metabolic reprogramming in the progression of cancer cachexia by screening for metabolites and investigating their direct effect on muscle atrophy. Treatment with 93 μM D-2-hydroxyglutarate (D2HG) resulted in reduced myotube width and increased expression of E3 ubiquitin ligases. Isocitrate Dehydrogenase 1 (IDH1) mutant patients had higher D2HG than non-mutant patients. In the in vivo murine cancer cachexia model, mutant IDH1 in CT26 cancer cells accelerated cachexia progression and worsened overall survival. Transcriptomics and metabolomics revealed a distinct D2HG-induced metabolic imbalance. Treatment with the IDH1 inhibitor ivosidenib delayed the progression of cancer cachexia in murine GL261 glioma model and CT26 colorectal carcinoma models. These data demonstrate the contribution of IDH1 mutation mediated D2HG accumulation to the progression of cancer cachexia and highlight the individualized treatment of IDH1 mutation associated cancer cachexia.
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Affiliation(s)
- Xinting Zhu
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Juan Hao
- Department of Endocrinology, Shanghai Traditional Chinese Medicine, Integrated Hospital, Shanghai University of Traditional Chinese Medicine, 230 Baoding Road, Shanghai, 200082, China
| | - Hong Zhang
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Mengyi Chi
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Yaxian Wang
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Jinlu Huang
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Rong Xu
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Zhao Xincai
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Bo Xin
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Xipeng Sun
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Jianping Zhang
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Shumin Zhou
- Institution of microsurgery on extremities, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Dongdong Cheng
- Department of Bone Oncology, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of MedicineShanghai Shanghai, Shanghai, P. R. China
| | - Ting Yuan
- Department of Bone Oncology, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of MedicineShanghai Shanghai, Shanghai, P. R. China
| | - Jun Ding
- Department of Neurosurgery, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Shuier Zheng
- Department of Oncology, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China
| | - Cheng Guo
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China.
| | - Quanjun Yang
- Department of Pharmacy, Shanghai Sixth People's Hospital affiliated Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Shanghai, 200233, China.
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12
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Chen Y, Wu Y, Li J, Chen K, Wang W, Ye Z, Feng K, Yang Y, Xu Y, Kang J, Guo X. Cooperative regulation of Zhx1 and hnRNPA1 drives the cardiac progenitor-specific transcriptional activation during cardiomyocyte differentiation. Cell Death Discov 2023; 9:244. [PMID: 37452012 PMCID: PMC10349095 DOI: 10.1038/s41420-023-01548-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The zinc finger proteins (ZNFs) mediated transcriptional regulation is critical for cell fate transition. However, it is still unclear how the ZNFs realize their specific regulatory roles in the stage-specific determination of cardiomyocyte differentiation. Here, we reported that the zinc fingers and homeoboxes 1 (Zhx1) protein, transiently expressed during the cell fate transition from mesoderm to cardiac progenitors, was indispensable for the proper cardiomyocyte differentiation of mouse and human embryonic stem cells. Moreover, Zhx1 majorly promoted the specification of cardiac progenitors via interacting with hnRNPA1 and co-activated the transcription of a wide range of genes. In-depth mechanistic studies showed that Zhx1 was bound with hnRNPA1 by the amino acid residues (Thr111-His120) of the second Znf domain, thus participating in the formation of cardiac progenitors. Together, our study highlights the unrevealed interaction of Zhx1/hnRNPA1 for activating gene transcription during cardiac progenitor specification and also provides new evidence for the specificity of cell fate determination in cardiomyocyte differentiation.
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Affiliation(s)
- Yang Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jianguo Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Kai Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Wuchan Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Zihui Ye
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Ke Feng
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yiwei Yang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yanxin Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Institute for Advanced Study, Tongji University, Shanghai, 200092, China.
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13
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Hedaya OM, Subbaiah KCV, Jiang F, Xie LH, Wu J, Khor E, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545153. [PMID: 37397986 PMCID: PMC10312771 DOI: 10.1101/2023.06.15.545153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we identified a double-stranded RNA (dsRNA) structure residing within the GATA4 uORF that augments uORF translation and inhibits mORF translation. Antisense oligonucleotides (ASOs) that disrupt this dsRNA structure promote mORF translation, while ASOs that base-pair immediately downstream (i.e., forming a bimolecular double-stranded region) of either the uORF or mORF start codon enhance uORF or mORF translation, respectively. Human cardiomyocytes and mice treated with a uORF-enhancing ASO showed reduced cardiac GATA4 protein levels and increased resistance to cardiomyocyte hypertrophy. We further show the general utility of uORF-dsRNA- or mORF- targeting ASO to regulate mORF translation for other mRNAs. Our work demonstrates a regulatory paradigm that controls translational efficiency and a useful strategy to alter protein expression and cellular phenotypes by targeting or generating dsRNA downstream of a uORF or mORF start codon. Bullet points for discoveries dsRNA within GATA4 uORF activates uORF translation and inhibits mORF translation. ASOs that target the dsRNA can either inhibit or enhance GATA4 mORF translation. ASOs can be used to impede hypertrophy in human cardiomyocytes and mouse hearts.uORF- and mORF-targeting ASOs can be used to control translation of multiple mRNAs.
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Affiliation(s)
- Omar M. Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Kadiam C. Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Li Huitong Xie
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - EngSoon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - David H. Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Chris Proschel
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
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14
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Li C, Dong X, Lin Y, Sun X, Cai L, Yang X, Cui Y, Qin L, Wang J. Establishing a human embryonic stem cell line (SKLRMe005-A) from a blastocyst with congenital heart disease (CHD). Stem Cell Res 2023; 68:103049. [PMID: 36805323 DOI: 10.1016/j.scr.2023.103049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/20/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
GATA binding protein 6 (GATA6) is an important transcription factor of cardiovascular endothelial cells, has the potential to regulate the process of cardiac development. Consequently, its abnormal expression is related to congenital heart disease.Human GATA6 gene clones were on chromosome 18 q11.1- q 11.2, consists of 7 exons and 6 intron.Now, a human embryonic stem cell line with GATA6 c.620_647del (p.S208Afs*77) mutation was generated. Interestingly, the ESC line displayed a normal karyotype, pluripotency and morphology of stem cells.This cell line has the ability to undergo differentiation into three germ layers in vivo.
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Affiliation(s)
- Chuyu Li
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China
| | - Xiaohan Dong
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China
| | - Yuting Lin
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China
| | - Xueping Sun
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China
| | - Lingbo Cai
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China
| | - Xiaoyu Yang
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China
| | - Yugui Cui
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China
| | - Lianju Qin
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China.
| | - Jing Wang
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 210029 Nanjing, Jiangsu, China.
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15
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Ward EJ, Bert S, Fanti S, Malone KM, Maughan RT, Gkantsinikoudi C, Prin F, Volpato LK, Piovezan AP, Graham GJ, Dufton NP, Perretti M, Marelli-Berg FM, Nadkarni S. Placental Inflammation Leads to Abnormal Embryonic Heart Development. Circulation 2023; 147:956-972. [PMID: 36484244 PMCID: PMC10022676 DOI: 10.1161/circulationaha.122.061934] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Placental heart development and embryonic heart development occur in parallel, and these organs have been proposed to exert reciprocal regulation during gestation. Poor placentation has been associated with congenital heart disease, an important cause of infant mortality. However, the mechanisms by which altered placental development can lead to congenital heart disease remain unresolved. METHODS In this study, we use an in vivo neutrophil-driven placental inflammation model through antibody depletion of maternal circulating neutrophils at key stages during time-mated murine pregnancy: embryonic days 4.5 and 7.5. Pregnant mice were culled at embryonic day 14.5 to assess placental and embryonic heart development. A combination of flow cytometry, histology, and bulk RNA sequencing was used to assess placental immune cell composition and tissue architecture. We also used flow cytometry and single-cell sequencing to assess embryonic cardiac immune cells at embryonic day 14.5 and histology and gene analyses to investigate embryonic heart structure and development. In some cases, offspring were culled at postnatal days 5 and 28 to assess any postnatal cardiac changes in immune cells, structure, and cardiac function, as measured by echocardiography. RESULTS In the present study, we show that neutrophil-driven placental inflammation leads to inadequate placental development and loss of barrier function. Consequently, placental inflammatory monocytes of maternal origin become capable of migration to the embryonic heart and alter the normal composition of resident cardiac macrophages and cardiac tissue structure. This cardiac impairment continues into postnatal life, hindering normal tissue architecture and function. Last, we show that tempering placental inflammation can prevent this fetal cardiac defect and is sufficient to promote normal cardiac function in postnatal life. CONCLUSIONS Taken together, these observations provide a mechanistic paradigm whereby neutrophil-driven inflammation in pregnancy can preclude normal embryonic heart development as a direct consequence of poor placental development, which has major implications on cardiac function into adult life.
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Affiliation(s)
- Eleanor J. Ward
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, UK (E.J.W., S.B., S.F., C.G., N.P.D., M.P., F.M.M.-B., S.N.)
| | - Serena Bert
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, UK (E.J.W., S.B., S.F., C.G., N.P.D., M.P., F.M.M.-B., S.N.)
| | - Silvia Fanti
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, UK (E.J.W., S.B., S.F., C.G., N.P.D., M.P., F.M.M.-B., S.N.)
| | - Kerri M. Malone
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK (K.M.M.)
| | - Robert T. Maughan
- National Heart and Lung Institute, Imperial College London, UK (R.T.M.)
| | - Christina Gkantsinikoudi
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, UK (E.J.W., S.B., S.F., C.G., N.P.D., M.P., F.M.M.-B., S.N.)
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, the Francis Crick Institute, London, UK (F.P.)
| | - Lia Karina Volpato
- Postgraduate Program in Health Science, University of Southern Catarina, Campus Pedra Branca, Palhoça, SC, Brazil (L.K.V., A.P.P.)
| | - Anna Paula Piovezan
- Postgraduate Program in Health Science, University of Southern Catarina, Campus Pedra Branca, Palhoça, SC, Brazil (L.K.V., A.P.P.)
| | - Gerard J. Graham
- Institute of Infection, Immunity and Inflammation, University of Glasgow, UK (G.J.G.)
| | - Neil P. Dufton
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, UK (E.J.W., S.B., S.F., C.G., N.P.D., M.P., F.M.M.-B., S.N.)
| | - Mauro Perretti
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, UK (E.J.W., S.B., S.F., C.G., N.P.D., M.P., F.M.M.-B., S.N.)
| | - Federica M. Marelli-Berg
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, UK (E.J.W., S.B., S.F., C.G., N.P.D., M.P., F.M.M.-B., S.N.)
| | - Suchita Nadkarni
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, UK (E.J.W., S.B., S.F., C.G., N.P.D., M.P., F.M.M.-B., S.N.)
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16
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Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. A transcription factor atlas of directed differentiation. Cell 2023; 186:209-229.e26. [PMID: 36608654 PMCID: PMC10344468 DOI: 10.1016/j.cell.2022.11.026] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/04/2022] [Accepted: 11/23/2022] [Indexed: 01/07/2023]
Abstract
Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular processes and cell states. To comprehensively understand TFs and the programs they control, we created a barcoded library of all annotated human TF splice isoforms (>3,500) and applied it to build a TF Atlas charting expression profiles of human embryonic stem cells (hESCs) overexpressing each TF at single-cell resolution. We mapped TF-induced expression profiles to reference cell types and validated candidate TFs for generation of diverse cell types, spanning all three germ layers and trophoblasts. Targeted screens with subsets of the library allowed us to create a tailored cellular disease model and integrate mRNA expression and chromatin accessibility data to identify downstream regulators. Finally, we characterized the effects of combinatorial TF overexpression by developing and validating a strategy for predicting combinations of TFs that produce target expression profiles matching reference cell types to accelerate cellular engineering efforts.
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Affiliation(s)
- Julia Joung
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Sai Ma
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn R Geiger-Schuller
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul C Kirchgatterer
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Vanessa K Verdine
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Baolin Guo
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mario A Arias-Garcia
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William E Allen
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA; Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Ankita Singh
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Olena Kuksenko
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Omar O Abudayyeh
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Jonathan S Gootenberg
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Zhanyan Fu
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rhiannon K Macrae
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Feng Zhang
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
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17
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Chowdhary S, Hadjantonakis AK. Journey of the mouse primitive endoderm: from specification to maturation. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210252. [PMID: 36252215 PMCID: PMC9574636 DOI: 10.1098/rstb.2021.0252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/25/2022] [Indexed: 12/22/2022] Open
Abstract
The blastocyst is a conserved stage and distinct milestone in the development of the mammalian embryo. Blastocyst stage embryos comprise three cell lineages which arise through two sequential binary cell fate specification steps. In the first, extra-embryonic trophectoderm (TE) cells segregate from inner cell mass (ICM) cells. Subsequently, ICM cells acquire a pluripotent epiblast (Epi) or extra-embryonic primitive endoderm (PrE, also referred to as hypoblast) identity. In the mouse, nascent Epi and PrE cells emerge in a salt-and-pepper distribution in the early blastocyst and are subsequently sorted into adjacent tissue layers by the late blastocyst stage. Epi cells cluster at the interior of the ICM, while PrE cells are positioned on its surface interfacing the blastocyst cavity, where they display apicobasal polarity. As the embryo implants into the maternal uterus, cells at the periphery of the PrE epithelium, at the intersection with the TE, break away and migrate along the TE as they mature into parietal endoderm (ParE). PrE cells remaining in association with the Epi mature into visceral endoderm. In this review, we discuss our current understanding of the PrE from its specification to its maturation. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.
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Affiliation(s)
- Sayali Chowdhary
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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18
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Lorenzana-Carrillo MA, Gopal K, Byrne NJ, Tejay S, Saleme B, Das SK, Zhang Y, Haromy A, Eaton F, Mendiola Pla M, Bowles DE, Dyck JR, Ussher JR, Michelakis ED, Sutendra G. TRIM35-mediated degradation of nuclear PKM2 destabilizes GATA4/6 and induces P53 in cardiomyocytes to promote heart failure. Sci Transl Med 2022; 14:eabm3565. [DOI: 10.1126/scitranslmed.abm3565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Pyruvate kinase M2 (PKM2) is a glycolytic enzyme that translocates to the nucleus to regulate transcription factors in different tissues or pathologic states. Although studied extensively in cancer, its biological role in the heart remains unresolved. PKM1 is more abundant than the PKM2 isoform in cardiomyocytes, and thus, we speculated that PKM2 is not genetically redundant to PKM1 and may be critical in regulating cardiomyocyte-specific transcription factors important for cardiac survival. Here, we showed that nuclear PKM2 (
S37
P-PKM2) in cardiomyocytes interacts with prosurvival and proapoptotic transcription factors, including GATA4, GATA6, and P53. Cardiomyocyte-specific PKM2-deficient mice (
Pkm2
Mut Cre
+
) developed age-dependent dilated cardiac dysfunction and had decreased amounts of GATA4 and GATA6 (GATA4/6) but increased amounts of P53 compared to Control Cre
+
hearts. Nuclear PKM2 prevented caspase-1–dependent cleavage and degradation of GATA4/6 while also providing a molecular platform for MDM2-mediated reduction of P53. In a preclinical heart failure mouse model, nuclear PKM2 and GATA4/6 were decreased, whereas P53 was increased in cardiomyocytes. Loss of nuclear PKM2 was ubiquitination dependent and associated with the induction of the E3 ubiquitin ligase TRIM35. In mice, cardiomyocyte-specific TRIM35 overexpression resulted in decreased
S37
P-PKM2 and GATA4/6 along with increased P53 in cardiomyocytes compared to littermate controls and similar cardiac dysfunction to
Pkm2
Mut Cre
+
mice. In patients with dilated left ventricles, increase in TRIM35 was associated with decreased
S37
P-PKM2 and GATA4/6 and increased P53. This study supports a previously unrecognized role for PKM2 as a molecular platform that mediates cell signaling events essential for cardiac survival.
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Affiliation(s)
- Maria Areli Lorenzana-Carrillo
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Keshav Gopal
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H1, Canada
| | - Nikole J. Byrne
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Saymon Tejay
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Bruno Saleme
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Subhash K. Das
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Yongneng Zhang
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Alois Haromy
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Farah Eaton
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H1, Canada
| | | | - Dawn E. Bowles
- Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Jason R. B. Dyck
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - John R. Ussher
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2H1, Canada
| | - Evangelos D. Michelakis
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Gopinath Sutendra
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB T6G 2B7, Canada
- Cardiovascular Research Centre, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB T6G 2E1, Canada
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19
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Shichiri Y, Kato Y, Inagaki H, Kato T, Ishihara N, Miyata M, Boda H, Kojima A, Miyake M, Kurahashi H. A case of 46,XY disorders of sex development with congenital heart disease caused by a GATA4 variant. Congenit Anom (Kyoto) 2022; 62:203-207. [PMID: 35751412 DOI: 10.1111/cga.12482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 11/30/2022]
Abstract
GATA4 is known to be a causative gene for congenital heart disease, but has also now been associated with disorders of sexual development (DSD). We here report a pathogenic variant of GATA4 in a 46,XY DSD patient with an atrial septal defect, identified by whole-exome sequencing to be c.487C>T (p.Pro163Ser). This mutation resulted in reduced transcriptional activity of the downstream gene. When we compared this transcriptional activity level with other GATA4 variants, those that had been identified in patients with cardiac defects and DSD showed less activity than those in patients with cardiac defect only. This suggests that the normal development of the heart requires more strict regulation of GATA4 transcription than testicular development. Further, when the different variants were co-expressed with wild-type, the transcriptional activities were consistently lower than would be expected from an additive effect, suggesting a dominant-negative impact of the variant via dimer formation of the GATA4 protein. Since these pathogenic GATA4 variants are occasionally identified in healthy parents, a threshold model of quantitative traits may explain the cardiac defect or DSD phenotypes that they cause.
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Affiliation(s)
- Yui Shichiri
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Yoshimi Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Naoko Ishihara
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Masafumi Miyata
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroko Boda
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Arisa Kojima
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Misa Miyake
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
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20
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Sugiyama A, Hirashima M. Fetal nuchal edema and developmental anomalies caused by gene mutations in mice. Front Cell Dev Biol 2022; 10:949013. [PMID: 36111337 PMCID: PMC9468611 DOI: 10.3389/fcell.2022.949013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Fetal nuchal edema, a subcutaneous accumulation of extracellular fluid in the fetal neck, is detected as increased nuchal translucency (NT) by ultrasonography in the first trimester of pregnancy. It has been demonstrated that increased NT is associated with chromosomal anomalies and genetic syndromes accompanied with fetal malformations such as defective lymphatic vascular development, cardiac anomalies, anemia, and a wide range of other fetal anomalies. However, in many clinical cases of increased NT, causative genes, pathogenesis and prognosis have not been elucidated in humans. On the other hand, a large number of gene mutations have been reported to induce fetal nuchal edema in mouse models. Here, we review the relationship between the gene mutants causing fetal nuchal edema with defective lymphatic vascular development, cardiac anomalies, anemia and blood vascular endothelial barrier anomalies in mice. Moreover, we discuss how studies using gene mutant mouse models will be useful in developing diagnostic method and predicting prognosis.
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21
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Afouda BA. Towards Understanding the Gene-Specific Roles of GATA Factors in Heart Development: Does GATA4 Lead the Way? Int J Mol Sci 2022; 23:5255. [PMID: 35563646 PMCID: PMC9099915 DOI: 10.3390/ijms23095255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 02/04/2023] Open
Abstract
Transcription factors play crucial roles in the regulation of heart induction, formation, growth and morphogenesis. Zinc finger GATA transcription factors are among the critical regulators of these processes. GATA4, 5 and 6 genes are expressed in a partially overlapping manner in developing hearts, and GATA4 and 6 continue their expression in adult cardiac myocytes. Using different experimental models, GATA4, 5 and 6 were shown to work together not only to ensure specification of cardiac cells but also during subsequent heart development. The complex involvement of these related gene family members in those processes is demonstrated through the redundancy among them and crossregulation of each other. Our recent identification at the genome-wide level of genes specifically regulated by each of the three family members and our earlier discovery that gata4 and gata6 function upstream, while gata5 functions downstream of noncanonical Wnt signalling during cardiac differentiation, clearly demonstrate the functional differences among the cardiogenic GATA factors. Such suspected functional differences are worth exploring more widely. It appears that in the past few years, significant advances have indeed been made in providing a deeper understanding of the mechanisms by which each of these molecules function during heart development. In this review, I will therefore discuss current evidence of the role of individual cardiogenic GATA factors in the process of heart development and emphasize the emerging central role of GATA4.
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Affiliation(s)
- Boni A Afouda
- Institute of Medical Sciences, Foresterhill Health Campus, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, UK
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22
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The nuclear receptor ERR cooperates with the cardiogenic factor GATA4 to orchestrate cardiomyocyte maturation. Nat Commun 2022; 13:1991. [PMID: 35418170 PMCID: PMC9008061 DOI: 10.1038/s41467-022-29733-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/30/2022] [Indexed: 12/19/2022] Open
Abstract
Estrogen-related receptors (ERR) α and γ were shown recently to serve as regulators of cardiac maturation, yet the underlying mechanisms have not been delineated. Herein, we find that ERR signaling is necessary for induction of genes involved in mitochondrial and cardiac-specific contractile processes during human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) differentiation. Genomic interrogation studies demonstrate that ERRγ occupies many cardiomyocyte enhancers/super-enhancers, often co-localizing with the cardiogenic factor GATA4. ERRγ interacts with GATA4 to cooperatively activate transcription of targets involved in cardiomyocyte-specific processes such as contractile function, whereas ERRγ-mediated control of metabolic genes occurs independent of GATA4. Both mechanisms require the transcriptional coregulator PGC-1α. A disease-causing GATA4 mutation is shown to diminish PGC-1α/ERR/GATA4 cooperativity and expression of ERR target genes are downregulated in human heart failure samples suggesting that dysregulation of this circuitry may contribute to congenital and acquired forms of heart failure. Mature cardiac muscle requires high mitochondrial ATP production and specialized contractile proteins. Here the authors demonstrate that cardiomyocyte-specific contractile maturation involves cooperation between the nuclear receptor ERRγ and cardiogenic transcription factor GATA4, but ERRγ controls metabolic genes independently.
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23
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Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D. Transcription factor protein interactomes reveal genetic determinants in heart disease. Cell 2022; 185:794-814.e30. [PMID: 35182466 PMCID: PMC8923057 DOI: 10.1016/j.cell.2022.01.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/20/2021] [Accepted: 01/25/2022] [Indexed: 02/08/2023]
Abstract
Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains challenging. We hypothesized that genetic determinants for CHDs may lie in the protein interactomes of transcription factors whose mutations cause CHDs. Defining the interactomes of two transcription factors haplo-insufficient in CHD, GATA4 and TBX5, within human cardiac progenitors, and integrating the results with nearly 9,000 exomes from proband-parent trios revealed an enrichment of de novo missense variants associated with CHD within the interactomes. Scoring variants of interactome members based on residue, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied and co-activated cardiac developmental genes, and the identified GLYR1 missense variant disrupted interaction with GATA4, impairing in vitro and in vivo function in mice. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating genetic variants in heart disease.
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Affiliation(s)
- Barbara Gonzalez-Teran
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Maureen Pittman
- Gladstone Institutes, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Franco Felix
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | | | - Desmond Richmond-Buccola
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | | | | | - Mauro W Costa
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Yu Huang
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michael Alexanian
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Clara Youngna Lee
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Bonnie E J Maven
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Kaitlen Samse-Knapp
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Sarah U Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Michael McGregor
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Casey A Gifford
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA; Division of Cardiology, Department of Pediatrics, UCSF School of Medicine, San Francisco, CA, USA
| | - Nevan J Krogan
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Division of Cardiology, Department of Pediatrics, UCSF School of Medicine, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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Miyajima Y, Noguchi S, Tanaka Y, Li JR, Nishimura H, Kishima M, Lim J, Furuhata E, Suzuki T, Kasukawa T, Suzuki H. Prediction of transcription factors associated with DNA demethylation during human cellular development. Chromosome Res 2022; 30:109-121. [PMID: 35142952 PMCID: PMC8942926 DOI: 10.1007/s10577-022-09685-6] [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: 10/27/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 12/19/2022]
Abstract
DNA methylation of CpG dinucleotides is an important epigenetic modification involved in the regulation of mammalian gene expression, with each type of cell developing a specific methylation profile during its differentiation. Recently, it has been shown that a small subgroup of transcription factors (TFs) might promote DNA demethylation at their binding sites. We developed a bioinformatics pipeline to predict from genome-wide DNA methylation data TFs that promote DNA demethylation at their binding site. We applied the pipeline to International Human Epigenome Consortium methylome data and selected 393 candidate transcription factor binding motifs and associated 383 TFs that are likely associated with DNA demethylation. Validation of a subset of the candidate TFs using an in vitro assay suggested that 28 of 49 TFs from various TF families had DNA-demethylation-promoting activity; TF families, such as bHLH and ETS, contained both TFs with and without the activity. The identified TFs showed large demethylated/methylated CpG ratios and their demethylated CpGs showed significant bias toward hypermethylation in original cells. Furthermore, the identified TFs promoted demethylation of distinct sets of CpGs, with slight overlap of the targeted CpGs among TF family members, which was consistent with the results of a gene ontology (GO) term analysis of the identified TFs. Gene expression analysis of the identified TFs revealed that multiple TFs from various families are specifically expressed in human cells and tissues. Together, our results suggest that a large number of TFs from various TF families are associated with cell-type-specific DNA demethylation during human cellular development.
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Affiliation(s)
- Yurina Miyajima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuki Tanaka
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan
| | - Jing-Ru Li
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hajime Nishimura
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Mami Kishima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Joanne Lim
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Erina Furuhata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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Bang J, Han M, Yoo TJ, Qiao L, Jung J, Na J, Carlson BA, Gladyshev VN, Hatfield DL, Kim JH, Kim LK, Lee BJ. Identification of Signaling Pathways for Early Embryonic Lethality and Developmental Retardation in Sephs1-/- Mice. Int J Mol Sci 2021; 22:ijms222111647. [PMID: 34769078 PMCID: PMC8583877 DOI: 10.3390/ijms222111647] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022] Open
Abstract
Selenophosphate synthetase 1 (SEPHS1) plays an essential role in cell growth and survival. However, the underlying molecular mechanisms remain unclear. In the present study, the pathways regulated by SEPHS1 during gastrulation were determined by bioinformatical analyses and experimental verification using systemic knockout mice targeting Sephs1. We found that the coagulation system and retinoic acid signaling were most highly affected by SEPHS1 deficiency throughout gastrulation. Gene expression patterns of altered embryo morphogenesis and inhibition of Wnt signaling were predicted with high probability at E6.5. These predictions were verified by structural abnormalities in the dermal layer of Sephs1−/− embryos. At E7.5, organogenesis and activation of prolactin signaling were predicted to be affected by Sephs1 knockout. Delay of head fold formation was observed in the Sephs1−/− embryos. At E8.5, gene expression associated with organ development and insulin-like growth hormone signaling that regulates organ growth during development was altered. Consistent with these observations, various morphological abnormalities of organs and axial rotation failure were observed. We also found that the gene sets related to redox homeostasis and apoptosis were gradually enriched in a time-dependent manner until E8.5. However, DNA damage and apoptosis markers were detected only when the Sephs1−/− embryos aged to E9.5. Our results suggest that SEPHS1 deficiency causes a gradual increase of oxidative stress which changes signaling pathways during gastrulation, and afterwards leads to apoptosis.
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Affiliation(s)
- Jeyoung Bang
- Interdisciplinary Program in Bioinformatics, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (J.B.); (M.H.)
| | - Minguk Han
- Interdisciplinary Program in Bioinformatics, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (J.B.); (M.H.)
| | - Tack-Jin Yoo
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (T.-J.Y.); (L.Q.); (J.J.); (J.N.); (J.-H.K.)
| | - Lu Qiao
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (T.-J.Y.); (L.Q.); (J.J.); (J.N.); (J.-H.K.)
| | - Jisu Jung
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (T.-J.Y.); (L.Q.); (J.J.); (J.N.); (J.-H.K.)
| | - Jiwoon Na
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (T.-J.Y.); (L.Q.); (J.J.); (J.N.); (J.-H.K.)
| | - Bradley A. Carlson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.A.C.); (D.L.H.)
| | - Vadim N. Gladyshev
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Dolph L. Hatfield
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.A.C.); (D.L.H.)
| | - Jin-Hong Kim
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (T.-J.Y.); (L.Q.); (J.J.); (J.N.); (J.-H.K.)
| | - Lark Kyun Kim
- Severance Biomedical Science Institute, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06230, Korea
- Correspondence: (L.K.K.); (B.J.L.); Tel.: +82-2-880-6775 (B.J.L.)
| | - Byeong Jae Lee
- Interdisciplinary Program in Bioinformatics, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (J.B.); (M.H.)
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea; (T.-J.Y.); (L.Q.); (J.J.); (J.N.); (J.-H.K.)
- Correspondence: (L.K.K.); (B.J.L.); Tel.: +82-2-880-6775 (B.J.L.)
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Jaiswal SK, Raj S, DePamphilis ML. Developmental Acquisition of p53 Functions. Genes (Basel) 2021; 12:genes12111675. [PMID: 34828285 PMCID: PMC8622856 DOI: 10.3390/genes12111675] [Citation(s) in RCA: 3] [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: 08/27/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
Remarkably, the p53 transcription factor, referred to as “the guardian of the genome”, is not essential for mammalian development. Moreover, efforts to identify p53-dependent developmental events have produced contradictory conclusions. Given the importance of pluripotent stem cells as models of mammalian development, and their applications in regenerative medicine and disease, resolving these conflicts is essential. Here we attempt to reconcile disparate data into justifiable conclusions predicated on reports that p53-dependent transcription is first detected in late mouse blastocysts, that p53 activity first becomes potentially lethal during gastrulation, and that apoptosis does not depend on p53. Furthermore, p53 does not regulate expression of genes required for pluripotency in embryonic stem cells (ESCs); it contributes to ESC genomic stability and differentiation. Depending on conditions, p53 accelerates initiation of apoptosis in ESCs in response to DNA damage, but cell cycle arrest as well as the rate and extent of apoptosis in ESCs are p53-independent. In embryonic fibroblasts, p53 induces cell cycle arrest to allow repair of DNA damage, and cell senescence to prevent proliferation of cells with extensive damage.
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Affiliation(s)
- Sushil K. Jaiswal
- National Institute of Child Health and Human Development, Bethesda, MD 20892, USA;
- National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Sonam Raj
- National Cancer Institute, Bethesda, MD 20892, USA;
| | - Melvin L. DePamphilis
- National Institute of Child Health and Human Development, Bethesda, MD 20892, USA;
- Correspondence:
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Genetics of diaphragmatic hernia. Eur J Hum Genet 2021; 29:1729-1733. [PMID: 34621023 PMCID: PMC8632982 DOI: 10.1038/s41431-021-00972-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 01/14/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a life-threatening malformation characterised by failure of diaphragmatic development with lung hypoplasia and persistent pulmonary hypertension of the newborn (PPHN). The incidence is 1:2000 corresponding to 8% of all major congenital malformations. Morbidity and mortality in affected newborns are very high and at present, there is no precise prenatal or early postnatal prognostication parameter to predict clinical outcome in CDH patients. Most cases occur sporadically, however, genetic causes have long been discussed to explain a proportion of cases. These range from aneuploidy to complex chromosomal aberrations and specific mutations often causing a complex phenotype exhibiting multiple malformations along with CDH. This review summarises the genetic variations which have been observed in syndromic and isolated cases of congenital diaphragmatic hernia.
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Huang GJ, Xie XL, Zou Y. MiR-23b targets GATA6 to down-regulate IGF-1 and promote the development of congenital heart disease. Acta Cardiol 2021; 77:375-384. [PMID: 34582317 DOI: 10.1080/00015385.2021.1948207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most universal congenital defect disease. This study explores the interrelationship between miR-23b and GTAT6 in the development of CHD. METHODS We collected clinical samples and constructed in vitro cell models to evaluate the expression of miR-23b, GATA6, and IGF-1. CHD cell models were constructed by hypoxia in H9C2 cells. The expression levels of GATA6 and IGF-1 in H9C2 cells were determined by western blot and qPCR. MiR-23b was knocked down by transfection miR-23b inhibitor. GATA6 knockdown or overexpression vectors were established by the lentiviral approach and cell transfection, respectively. According to the CCK-8 assay and flow cytometry analysis, the proliferation and apoptosis of H9C2 cells were detected. The binding relationship between GATA6 and miR-23b was detected by luciferase reporter assay. RESULTS The expression level of miR-23b was escalated abnormally, while the expression levels of GATA6 and IGF-1 were decreased in the serum of CHD clinical patients and cell models. miR-23b knockdown in H9C2 cells could up-regulate the expression of GATA6, thus improved the proliferation and decreased apoptosis of H9C2 cells. Overexpression of GATA6 could up-regulate IGF-1 to promote proliferation and inhibit apoptosis in H9C2 cells. MiR-23b could target GATA6 and regulated IGF-1, thus affecting cell proliferation and apoptosis. CONCLUSION The expression level of miR-23b was remarkably up-regulated in serum of CHD patients and H9C2 cells in vitro, while the expression of GATA6 and IGF-1 was significantly decreased. MiR-23b could influence the proliferation and apoptosis of cardiomyocytes by targeting the down-regulation of the GATA6/IGF-1 axis.
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Affiliation(s)
- Guo-Jin Huang
- Pediatric Heart Disease Treatment Center of Jiangxi Province, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Xue-Liang Xie
- Pediatric Heart Disease Treatment Center of Jiangxi Province, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Yong Zou
- Pediatric Heart Disease Treatment Center of Jiangxi Province, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
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29
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Nachtigall PG, Bovolenta LA, Patton JG, Fromm B, Lemke N, Pinhal D. A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks. BMC Genomics 2021; 22:153. [PMID: 33663371 PMCID: PMC7931589 DOI: 10.1186/s12864-021-07441-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/12/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND During vertebrate evolution, the heart has undergone remarkable changes that lead to morphophysiological differences in the fully formed heart of these species, such as chamber septation, heart rate frequency, blood pressure, and cardiac output volume. Despite these differences, the heart developmental process is guided by a core gene set conserved across vertebrates. Nonetheless, the regulatory mechanisms controlling the expression of genes involved in heart development and maintenance are largely uncharted. MicroRNAs (miRNAs) have been described as important regulatory elements in several biological processes, including heart biology. These small RNA molecules are broadly conserved in sequence and genomic context in metazoans. Mutations may occur in miRNAs and/or genes that contribute to the establishment of distinct repertoires of miRNA-target interactions, thereby favoring the differential control of gene expression and, consequently, the origin of novel phenotypes. In fact, several studies showed that miRNAs are integrated into genetic regulatory networks (GRNs) governing specific developmental programs and diseases. However, studies integrating miRNAs in vertebrate heart GRNs under an evolutionary perspective are still scarce. RESULTS We comprehensively examined and compared the heart miRNome of 20 species representatives of the five major vertebrate groups. We found 54 miRNA families with conserved expression and a variable number of miRNA families with group-specific expression in fishes, amphibians, reptiles, birds, and mammals. We also detected that conserved miRNAs present higher expression levels and a higher number of targets, whereas the group-specific miRNAs present lower expression levels and few targets. CONCLUSIONS Both the conserved and group-specific miRNAs can be considered modulators orchestrating the core and peripheral genes of heart GRNs of vertebrates, which can be related to the morphophysiological differences and similarities existing in the heart of distinct vertebrate groups. We propose a hypothesis to explain evolutionary differences in the putative functional roles of miRNAs in the heart GRNs analyzed. Furthermore, we present new insights into the molecular mechanisms that could be helping modulate the diversity of morphophysiology in the heart organ of vertebrate species.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório Especial de Toxinologia Aplicada (LETA), CeTICS, Instituto Butantan, São Paulo, Brazil. .,Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil.
| | - Luiz A Bovolenta
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute (MBW), Stockholm University, Stockholm, Sweden
| | - Ney Lemke
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
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Abstract
Congenital heart disease is the most common congenital defect observed in newborns. Within the spectrum of congenital heart disease are left‐sided obstructive lesions (LSOLs), which include hypoplastic left heart syndrome, aortic stenosis, bicuspid aortic valve, coarctation of the aorta, and interrupted aortic arch. These defects can arise in isolation or as a component of a defined syndrome; however, nonsyndromic defects are often observed in multiple family members and associated with high sibling recurrence risk. This clear evidence for a heritable basis has driven a lengthy search for disease‐causing variants that has uncovered both rare and common variants in genes that, when perturbed in cardiac development, can result in LSOLs. Despite advancements in genetic sequencing platforms and broadening use of exome sequencing, the currently accepted LSOL‐associated genes explain only 10% to 20% of patients. Further, the combinatorial effects of common and rare variants as a cause of LSOLs are emerging. In this review, we highlight the genes and variants associated with the different LSOLs and discuss the strengths and weaknesses of the present genetic associations. Furthermore, we discuss the research avenues needed to bridge the gaps in our current understanding of the genetic basis of nonsyndromic congenital heart disease.
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Affiliation(s)
- Lauren E Parker
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC
| | - Andrew P Landstrom
- Division of Cardiology Department of Pediatrics Duke University School of Medicine Durham NC.,Department of Cell Biology Duke University School of Medicine Durham NC
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31
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Jiao H, Walczak BE, Lee MS, Lemieux ME, Li WJ. GATA6 regulates aging of human mesenchymal stem/stromal cells. STEM CELLS (DAYTON, OHIO) 2020; 39:62-77. [PMID: 33252174 DOI: 10.1002/stem.3297] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 03/29/2020] [Accepted: 10/12/2020] [Indexed: 12/17/2022]
Abstract
Cellular reprogramming forcing the expression of pluripotency markers can reverse aging of cells, but how molecular mechanisms through which reprogrammed cells alter aging-related cellular activities still remains largely unclear. In this study, we reprogrammed human synovial fluid-derived mesenchymal stem cells (MSCs) into induced pluripotent stem cells (iPSCs) using six reprogramming factors and reverted the iPSCs back to MSCs, as an approach to cell rejuvenation. Using the parental and reprogrammed MSCs as control nonrejuvenated and rejuvenated cells, respectively, for comparative analysis, we found that aging-related activities were greatly reduced in reprogrammed MSCs compared with those in their parental lines, indicating reversal of cell aging. Global transcriptome analysis revealed differences in activities of regulatory networks associated with inflammation and proliferation. Mechanistically, we demonstrated that, compared with control cells, the expression of GATA binding protein 6 (GATA6) in reprogrammed cells was attenuated, resulting in an increase in the activity of sonic hedgehog signaling and the expression level of downstream forkhead box P1 (FOXP1), in turn ameliorating cellular hallmarks of aging. Lower levels of GATA6 expression were also found in cells harvested from younger mice or lower passage cultures. Our findings suggest that GATA6 is a critical regulator increased in aged MSCs that controls the downstream sonic hedgehog signaling and FOXP1 pathway to modulate cellular senescence and aging-related activities.
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Affiliation(s)
- Hongli Jiao
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian E Walczak
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ming-Song Lee
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Wan-Ju Li
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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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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Sam J, Mercer EJ, Torregroza I, Banks KM, Evans T. Specificity, redundancy and dosage thresholds among gata4/5/6 genes during zebrafish cardiogenesis. Biol Open 2020; 9:9/6/bio053611. [PMID: 32580940 PMCID: PMC7327998 DOI: 10.1242/bio.053611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Gata4/5/6 sub-family of zinc finger transcription factors regulate many aspects of cardiogenesis. However, critical roles in extra-embryonic endoderm also challenge comprehensive analysis during early mouse cardiogenesis, while zebrafish models have previously relied on knockdown assays. We generated targeted deletions to disrupt each gata4/5/6 gene in zebrafish and analyzed cardiac phenotypes in single, double and triple mutants. The analysis confirmed that loss of gata5 causes cardia bifida and validated functional redundancies for gata5/6 in cardiac precursor specification. Surprisingly, we discovered that gata4 is dispensable for early zebrafish development, while loss of one gata4 allele can suppress the bifid phenotype of the gata5 mutant. The gata4 mutants eventually develop an age-dependent cardiomyopathy. By combining combinations of mutant alleles, we show that cardiac specification depends primarily on an overall dosage of gata4/5/6 alleles rather than a specific gene. We also identify a specific role for gata6 in controlling ventricle morphogenesis through regulation of both the first and second heart field, while loss of both gata4/6 eliminates the ventricle. Thus, different developmental programs are dependent on total dosage, certain pairs, or specific gata4/5/6 genes during embryonic cardiogenesis. This article has an associated First Person interview with the first author of the paper. Summary: Targeted mutations were generated for each of the three gata4/5/6 genes in zebrafish to define functions for individual or combinations of these related transcription factors during cardiogenesis.
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Affiliation(s)
- Jessica Sam
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Emily J Mercer
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ingrid Torregroza
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Kelly M Banks
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY 10065, USA
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Gharibeh L, Komati H, Bossé Y, Boodhwani M, Heydarpour M, Fortier M, Hassanzadeh R, Ngu J, Mathieu P, Body S, Nemer M. GATA6 Regulates Aortic Valve Remodeling, and Its Haploinsufficiency Leads to Right-Left Type Bicuspid Aortic Valve. Circulation 2019; 138:1025-1038. [PMID: 29567669 DOI: 10.1161/circulationaha.117.029506] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Bicuspid aortic valve (BAV), the most common congenital heart defect affecting 1% to 2% of the population, is a major risk factor for premature aortic valve disease and accounts for the majority of valve replacement. The genetic basis and mechanisms of BAV etiology and pathogenesis remain largely undefined. METHODS Cardiac structure and function was assessed in mice lacking a Gata6 allele. Human GATA6 gene variants were analyzed in 452 BAV cases from the BAV consortium and 1849 controls from the Framingham GWAS (Genome Wide Association Study). GATA6 expression was determined in mice and human tissues using quantitative real-time polymerase chain reaction and immunohistochemistry. Mechanistic studies were carried out in cultured cells. RESULTS Gata6 heterozygous mice have highly penetrant right-left (RL)-type BAV, the most frequent type in humans. GATA6 transcript levels are lower in human BAV compared with normal tricuspid valves. Mechanistically, Gata6 haploinsufficiency disrupts valve remodeling and extracellular matrix composition through dysregulation of important signaling molecules, including matrix metalloproteinase 9. Cell-specific inactivation of Gata6 reveals an essential role for GATA6 in secondary heart field myocytes because loss of 1 Gata6 allele from Isl- 1-positive cells-but not from endothelial or neural crest cells-recapitulates the phenotype of Gata6 heterozygous mice. CONCLUSIONS The data identify a new cellular and molecular mechanism underlying BAV. The availability of an animal model for the most frequent human BAV opens the way for the elucidation of BAV pathogenesis and the development of much needed therapies.
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Affiliation(s)
- Lara Gharibeh
- Department of Biochemistry, Microbiology, and Immunology, Molecular Genetics and Cardiac Regeneration Laboratory, University of Ottawa, Ontario, Canada (L.G., H.K., R.H., M.T., M.N.)
| | - Hiba Komati
- Department of Biochemistry, Microbiology, and Immunology, Molecular Genetics and Cardiac Regeneration Laboratory, University of Ottawa, Ontario, Canada (L.G., H.K., R.H., M.T., M.N.)
| | - Yohan Bossé
- Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Canada (Y.B., P.M.)
| | - Munir Boodhwani
- Division of Cardiac Surgery, University of Ottawa Heart Institute, Ontario, Canada (M.B., J.N.)
| | - Mahyar Heydarpour
- Department of Biochemistry, Microbiology, and Immunology, Molecular Genetics and Cardiac Regeneration Laboratory, University of Ottawa, Ontario, Canada (L.G., H.K., R.H., M.T., M.N.)
| | | | - Romina Hassanzadeh
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (M.H., S.B.)
| | - Janet Ngu
- Division of Cardiac Surgery, University of Ottawa Heart Institute, Ontario, Canada (M.B., J.N.)
| | - Patrick Mathieu
- Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Canada (Y.B., P.M.)
| | - Simon Body
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (M.H., S.B.)
| | - Mona Nemer
- Department of Biochemistry, Microbiology, and Immunology, Molecular Genetics and Cardiac Regeneration Laboratory, University of Ottawa, Ontario, Canada (L.G., H.K., R.H., M.T., M.N.)
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Maliken BD, Kanisicak O, Karch J, Khalil H, Fu X, Boyer JG, Prasad V, Zheng Y, Molkentin JD. Gata4-Dependent Differentiation of c-Kit +-Derived Endothelial Cells Underlies Artefactual Cardiomyocyte Regeneration in the Heart. Circulation 2019; 138:1012-1024. [PMID: 29666070 PMCID: PMC6125755 DOI: 10.1161/circulationaha.118.033703] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Supplemental Digital Content is available in the text. Background: Although c-Kit+ adult progenitor cells were initially reported to produce new cardiomyocytes in the heart, recent genetic evidence suggests that such events are exceedingly rare. However, to determine if these rare events represent true de novo cardiomyocyte formation, we deleted the necessary cardiogenic transcription factors Gata4 and Gata6 from c-Kit–expressing cardiac progenitor cells. Methods: Kit allele–dependent lineage tracing and fusion analysis were performed in mice following simultaneous Gata4 and Gata6 cell type–specific deletion to examine rates of putative de novo cardiomyocyte formation from c-Kit+ cells. Bone marrow transplantation experiments were used to define the contribution of Kit allele–derived hematopoietic cells versus Kit lineage–dependent cells endogenous to the heart in contributing to apparent de novo lineage-traced cardiomyocytes. A Tie2CreERT2 transgene was also used to examine the global impact of Gata4 deletion on the mature cardiac endothelial cell network, which was further evaluated with select angiogenesis assays. Results: Deletion of Gata4 in Kit lineage–derived endothelial cells or in total endothelial cells using the Tie2CreERT2 transgene, but not from bone morrow cells, resulted in profound endothelial cell expansion, defective endothelial cell differentiation, leukocyte infiltration into the heart, and a dramatic increase in Kit allele–dependent lineage-traced cardiomyocytes. However, this increase in labeled cardiomyocytes was an artefact of greater leukocyte-cardiomyocyte cellular fusion because of defective endothelial cell differentiation in the absence of Gata4. Conclusions: Past identification of presumed de novo cardiomyocyte formation in the heart from c-Kit+ cells using Kit allele lineage tracing appears to be an artefact of labeled leukocyte fusion with cardiomyocytes. Deletion of Gata4 from c-Kit+ endothelial progenitor cells or adult endothelial cells negatively impacted angiogenesis and capillary network integrity.
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Affiliation(s)
- Bryan D Maliken
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (B.D.M., O.K., J.K., H.K., X.F., J.G.B., V.P., Y.Z., J.D.M.)
| | - Onur Kanisicak
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (B.D.M., O.K., J.K., H.K., X.F., J.G.B., V.P., Y.Z., J.D.M.)
| | - Jason Karch
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (B.D.M., O.K., J.K., H.K., X.F., J.G.B., V.P., Y.Z., J.D.M.)
| | - Hadi Khalil
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (B.D.M., O.K., J.K., H.K., X.F., J.G.B., V.P., Y.Z., J.D.M.)
| | | | - Justin G Boyer
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (B.D.M., O.K., J.K., H.K., X.F., J.G.B., V.P., Y.Z., J.D.M.).,Howard Hughes Medical Institute, Cincinnati Children's Hospital Research Foundation, OH (J.G.B., J.D.M)
| | - Vikram Prasad
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (B.D.M., O.K., J.K., H.K., X.F., J.G.B., V.P., Y.Z., J.D.M.)
| | - Yi Zheng
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (B.D.M., O.K., J.K., H.K., X.F., J.G.B., V.P., Y.Z., J.D.M.)
| | - Jeffery D Molkentin
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, OH (B.D.M., O.K., J.K., H.K., X.F., J.G.B., V.P., Y.Z., J.D.M.).,Howard Hughes Medical Institute, Cincinnati Children's Hospital Research Foundation, OH (J.G.B., J.D.M)
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36
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Peng T, Deng X, Tian F, Li Z, Jiang P, Zhao X, Chen G, Chen Y, Zheng P, Li D, Wang S. The interaction of LOXL2 with GATA6 induces VEGFA expression and angiogenesis in cholangiocarcinoma. Int J Oncol 2019; 55:657-670. [PMID: 31322171 PMCID: PMC6685595 DOI: 10.3892/ijo.2019.4837] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/27/2019] [Indexed: 12/15/2022] Open
Abstract
Cholangiocarcinoma (CCA) is the second most common hepatobiliary cancer after hepatocellular carcinoma. Antiangiogenic therapy has been administered to patients with CCA, but the benefits of this therapy remain unsatisfactory. Improved understanding of the molecular mechanisms underlying angiogenesis in CCA is required. In the present study, the expression of GATA-binding protein 6 (GATA6), lysyl oxidase-like 2 (LOXL2) and vascular endothelial growth factor A (VEGFA), in addition to the microvessel density (MVD), were evaluated by performing immunohistochemical staining of human CCA microarrays. The expression of GATA6/LOXL2 was associated with poor overall survival (P=0.01) and disease-free survival (P=0.02), and was positively associated with VEGFA expression (P=0.02) and MVD (P=0.04). In vitro, western blotting, reverse transcription-quantitative PCR analysis and ELISAs revealed that altered GATA6 and LOXL2 expression regulated the expression levels of secreted VEGFA. Co-immunoprecipitation demonstrated a physical interaction between GATA6 and LOXL2 in CCA cell lines, and the scavenger receptor cysteine-rich domain of LOXL2 interacted with GATA6, which regulated VEGFA mRNA expression and protein secretion, and promoted tube formation. In vivo analyses further revealed that GATA6/LOXL2 promoted VEGFA expression, angiogenesis and tumor growth. The GATA6/LOXL2 complex represents a novel candidate prognostic marker for stratifying patients with CCA. Drugs targeting this complex may possess great therapeutic value in the treatment of CCA.
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Affiliation(s)
- Tao Peng
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Xiang Deng
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Feng Tian
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Zhonghu Li
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Peng Jiang
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Xin Zhao
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Guangyu Chen
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Yan Chen
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Ping Zheng
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Dajiang Li
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
| | - Shuguang Wang
- Hepatobiliary Surgery Institute, Southwest Hospital, Army Medical University, Chongqing 400038, P.R. China
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37
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Škorić-Milosavljević D, Tjong FVY, Barc J, Backx APCM, Clur SAB, van Spaendonck-Zwarts K, Oostra RJ, Lahrouchi N, Beekman L, Bökenkamp R, Barge-Schaapveld DQCM, Mulder BJ, Lodder EM, Bezzina CR, Postma AV. GATA6 mutations: Characterization of two novel patients and a comprehensive overview of the GATA6 genotypic and phenotypic spectrum. Am J Med Genet A 2019; 179:1836-1845. [PMID: 31301121 PMCID: PMC6772993 DOI: 10.1002/ajmg.a.61294] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/29/2019] [Accepted: 06/11/2019] [Indexed: 12/26/2022]
Abstract
The first human mutations in GATA6 were described in a cohort of patients with persistent truncus arteriosus, and the phenotypic spectrum has expanded since then. This study underscores the broad phenotypic spectrum by presenting two patients with de novo GATA6 mutations, both exhibiting complex cardiac defects, pancreatic, and other abnormalities. Furthermore, we provided a detailed overview of all published human genetic variation in/near GATA6 published to date and the associated phenotypes (n = 78). We conclude that the most common phenotypes associated with a mutation in GATA6 were structural cardiac and pancreatic abnormalities, with a penetrance of 87 and 60%, respectively. Other common malformations were gallbladder agenesis, congenital diaphragmatic hernia, and neurocognitive abnormalities, mostly developmental delay. Fifty-eight percent of the mutations were de novo, and these patients more often had an anomaly of intracardiac connections, an anomaly of the great arteries, and hypothyroidism, compared with those with inherited mutations. Functional studies mostly support loss-of-function as the pathophysiological mechanism. In conclusion, GATA6 mutations give a wide range of phenotypic defects, most frequently malformations of the heart and pancreas. This highlights the importance of detailed clinical evaluation of identified carriers to evaluate their full phenotypic spectrum.
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Affiliation(s)
- Doris Škorić-Milosavljević
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
| | - Fleur V Y Tjong
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
| | - Julien Barc
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
| | - Ad P C M Backx
- Department of Pediatric Cardiology, Amsterdam UMC, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Sally-Ann B Clur
- Department of Pediatric Cardiology, Amsterdam UMC, Emma Children's Hospital, Amsterdam, The Netherlands
| | | | - Roelof-Jan Oostra
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Najim Lahrouchi
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
| | - Leander Beekman
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
| | - Regina Bökenkamp
- Department of Pediatric Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Barbara J Mulder
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
| | - Elisabeth M Lodder
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Heart Centre, Amsterdam, The Netherlands
| | - Connie R Bezzina
- Department of Clinical and Experimental Cardiology, Amsterdam UMC, University of Amsterdam, Heart Centre, 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
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Yee J, Kim W, Chang BC, Chung JE, Lee KE, Gwak HS. Genetic variations in the transcription factors GATA4 and GATA6 and bleeding complications in patients receiving warfarin therapy. DRUG DESIGN DEVELOPMENT AND THERAPY 2019; 13:1717-1727. [PMID: 31190750 PMCID: PMC6529806 DOI: 10.2147/dddt.s198018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/19/2019] [Indexed: 12/17/2022]
Abstract
Purpose: GATA4 and GATA6 are known to have potential roles in vascular regulation by affecting vascular smooth muscle cell differentiation and atrial natriuretic peptide levels. The aim of this retrospective study was to investigate the associations between GATA4 and GATA6 polymorphisms and bleeding complication risk at a therapeutic international normalized ratio (INR) in patients with mechanical heart valves. Patients and methods: Study patients were included from the Ewha-Severance Treatment (EAST) Group of Warfarin. It consisted of 229 patients who received warfarin therapy after undergoing mechanical heart valve replacement and maintained a stable INR (INR of 2.0–3.0 for at least three consecutive times). Twenty single-nucleotide polymorphisms including VKORC1, CYP2C9, GATA4, and GATA6 were analyzed. Multivariate logistic regression analysis was employed to investigate the independent risk factors for bleeding complications. To evaluate the potential clinical value of genotyping for preventing bleeding complications in patients with high-risk genotype, the number needed to genotype (NNG) was also calculated. Results: One hundred forty-two patients were included in this study, 21 of whom had bleeding complications. After adjusting covariates, TT genotype carriers of rs13273672 in GATA4 and CC genotype carriers of rs10454095 in GATA6 showed 5.0- (95% CI, 1.6–15.7) and 3.1-fold (95% CI, 1.1–8.7) higher bleeding complications than carriers of C allele and T allele, respectively. NNG for preventing one patient from experiencing bleeding complications in patients with TT genotype of rs13273672 and CC genotype of rs10454095 was 22.2 and 17.5, respectively. Patients with both TT genotype in rs13273672 and CC genotype in rs10454095 showed 8.7-fold (95% CI, 1.7–46.1) higher bleeding complications than those with other genotypes. NNG in patients having both TT genotype in rs13273672 and CC genotype in rs10454095 was calculated to be 40.0. Conclusions: This study showed that GATA4 and GATA6 gene polymorphisms could affect bleeding complications during warfarin treatment in patients with mechanical heart valves.
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Affiliation(s)
- Jeong Yee
- College of Pharmacy & Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Woorim Kim
- College of Pharmacy, Chungbuk National University, Cheongju-si 28160, Korea
| | - Byung Chul Chang
- Department of Thoracic and Cardiovascular Surgery, Bundang CHA Medical Center, CHA University, Seongnam, Gyeonggi-do, Korea.,Department of Thoracic & Cardiovascular Surgery, Yonsei University Medical Center, Seoul 03722, Korea
| | - Jee Eun Chung
- College of Pharmacy, Hanyang University, Ansan 15588, Korea
| | - Kyung Eun Lee
- College of Pharmacy, Chungbuk National University, Cheongju-si 28160, Korea
| | - Hye Sun Gwak
- College of Pharmacy & Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
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Perl E, Waxman JS. Reiterative Mechanisms of Retinoic Acid Signaling during Vertebrate Heart Development. J Dev Biol 2019; 7:jdb7020011. [PMID: 31151214 PMCID: PMC6631158 DOI: 10.3390/jdb7020011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 01/07/2023] Open
Abstract
Tightly-regulated levels of retinoic acid (RA) are critical for promoting normal vertebrate development. The extensive history of research on RA has shown that its proper regulation is essential for cardiac progenitor specification and organogenesis. Here, we discuss the roles of RA signaling and its establishment of networks that drive both early and later steps of normal vertebrate heart development. We focus on studies that highlight the drastic effects alternative levels of RA have on early cardiomyocyte (CM) specification and cardiac chamber morphogenesis, consequences of improper RA synthesis and degradation, and known effectors downstream of RA. We conclude with the implications of these findings to our understanding of cardiac regeneration and the etiologies of congenital heart defects.
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Affiliation(s)
- Eliyahu Perl
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
- The Heart Institute and Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Joshua S Waxman
- The Heart Institute and Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45267, USA.
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40
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Liu J, Cheng H, Xiang M, Zhou L, Wu B, Moskowitz IP, Zhang K, Xie L. Gata4 regulates hedgehog signaling and Gata6 expression for outflow tract development. PLoS Genet 2019; 15:e1007711. [PMID: 31120883 PMCID: PMC6550424 DOI: 10.1371/journal.pgen.1007711] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 06/05/2019] [Accepted: 05/07/2019] [Indexed: 01/09/2023] Open
Abstract
Dominant mutations of Gata4, an essential cardiogenic transcription factor (TF), were known to cause outflow tract (OFT) defects in both human and mouse, but the underlying molecular mechanism was not clear. In this study, Gata4 haploinsufficiency in mice was found to result in OFT defects including double outlet right ventricle (DORV) and ventricular septum defects (VSDs). Gata4 was shown to be required for Hedgehog (Hh)-receiving progenitors within the second heart field (SHF) for normal OFT alignment. Restored cell proliferation in the SHF by knocking-down Pten failed to rescue OFT defects, suggesting that additional cell events under Gata4 regulation is important. SHF Hh-receiving cells failed to migrate properly into the proximal OFT cushion, which is associated with abnormal EMT and cell proliferation in Gata4 haploinsufficiency. The genetic interaction of Hh signaling and Gata4 is further demonstrated to be important for OFT development. Gata4 and Smo double heterozygotes displayed more severe OFT abnormalities including persistent truncus arteriosus (PTA). Restoration of Hedgehog signaling renormalized SHF cell proliferation and migration, and rescued OFT defects in Gata4 haploinsufficiency. In addition, there was enhanced Gata6 expression in the SHF of the Gata4 heterozygotes. The Gata4-responsive repressive sites were identified within 1kbp upstream of the transcription start site of Gata6 by both ChIP-qPCR and luciferase reporter assay. These results suggested a SHF regulatory network comprising of Gata4, Gata6 and Hh-signaling for OFT development. Gata4 is an important transcription factor that regulates the development of the heart. Human possessing a single copy of Gata4 mutation display congenital heart defects (CHD), including double outlet right ventricle (DORV). DORV is an alignment problem in which both the Aorta and Pulmonary Artery originate from the right ventricle, instead of originating from the left and the right ventricles, respectively. In this study, a Gata4 mutant mouse model was used to study how Gata4 mutations cause DORV. We showed that Gata4 is required in the cardiac precursor cells for the normal alignment of the great arteries. Although Gata4 mutations inhibit the rapid increase in the cardiac precursor cell numbers, resolving this problem does not recover the normal alignment of the great arteries. It indicates that there is a migratory issue of the cardiac precursor cells as they navigate to the great arteries during development. The study further showed that a specific molecular signaling, Hh-signaling and Gata6 are responsible to the Gata4 action in the cardiac precursor cells. Importantly, over-activation of the Hh-signaling pathways rescues the DORV in the Gata4 mutant embryos. This study provides a molecular model to explain the ontogeny of a subtype of CHD.
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Affiliation(s)
- Jielin Liu
- Department of Nutrition and Food Sciences, Texas A&M University, College Station, Texas, United States of America
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, North Dakota, United States of America
| | - Henghui Cheng
- Department of Nutrition and Food Sciences, Texas A&M University, College Station, Texas, United States of America
- Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Menglan Xiang
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, North Dakota, United States of America
| | - Lun Zhou
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, North Dakota, United States of America
- Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bingruo Wu
- Departments of Genetics, Pediatrics, and Medicine (Cardiology), Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, United States of America
| | - Ivan P. Moskowitz
- Departments of Pathology and Pediatrics, The University of Chicago, Chicago, Illinois, United States of America
| | - Ke Zhang
- Department of Nutrition and Food Sciences, Texas A&M University, College Station, Texas, United States of America
- Center for Epigenetics & Disease Prevention, Institute of Biosciences & Technology, College of Medicine, Texas A&M University, Houston, Texas, United States of America
| | - Linglin Xie
- Department of Nutrition and Food Sciences, Texas A&M University, College Station, Texas, United States of America
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, North Dakota, United States of America
- * E-mail:
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Asymptomatic Right Ventricular Hypoplasia in Twin Siblings: A Normal Variant or Cause of Early Mortality? Case Rep Pediatr 2019; 2019:6871340. [PMID: 30805240 PMCID: PMC6360540 DOI: 10.1155/2019/6871340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/03/2019] [Indexed: 11/18/2022] Open
Abstract
Right ventricular (RV) hypoplasia may develop secondary to pulmonary or tricuspid valve atresia. These patients are usually symptomatic early in life and need prompt intervention. Isolated RV hypoplasia is a rare congenital heart disease. We report a case of 23-year-old twins who have been monitored for the last 14 years for isolated right ventricular hypoplasia. ECHO and MRI studies showed a small, heavily trabeculated, nonapex-forming RV and mild tricuspid valve insufficiency. The girl has a patent foramen ovale (PFO). Otherwise, the cardiac anatomy and function was normal. They have both been completely asymptomatic from the cardiac standpoint. The family history is remarkable for death of father at the age of 30 years with autopsy suggestive of a hypoplastic RV. The paternal uncle also died at the age of 46 years, and his son has an unidentified congenital heart disease. The family history appears to suggest an autosomal dominant pattern of inheritance with variable expressivity. However, the chromosome microarray analysis of the twins did not identify any variations of clinical significance.
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Thangavel C, Gomes CM, Zderic SA, Javed E, Addya S, Singh J, Das S, Birbe R, Den RB, Rattan S, Deshpande DA, Penn RB, Chacko S, Boopathi E. NF-κB and GATA-Binding Factor 6 Repress Transcription of Caveolins in Bladder Smooth Muscle Hypertrophy. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:847-867. [PMID: 30707892 DOI: 10.1016/j.ajpath.2018.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 12/03/2018] [Accepted: 12/17/2018] [Indexed: 12/26/2022]
Abstract
Caveolins (CAVs) are structural proteins of caveolae that function as signaling platforms to regulate smooth muscle contraction. Loss of CAV protein expression is associated with impaired contraction in obstruction-induced bladder smooth muscle (BSM) hypertrophy. In this study, microarray analysis of bladder RNA revealed down-regulation of CAV1, CAV2, and CAV3 gene transcription in BSM from models of obstructive bladder disease in mice and humans. We identified and characterized regulatory regions responsible for CAV1, CAV2, and CAV3 gene expression in mice with obstruction-induced BSM hypertrophy, and in men with benign prostatic hyperplasia. DNA affinity chromatography and chromatin immunoprecipitation assays revealed a greater increase in binding of GATA-binding factor 6 (GATA-6) and NF-κB to their cognate binding motifs on CAV1, CAV2, and CAV3 promoters in obstructed BSM relative to that observed in control BSM. Knockout of NF-κB subunits, shRNA-mediated knockdown of GATA-6, or pharmacologic inhibition of GATA-6 and NF-κB in BSM increased CAV1, CAV2, and CAV3 transcription and promoter activity. Conversely, overexpression of GATA-6 decreased CAV2 and CAV3 transcription and promoter activity. Collectively, these data provide new insight into the mechanisms by which CAV gene expression is repressed in hypertrophied BSM in obstructive bladder disease.
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Affiliation(s)
| | - Cristiano M Gomes
- Division of Urology, University of Sao Paulo School of Medicine, Hospital das Clinicas, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Stephen A Zderic
- Department of Urology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elham Javed
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Sankar Addya
- Kimmel Cancer Centre, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jagmohan Singh
- Division of Gastroenterology and Hepatology, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Sreya Das
- Kimmel Cancer Centre, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ruth Birbe
- Department of Pathology and Laboratory Medicine, Cooper University Health Care, Camden, New Jersey
| | - Robert B Den
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Satish Rattan
- Division of Gastroenterology and Hepatology, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Deepak A Deshpande
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Raymond B Penn
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Samuel Chacko
- Division of Urology, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ettickan Boopathi
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania; Division of Urology, University of Pennsylvania, Philadelphia, Pennsylvania.
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43
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Chen J, Wang S, Pang S, Cui Y, Yan B, Hawley RG. Functional genetic variants of the GATA4 gene promoter in acute myocardial infarction. Mol Med Rep 2019; 19:2861-2868. [PMID: 30720078 DOI: 10.3892/mmr.2019.9914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/25/2019] [Indexed: 11/05/2022] Open
Abstract
Coronary artery disease (CAD), including acute myocardial infarction (AMI), is a common complex disease; however, the genetic causes remain largely unknown. Recent epidemiological investigations indicated that the incidence of CAD in patients with congenital heart diseases is markedly higher than that observed in healthy controls. It was therefore hypothesized that the dysregulated expression of cardiac developmental genes may be involved in CAD development. GATA binding protein 4 (GATA4) serves essential roles in heart development and coronary vessel formation. In the present study, the GATA4 gene promoter was analyzed in patients with AMI (n=395) and in ethnically‑matched healthy controls (n=397). A total of 14 DNA variants were identified, including two single‑nucleotide polymorphisms. Three novel heterozygous DNA variants (g.31806C>T, g.31900G>C and g.32241C>T) were reported in three patients with AMI. These DNA variants significantly increased the activity of the GATA4 gene promoter. The electrophoretic mobility shift assay revealed that the DNA variant g.32241C>T influenced the binding ability of transcription factors. Taken together, the DNA variants may alter GATA4 gene promoter activity and affect GATA4 levels, thus contributing to AMI development.
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Affiliation(s)
- Jing Chen
- Department of Medicine, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Shuai Wang
- Department of Medicine, Shandong University School of Medicine, Jinan, Shandong 250012, P.R. China
| | - Shuchao Pang
- Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Yinghua Cui
- Division of Cardiology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Bo Yan
- Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Robert G Hawley
- Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC 20037, USA
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44
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Yuan SM. Fetal arrhythmias: Surveillance and management. Hellenic J Cardiol 2018; 60:72-81. [PMID: 30576831 DOI: 10.1016/j.hjc.2018.12.003] [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: 05/30/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022] Open
Abstract
Fetal arrhythmias warrant sophisticated surveillance and management, especially for the high-risk pregnancies. Clinically, fetal arrhythmias can be categorized into 3 types: premature contractions, tachyarrhythmias, and bradyarrhythmias. Fetal arrhythmias include electrocardiography, cardiotocography, echocardiography and magnetocardiography. Oxygen saturation monitoring can be an effective way of fetal surveillance for congenital complete AV block or SVT during labor. Genetic surveillance of fetal arrhythmias may facilitate the understanding of the mechanisms of the arrhythmias and provide theoretical basis for diagnosis and treatment. For fetal benign arrhythmias, usually no treatment but a close follow-up is need, while persistant fetal arrhythmias with congestive heart dysfunction or hydrops fetalis, intrauterine or postnatal treatments are required. The prognoses of fetal arrhythmias depend on the type and severity of fetal arrhythmias and the associated fetal conditions. Responses of fetal arrhythmias to individual treatments and clinical schemes are heterogeneous, and the prognoses are poor particularly under such circumstances.
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Affiliation(s)
- Shi-Min Yuan
- Department of Cardiothoracic Surgery, The First Hospital of Putian, Teaching Hospital, Fujian Medical University, Putian, Fujian Province, People's Republic of China.
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45
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Thompson JJ, Kaur R, Sosa CP, Lee JH, Kashiwagi K, Zhou D, Robertson KD. ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation. Nucleic Acids Res 2018; 46:10034-10051. [PMID: 30085123 PMCID: PMC6212772 DOI: 10.1093/nar/gky682] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
The interplay between transcription factors and epigenetic writers like the DNA methyltransferases (DNMTs), and the role of this interplay in gene expression, is being increasingly appreciated. ZBTB24, a poorly characterized zinc-finger protein, or the de novo methyltransferase DNMT3B, when mutated, cause Immunodeficiency, Centromere Instability, and Facial anomalies (ICF) syndrome, suggesting an underlying mechanistic link. Chromatin immunoprecipitation coupled with loss-of-function approaches in model systems revealed common loci bound by ZBTB24 and DNMT3B, where they function to regulate gene body methylation. Genes coordinately regulated by ZBTB24 and DNMT3B are enriched for molecular mechanisms essential for cellular homeostasis, highlighting the importance of the ZBTB24-DNMT3B interplay in maintaining epigenetic patterns required for normal cellular function. We identify a ZBTB24 DNA binding motif, which is contained within the promoters of most of its transcriptional targets, including CDCA7, AXIN2, and OSTC. Direct binding of ZBTB24 at the promoters of these genes targets them for transcriptional activation. ZBTB24 binding at the promoters of RNF169 and CAMKMT, however, targets them for transcriptional repression. The involvement of ZBTB24 targets in diverse cellular programs, including the VDR/RXR and interferon regulatory pathways, suggest that ZBTB24's role as a transcriptional regulator is not restricted to immune cells.
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Affiliation(s)
- Joyce J Thompson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
| | - Rupinder Kaur
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
| | - Carlos P Sosa
- Clinical Genome Sequencing Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Stabile12-58, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Epigenomics Translational Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Katsunobu Kashiwagi
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Dan Zhou
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Stabile 12-58, Rochester, MN 55905, USA
- Epigenomics Translational Program, Mayo Clinic, Rochester, MN 55905, USA
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46
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Mesothelial to mesenchyme transition as a major developmental and pathological player in trunk organs and their cavities. Commun Biol 2018; 1:170. [PMID: 30345394 PMCID: PMC6191446 DOI: 10.1038/s42003-018-0180-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/28/2018] [Indexed: 12/18/2022] Open
Abstract
The internal organs embedded in the cavities are lined by an epithelial monolayer termed the mesothelium. The mesothelium is increasingly implicated in driving various internal organ pathologies, as many of the normal embryonic developmental pathways acting in mesothelial cells, such as those regulating epithelial-to-mesenchymal transition, also drive disease progression in adult life. Here, we summarize observations from different animal models and organ systems that collectively point toward a central role of epithelial-to-mesenchymal transition in driving tissue fibrosis, acute scarring, and cancer metastasis. Thus, drugs targeting pathways of mesothelium’s transition may have broad therapeutic benefits in patients suffering from these diseases. Tim Koopmans and Yuval Rinkevich review recent findings linking the mesothelium’s embryonic programs that drive epithelial-to-mesenchyme transition with adult pathologies, such as fibrosis, acute scarring, and cancer metastasis. They highlight new avenues for drug development that would target pathways of the mesothelium’s mesenchymal transition.
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47
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Akthar IST, Pichiah PBT, Arunachalam S, Raja S. Adriamycin inhibits embryonic development in zebrafish through downregulation of Kruppel-like factor4. J Biochem Mol Toxicol 2018; 33:e22235. [PMID: 30286259 DOI: 10.1002/jbt.22235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/21/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022]
Abstract
Adriamycin is an effective anticancer drug used in a wide range of cancers. Anticancer drugs modulate oncogenes and nodal regulatory molecules that affect cell differentiation and organismal development. In this study, we explore the effect of adriamycin on Kruppel-like factor4 (Klf4), an essential pluripotent factor by choosing zebrafish embryos as a model system. Klf4 is involved in the regulation of cellular growth, proliferation, and differentiation. In zebrafish embryogenesis, Klf4 is a major regulator of differentiation of polster in the anterior mesendoderm region of cells into hatching gland cells. The importance of this study is to check the effect of adriamycin on embryonic development. We found, adriamycin dose dependently altered the gene expression level of Klf4 that occurs in parallel to its detrimental effect on hatching. Supportively, cathepsin L and cyclase-associated protein1 are the other two markers of hatching that are altered along with Klf4.
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Affiliation(s)
- I Syeda Thabassum Akthar
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamilnadu, India
| | - P B Tirupathi Pichiah
- Department of Animal Sciences, Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - Sankarganesh Arunachalam
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu, India
| | - Sudhakaran Raja
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamilnadu, India
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48
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Swanson JB, Vagnozzi AN, Veniaminova NA, Wong SY. Loss of Gata6 causes dilation of the hair follicle canal and sebaceous duct. Exp Dermatol 2018; 28:345-349. [PMID: 30033638 DOI: 10.1111/exd.13757] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/20/2018] [Indexed: 12/17/2022]
Abstract
The uppermost aspect of the hair follicle, known as the infundibulum or hair canal, provides a passageway for hair shaft egress and sebum secretion. Recent studies have indicated that the infundibulum and sebaceous ducts are lined by molecularly distinct differentiated cells expressing markers including Keratin 79 and Gata6. Here, we ablated Gata6 from the skin and observed dilation of both the hair canal and sebaceous ducts, independent of gender and hair cycle stage. Constitutive loss of Gata6 yielded only a mild delay in depilation-induced entry into anagen, while unperturbed mutant mice possessed overtly normal skin and hair. Furthermore, we noted that Keratin 79 and Gata6 expression and localization did not depend upon each other. Our findings implicate Gata6 in maintaining the upper hair follicle and suggest that regulation of this transcription factor may be compromised in pathologies such as acne or infundibular cystic diseases that are characterized by abnormal expansion of this follicular domain.
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Affiliation(s)
- Jacob B Swanson
- Departments of Dermatology and Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Alicia N Vagnozzi
- Departments of Dermatology and Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Natalia A Veniaminova
- Departments of Dermatology and Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Sunny Y Wong
- Departments of Dermatology and Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
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49
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Yoon CH, Kim TW, Koh SJ, Choi YE, Hur J, Kwon YW, Cho HJ, Kim HS. Gata6 in pluripotent stem cells enhance the potential to differentiate into cardiomyocytes. BMB Rep 2018; 51:85-91. [PMID: 29335067 PMCID: PMC5836562 DOI: 10.5483/bmbrep.2018.51.2.176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Indexed: 01/15/2023] Open
Abstract
Pluripotent stem cell (PSC) variations can cause significant differences in the efficiency of cardiac differentiation. This process is unpredictable, as there is not an adequate indicator at the undifferentiated stage of the PSCs. We compared global gene expression profiles of two PSCs showing significant differences in cardiac differentiation potential. We identified 12 up-regulated genes related to heart development, and we found that 4 genes interacted with multiple genes. Among these genes, Gata6 is the only gene that was significantly induced at the early stage of differentiation of PSCs to cardiomyocytes. Gata6 knock-down in PSCs decreased the efficiency of cardiomyocyte production. In addition, we analyzed 6 mESC lines and 3 iPSC lines and confirmed that a positive correlation exists between Gata6 levels and efficiency of differentiation into cardiomyocytes. In conclusion, Gata6 could be utilized as a biomarker to select the best PSC lines to produce PSC-derived cardiomyocytes for therapeutic purposes. [BMB Reports 2018; 51(2): 85-91].
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Affiliation(s)
- Chang-Hwan Yoon
- Cardiovascular Center & Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Tae-Won Kim
- Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea
| | - Seok-Jin Koh
- Cardiovascular Center & Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Young-Eun Choi
- Innovative Research Institute for Cell Therapy, Seoul National University Hospital, Seoul 03080, Korea
| | - Jin Hur
- Innovative Research Institute for Cell Therapy, Seoul National University Hospital, Seoul 03080, Korea
| | - Yoo-Wook Kwon
- Innovative Research Institute for Cell Therapy, Seoul National University Hospital, Seoul 03080, Korea
| | - Hyun-Jai Cho
- Innovative Research Institute for Cell Therapy, Seoul National University Hospital, Seoul 03080, Korea
| | - Hyo-Soo Kim
- Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080; Innovative Research Institute for Cell Therapy, Seoul National University Hospital, Seoul 03080, Korea
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50
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Marcu R, Choi YJ, Xue J, Fortin CL, Wang Y, Nagao RJ, Xu J, MacDonald JW, Bammler TK, Murry CE, Muczynski K, Stevens KR, Himmelfarb J, Schwartz SM, Zheng Y. Human Organ-Specific Endothelial Cell Heterogeneity. iScience 2018; 4:20-35. [PMID: 30240741 PMCID: PMC6147238 DOI: 10.1016/j.isci.2018.05.003] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022] Open
Abstract
The endothelium first forms in the blood islands in the extra-embryonic yolk sac and then throughout the embryo to establish circulatory networks that further acquire organ-specific properties during development to support diverse organ functions. Here, we investigated the properties of endothelial cells (ECs), isolated from four human major organs-the heart, lung, liver, and kidneys-in individual fetal tissues at three months' gestation, at gene expression, and at cellular function levels. We showed that organ-specific ECs have distinct expression patterns of gene clusters, which support their specific organ development and functions. These ECs displayed distinct barrier properties, angiogenic potential, and metabolic rate and support specific organ functions. Our findings showed the link between human EC heterogeneity and organ development and can be exploited therapeutically to contribute in organ regeneration, disease modeling, as well as guiding differentiation of tissue-specific ECs from human pluripotent stem cells.
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Affiliation(s)
- Raluca Marcu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Yoon Jung Choi
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jun Xue
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Chelsea L Fortin
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Yuliang Wang
- Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Ryan J Nagao
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jin Xu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - James W MacDonald
- Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Charles E Murry
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Kelly R Stevens
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jonathan Himmelfarb
- Department of Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, University of Washington, Seattle, WA, USA
| | | | - Ying Zheng
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, University of Washington, Seattle, WA, USA.
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