51
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Banerjee R, Bultman SJ, Holley D, Hillhouse C, Bain JR, Newgard CB, Muehlbauer MJ, Willis MS. Non-targeted metabolomics of Brg1/Brm double-mutant cardiomyocytes reveals a novel role for SWI/SNF complexes in metabolic homeostasis. Metabolomics 2015; 11:1287-1301. [PMID: 26392817 PMCID: PMC4574504 DOI: 10.1007/s11306-015-0786-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian SWI/SNF chromatin-remodeling complexes utilize either BRG1 or Brm as alternative catalytic subunits to alter the position of nucleosomes and regulate gene expression. Genetic studies have demonstrated that SWI/SNF complexes are required during cardiac development and also protect against cardiovascular disease and cancer. However, Brm constitutive null mutants do not exhibit a cardiomyocyte phenotype and inducible Brg1 conditional mutations in cardiomyocyte do not demonstrate differences until stressed with transverse aortic constriction, where they exhibit a reduction in cardiac hypertrophy. We recently demonstrated the overlapping functions of Brm and Brg1 in vascular endothelial cells and sought here to test if this overlapping function occurred in cardiomyocytes. Brg1/Brm double mutants died within 21 days of severe cardiac dysfunction associated with glycogen accumulation and mitochondrial defects based on histological and ultrastructural analyses. To determine the underlying defects, we performed nontargeted metabolomics analysis of cardiac tissue by GC/MS from a line of Brg1/Brm double-mutant mice, which lack both Brg1 and Brm in cardiomyocytes in an inducible manner, and two groups of controls. Metabolites contributing most significantly to the differences between Brg1/Brm double-mutant and control-group hearts were then determined using the variable importance in projection analysis. Increased cardiac linoleic acid and oleic acid suggest alterations in fatty acid utilization or intake are perturbed in Brg1/Brm double mutants. Conversely, decreased glucose-6-phosphate, fructose-6-phosphate, and myoinositol suggest that glycolysis and glycogen formation are impaired. These novel metabolomics findings provide insight into SWI/SNF-regulated metabolic pathways and will guide mechanistic studies evaluating the role of SWI/SNF complexes in homeostasis and cardiovascular disease prevention.
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Affiliation(s)
- Ranjan Banerjee
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Scott J. Bultman
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Darcy Holley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Carolyn Hillhouse
- Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - James R. Bain
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA. Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Christopher B. Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA. Division of Endocrinology, Metabolism, and Nutrition, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Michael J. Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Monte S. Willis
- Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA. McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA
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52
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van den Berg CW, Okawa S, Chuva de Sousa Lopes SM, van Iperen L, Passier R, Braam SR, Tertoolen LG, del Sol A, Davis RP, Mummery CL. Transcriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells. Development 2015. [PMID: 26209647 DOI: 10.1242/dev.123810] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Differentiated derivatives of human pluripotent stem cells (hPSCs) are often considered immature because they resemble foetal cells more than adult, with hPSC-derived cardiomyocytes (hPSC-CMs) being no exception. Many functional features of these cardiomyocytes, such as their cell morphology, electrophysiological characteristics, sarcomere organization and contraction force, are underdeveloped compared with adult cardiomyocytes. However, relatively little is known about how their gene expression profiles compare with the human foetal heart, in part because of the paucity of data on the human foetal heart at different stages of development. Here, we collected samples of matched ventricles and atria from human foetuses during the first and second trimester of development. This presented a rare opportunity to perform gene expression analysis on the individual chambers of the heart at various stages of development, allowing us to identify not only genes involved in the formation of the heart, but also specific genes upregulated in each of the four chambers and at different stages of development. The data showed that hPSC-CMs had a gene expression profile similar to first trimester foetal heart, but after culture in conditions shown previously to induce maturation, they cluster closer to the second trimester foetal heart samples. In summary, we demonstrate how the gene expression profiles of human foetal heart samples can be used for benchmarking hPSC-CMs and also contribute to determining their equivalent stage of development.
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Affiliation(s)
- Cathelijne W van den Berg
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Satoshi Okawa
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, Avenue du Swing, Belvaux L-4367, Luxembourg
| | | | - Liesbeth van Iperen
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Robert Passier
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Stefan R Braam
- Pluriomics B.V., Biopartner building 3, Galileiweg 8, Leiden 2333 BD, The Netherlands
| | - Leon G Tertoolen
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Antonio del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, Avenue du Swing, Belvaux L-4367, Luxembourg
| | - Richard P Davis
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Christine L Mummery
- Dept. of Anatomy & Embryology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
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53
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Elucidating the mechanisms of transcription regulation during heart development by next-generation sequencing. J Hum Genet 2015. [PMID: 26202577 DOI: 10.1038/jhg.2015.84] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dysregulation of transcription is associated with the pathogenesis of cardiovascular diseases, including congenital heart diseases and heart failure. However, it remains unclear how transcription factors regulate transcription in the heart and which genes are associated with cardiovascular diseases in humans. Development of genome-wide analyses using next-generation sequencers provides powerful methods to determine how these transcription factors and chromatin regulators control gene expressions and to identify causative genes in cardiovascular diseases. These technologies have revealed that transcription during heart development is elaborately regulated by multiple cardiac transcription factors. In this review, we discuss the recent progress toward understanding the molecular mechanisms of how transcriptional dysregulation leads to cardiovascular diseases.
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54
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Gaynullina D, Dweep H, Gloe T, Tarasova OS, Sticht C, Gretz N, Schubert R. Alteration of mRNA and microRNA expression profiles in rat muscular type vasculature in early postnatal development. Sci Rep 2015; 5:11106. [PMID: 26073182 PMCID: PMC4466593 DOI: 10.1038/srep11106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 05/15/2015] [Indexed: 12/23/2022] Open
Abstract
The vascular system is characterized by a high degree of plasticity. In particular, functional and structural remodeling of the arterial system takes place during early postnatal development. However, the mechanisms providing such alterations in the rapidly growing organisms are poorly understood, especially for the peripheral vasculature. To explore this, we performed mRNA- and miRNA microarray analysis on muscular type saphenous arteries of young (10-12 days) and adult (2-3 months) rats. Thirty-eight significant pathways (such as oxidative phosphorylation, MAPK signaling, metabolism, cell cycle, DNA replication and focal adhesion) were obtained on differentially regulated genes during postnatal development. Many differentially regulated genes were determined as target- and miRNA-hubs. We also found 92 miRNAs differentially expressed in arteries of young and adult rats. Several significantly regulated pathways were found on these regulated miRNAs. Interestingly, these biological cascades also contain those significantly enriched pathways that were previously identified based on the differently expressed genes. Our data indicate that the expression of many genes involved in the regulation of pathways that are relevant for different functions in arteries may be under the control of miRNAs and these miRNAs regulate the functional, and structural remodeling occurring in the vascular system during early postnatal development.
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Affiliation(s)
- Dina Gaynullina
- 1] Cardiovascular Physiology, Centre for Biomedicine and Medical Technology Mannheim, Ruprecht-Karls-University Heidelberg, 68167 Mannheim, Germany [2] Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia [3] Department of Physiology, Russian National Research Medical University, Ostrovityanova str. 1, 117997 Moscow, Russia
| | - Harsh Dweep
- Medical Research Center, University of Heidelberg, D-68167 Mannheim, Germany
| | - Torsten Gloe
- Cardiovascular Physiology, Centre for Biomedicine and Medical Technology Mannheim, Ruprecht-Karls-University Heidelberg, 68167 Mannheim, Germany
| | - Olga S Tarasova
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Carsten Sticht
- Medical Research Center, University of Heidelberg, D-68167 Mannheim, Germany
| | - Norbert Gretz
- Medical Research Center, University of Heidelberg, D-68167 Mannheim, Germany
| | - Rudolf Schubert
- Cardiovascular Physiology, Centre for Biomedicine and Medical Technology Mannheim, Ruprecht-Karls-University Heidelberg, 68167 Mannheim, Germany
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55
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Nelissen H, Eeckhout D, Demuynck K, Persiau G, Walton A, van Bel M, Vervoort M, Candaele J, De Block J, Aesaert S, Van Lijsebettens M, Goormachtig S, Vandepoele K, Van Leene J, Muszynski M, Gevaert K, Inzé D, De Jaeger G. Dynamic Changes in ANGUSTIFOLIA3 Complex Composition Reveal a Growth Regulatory Mechanism in the Maize Leaf. THE PLANT CELL 2015; 27:1605-19. [PMID: 26036253 PMCID: PMC4498210 DOI: 10.1105/tpc.15.00269] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/22/2015] [Indexed: 05/16/2023]
Abstract
Most molecular processes during plant development occur with a particular spatio-temporal specificity. Thus far, it has remained technically challenging to capture dynamic protein-protein interactions within a growing organ, where the interplay between cell division and cell expansion is instrumental. Here, we combined high-resolution sampling of the growing maize (Zea mays) leaf with tandem affinity purification followed by mass spectrometry. Our results indicate that the growth-regulating SWI/SNF chromatin remodeling complex associated with ANGUSTIFOLIA3 (AN3) was conserved within growing organs and between dicots and monocots. Moreover, we were able to demonstrate the dynamics of the AN3-interacting proteins within the growing leaf, since copurified GROWTH-REGULATING FACTORs (GRFs) varied throughout the growing leaf. Indeed, GRF1, GRF6, GRF7, GRF12, GRF15, and GRF17 were significantly enriched in the division zone of the growing leaf, while GRF4 and GRF10 levels were comparable between division zone and expansion zone in the growing leaf. These dynamics were also reflected at the mRNA and protein levels, indicating tight developmental regulation of the AN3-associated chromatin remodeling complex. In addition, the phenotypes of maize plants overexpressing miRNA396a-resistant GRF1 support a model proposing that distinct associations of the chromatin remodeling complex with specific GRFs tightly regulate the transition between cell division and cell expansion. Together, our data demonstrate that advancing from static to dynamic protein-protein interaction analysis in a growing organ adds insights in how developmental switches are regulated.
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Affiliation(s)
- Hilde Nelissen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Kirin Demuynck
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Michiel van Bel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Marieke Vervoort
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jasper Candaele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jolien De Block
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Stijn Aesaert
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Michael Muszynski
- Department of Genetics, Development, and Cell Biology, Iowa State University, Iowa 50011-3268
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
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56
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Affiliation(s)
- Pei Han
- a Krannert Institute of Cardiology and Division of Cardiology; Department of Medicine
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57
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Greco CM, Condorelli G. Epigenetic modifications and noncoding RNAs in cardiac hypertrophy and failure. Nat Rev Cardiol 2015; 12:488-97. [DOI: 10.1038/nrcardio.2015.71] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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58
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Yang J, Xu WW, Hu SJ. Heart failure: advanced development in genetics and epigenetics. BIOMED RESEARCH INTERNATIONAL 2015; 2015:352734. [PMID: 25949994 PMCID: PMC4407520 DOI: 10.1155/2015/352734] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/25/2015] [Accepted: 03/19/2015] [Indexed: 01/16/2023]
Abstract
Heart failure (HF) is a complex pathophysiological syndrome that arises from a primary defect in the ability of the heart to take in and/or eject sufficient blood. Genetic mutations associated with familial dilated cardiomyopathy, hypertrophic cardiomyopathy, and arrhythmogenic right ventricular cardiomyopathy can contribute to the various pathologies of HF. Therefore, genetic screening could be an approach for guiding individualized therapies and surveillance. In addition, epigenetic regulation occurs via key mechanisms, including ATP-dependent chromatin remodeling, DNA methylation, histone modification, and RNA-based mechanisms. MicroRNA is also a hot spot in HF research. This review gives an overview of genetic mutations associated with cardiomyopathy and the roles of some epigenetic mechanisms in HF.
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Affiliation(s)
- Jian Yang
- Department of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qing-Chun Road, Hangzhou 310003, China
| | - Wei-wei Xu
- Department of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qing-Chun Road, Hangzhou 310003, China
| | - Shen-jiang Hu
- Department of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qing-Chun Road, Hangzhou 310003, China
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59
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Nandi SS, Mishra PK. Harnessing fetal and adult genetic reprograming for therapy of heart disease. JOURNAL OF NATURE AND SCIENCE 2015; 1:e71. [PMID: 25879081 PMCID: PMC4394627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Heart is the first organ formed during organogenesis. The fetal heart undergoes several structural and functional modifications to form the four-chambered mammalian heart. The adult heart shows different adaptations during compensatory and decompensatory heart failure. However, one common adaptation in the pathological heart is fetal reprogramming, where the adult heart expresses several genes and miRNAs which are active in the fetal stage. The fetal reprogramming in the failing heart raises several questions, such as whether the switch of adult to fetal genetic programming is an adaptive response to cope with adverse remodeling of the heart, does the expression of fetal genes protect the heart during compensatory and/or decompensatory heart failure, does repressing the fetal gene in the failing heart is protective to the heart? To answer these questions, we need to understand the expression of genes and miRNAs that are reprogrammed in the failing heart. In view of this, we provided an overview of differentially expressed genes and miRNAs, and their regulation in this review. Further, we elaborated novel strategies for a plausible future therapy of cardiovascular diseases.
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Affiliation(s)
- Shyam Sundar Nandi
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Paras Kumar Mishra
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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60
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Xu K, Wen M, Duan W, Ren L, Hu F, Xiao J, Wang J, Tao M, Zhang C, Wang J, Zhou Y, Zhang Y, Liu Y, Liu S. Comparative Analysis of Testis Transcriptomes from Triploid and Fertile Diploid Cyprinid Fish1. Biol Reprod 2015; 92:95. [DOI: 10.1095/biolreprod.114.125609] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 03/03/2015] [Indexed: 02/02/2023] Open
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61
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Abstract
Dynamic packaging of DNA into strings of nucleosomes is a major mechanism whereby eukaryotic cells regulate gene expression. Intricate control of nucleosomal structure and assembly governs access of RNA polymerase II to DNA and consequent RNA synthesis. As part of this, post-translational modifications of histone proteins are central to the regulation of chromatin structure, playing vital roles in regulating the activation and repression of gene transcription. In the heart, dynamic homeostasis of histone modification-driven by the actions of modifiers and recruitment of downstream effectors-is a fundamental regulator of the transcriptional reprogramming that occurs in the setting of disease-related stress. Here, we examine the growing evidence for histone modification as a key mechanism governing pathological growth and remodeling of the myocardium.
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Affiliation(s)
- Thomas G Gillette
- From the Departments of Internal Medicine (Cardiology) (T.G.G., J.A.H.) and Molecular Biology (J.A.H.), University of Texas Southwestern Medical Center, Dallas.
| | - Joseph A Hill
- From the Departments of Internal Medicine (Cardiology) (T.G.G., J.A.H.) and Molecular Biology (J.A.H.), University of Texas Southwestern Medical Center, Dallas
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62
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Decoding the complex genetic causes of heart diseases using systems biology. Biophys Rev 2015; 7:141-159. [PMID: 28509974 DOI: 10.1007/s12551-014-0145-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022] Open
Abstract
The pace of disease gene discovery is still much slower than expected, even with the use of cost-effective DNA sequencing and genotyping technologies. It is increasingly clear that many inherited heart diseases have a more complex polygenic aetiology than previously thought. Understanding the role of gene-gene interactions, epigenetics, and non-coding regulatory regions is becoming increasingly critical in predicting the functional consequences of genetic mutations identified by genome-wide association studies and whole-genome or exome sequencing. A systems biology approach is now being widely employed to systematically discover genes that are involved in heart diseases in humans or relevant animal models through bioinformatics. The overarching premise is that the integration of high-quality causal gene regulatory networks (GRNs), genomics, epigenomics, transcriptomics and other genome-wide data will greatly accelerate the discovery of the complex genetic causes of congenital and complex heart diseases. This review summarises state-of-the-art genomic and bioinformatics techniques that are used in accelerating the pace of disease gene discovery in heart diseases. Accompanying this review, we provide an interactive web-resource for systems biology analysis of mammalian heart development and diseases, CardiacCode ( http://CardiacCode.victorchang.edu.au/ ). CardiacCode features a dataset of over 700 pieces of manually curated genetic or molecular perturbation data, which enables the inference of a cardiac-specific GRN of 280 regulatory relationships between 33 regulator genes and 129 target genes. We believe this growing resource will fill an urgent unmet need to fully realise the true potential of predictive and personalised genomic medicine in tackling human heart disease.
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63
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Abstract
Heart development comprises myocyte specification, differentiation and cardiac morphogenesis. These processes are regulated by a group of core cardiac transcription factors in a coordinated temporal and spatial manner. Histone methylation is an emerging epigenetic mechanism for regulating gene transcription. Interplay among cardiac transcription factors and histone lysine modifiers plays important role in heart development. Aberrant expression and mutation of the histone lysine modifiers during development and in adult life can cause either embryonic lethality or congenital heart diseases, and influences the response of adult hearts to pathological stresses. In this review, we describe current body of literature on the role of several common histone methylations and their modifying enzymes in heart development, congenital and adult heart diseases.
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Affiliation(s)
- Qing-Jun Zhang
- Department of Internal Medicine-Cardiology Division & Molecular Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75350, USA
| | - Zhi-Ping Liu
- Department of Internal Medicine-Cardiology Division & Molecular Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75350, USA
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64
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Aguirre A, Montserrat N, Zacchigna S, Nivet E, Hishida T, Krause MN, Kurian L, Ocampo A, Vazquez-Ferrer E, Rodriguez-Esteban C, Kumar S, Moresco JJ, Yates JR, Campistol JM, Sancho-Martinez I, Giacca M, Izpisua Belmonte JC. In vivo activation of a conserved microRNA program induces mammalian heart regeneration. Cell Stem Cell 2014; 15:589-604. [PMID: 25517466 DOI: 10.1016/j.stem.2014.10.003] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 08/19/2014] [Accepted: 10/08/2014] [Indexed: 01/14/2023]
Abstract
Heart failure is a leading cause of mortality and morbidity in the developed world, partly because mammals lack the ability to regenerate heart tissue. Whether this is due to evolutionary loss of regenerative mechanisms present in other organisms or to an inability to activate such mechanisms is currently unclear. Here we decipher mechanisms underlying heart regeneration in adult zebrafish and show that the molecular regulators of this response are conserved in mammals. We identified miR-99/100 and Let-7a/c and their protein targets smarca5 and fntb as critical regulators of cardiomyocyte dedifferentiation and heart regeneration in zebrafish. Although human and murine adult cardiomyocytes fail to elicit an endogenous regenerative response after myocardial infarction, we show that in vivo manipulation of this molecular machinery in mice results in cardiomyocyte dedifferentiation and improved heart functionality after injury. These data provide a proof of concept for identifying and activating conserved molecular programs to regenerate the damaged heart.
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Affiliation(s)
- Aitor Aguirre
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nuria Montserrat
- Center of Regenerative Medicine of Barcelona (CMRB), 08003 Barcelona, Spain
| | - Serena Zacchigna
- International Center for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Emmanuel Nivet
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tomoaki Hishida
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Marie N Krause
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Leo Kurian
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Alejandro Ocampo
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eric Vazquez-Ferrer
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Sachin Kumar
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR-11, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR-11, La Jolla, CA 92037, USA
| | - Josep M Campistol
- Renal Division, Hospital Clinic, University of Barcelona, IDIBAPS, 08036 Barcelona, Spain
| | - Ignacio Sancho-Martinez
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mauro Giacca
- International Center for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
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65
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Petriz BA, Almeida JA, Gomes CPC, Pereira RW, Murad AM, Franco OL. NanoUPLC/MS(E) proteomic analysis reveals modulation on left ventricle proteome from hypertensive rats after exercise training. J Proteomics 2014; 113:351-65. [PMID: 25451014 DOI: 10.1016/j.jprot.2014.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/03/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED NanoUPLC/MS(E) was used to verify the effects of 8weeks of low (SHR-LIT=4) and high (SHR-HIT=4) intensity training over the left ventricle proteome of hypertensive rats (SHR-C=4). Training enhanced the aerobic capacity and reduced the systolic blood pressure in all exercised rats. NanoUPLC/MS(E) identified 250 proteins, with 233 in common to all groups and 16 exclusive to SHR-C, 2 to SHR-LIT, and 2 to the SHR-HIT. Cardiac hypertrophy related proteins appeared only in SHR-C. The SHR-LIT enhanced the abundance of 30 proteins and diminished 6, while SHR-HIT enhanced the abundance of 39 proteins and reduced other 7. The levels of metabolic (β and γ-enolase, adenine phosphoribosultransferase, and cytochrome b-c1), myofibril (myosin light chain 4, tropomyosin α and β-chain), and transporter proteins (hemoglobin, serum albumin, and hemopexin) were increased by both intensities. Transcription regulator and histone variants were enhanced by SHR-LIT and SHR-HIT respectively. SHR-LIT reduced the concentration of myosin binding protein C, while desmin and membrane voltage dependent anion selective channel protein-3 were reduced only by SHR-HIT. In addition, polyubiquitin B and C, and transcription regulators decreased in both intensities. Exercise also increased the concentration of anti-oxidant proteins, peroxiredozin-6 and glutathione peroxidase-1. BIOLOGICAL SIGNIFICANCE Pathologic left ventricle hypertrophy if one of the major outcomes of hypertension being a strong predictor of heart failure. Among the various risk factors for cardiovascular disorders, arterial hypertension is responsible for the highest rates of mortality worldwide. In this way, this present study contribute to the understanding of the molecular mechanisms involved in the attenuation of hypertension and the regression of pathological cardiac hypertrophy induced by exercise training.
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Affiliation(s)
- Bernardo A Petriz
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; UDF - Centro Universitário, Brasília, DF, Brazil
| | - Jeeser A Almeida
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; UDF - Centro Universitário, Brasília, DF, Brazil; Programa de Pós Graduação em Ciências e Tecnologias em Saúde, Universidade de Brasília - UnB, Ceilândia-DF, Brazil
| | - Clarissa P C Gomes
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Rinaldo W Pereira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Programa de Pós-Graduação em Educação Física, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - André M Murad
- Embrapa Recursos Genéticos e Biotecnologia - Laboratório de Biologia Sintética, Brasília-DF, Brazil
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; S-Inova, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande MS, Brazil; Programa de Pós-Graduação em Educação Física, Universidade Católica de Brasília, Brasília-DF, Brazil.
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Waardenberg AJ, Ramialison M, Bouveret R, Harvey RP. Genetic networks governing heart development. Cold Spring Harb Perspect Med 2014; 4:a013839. [PMID: 25280899 PMCID: PMC4208705 DOI: 10.1101/cshperspect.a013839] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Animal genomes contain a code for construction of the body plan from a fertilized egg. Understanding how genome information is deciphered to create the complex multilayered regulatory systems that drive organismal development, and which become altered in disease, is one of the greatest challenges in the biological sciences. The development of methods that effectively represent and communicate the complexity inherent in gene regulatory networks remains a major barrier. This review introduces the philosophy of systems biology and discusses recent progress in understanding the development of the heart at a systems biology level.
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Affiliation(s)
- Ashley J Waardenberg
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Mirana Ramialison
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2052, Australia Stem Cells Australia, Melbourne Brain Centre, University of Melbourne, Victoria 3010, Australia
| | - Romaric Bouveret
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2052, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2052, Australia School of Biotechnology and Biomolecular Sciences, University of New South Wales Faculty of Science, New South Wales 2052, Australia Stem Cells Australia, Melbourne Brain Centre, University of Melbourne, Victoria 3010, Australia
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67
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Shameer K, Klee EW, Dalenberg AK, Kullo IJ. Whole Exome Sequencing Implicates an
INO80D
Mutation in a Syndrome of Aortic Hypoplasia, Premature Atherosclerosis, and Arterial Stiffness. ACTA ACUST UNITED AC 2014; 7:607-14. [DOI: 10.1161/circgenetics.113.000233] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Massively parallel, high-throughput sequencing technology is helping to generate new insights into the genetic basis of human diseases. We used whole exome sequencing to identify the mutation underlying a syndrome affecting 2 siblings with aortic hypoplasia, calcific atherosclerosis, systolic hypertension, and premature cataract.
Methods and Results—
Exonic regions were captured and sequenced using a next-generation sequencing platform to generate 100 bases paired-end reads. A computational genomic data analysis pipeline was used to perform quality control, align reads to a reference genome, and identify genetic variants; findings were confirmed using a different exome analyses pipeline. The 2 siblings were homozygous for a rare missense mutation (Ser818Cys) in
INO80D
, a subunit of the human INO80 chromatin remodeling complex. Homozygosity mapping and Sanger sequencing confirmed that the mutation is located in one of the runs of homozygosity on chromosome 2.
INO80D
encodes a key subunit of the human IN080 complex, a multiprotein complex involved in DNA binding, chromatin modification, organization of chromosome structure, and ATP-dependent nucleosome sliding. By introducing a new disulphide-bond in the protein product and also disrupting the composition of low-complexity regions, the Ser818Cys mutation may affect INO80D function, protein–protein interactions, and chromatin remodeling.
Conclusions—
Our findings suggest a link between the Ser818Cys mutation in
INO80D
, a subunit of the human INO80 chromatin remodeling complex, and accelerated arterial aging.
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Affiliation(s)
- Khader Shameer
- From the Division of Cardiovascular Diseases (K.S., A.K.D., I.J.K.) and Biomedical Statistics and Informatics, Departments of Health Sciences Research and Laboratory Medicine and Pathology (E.W.K.), Mayo Clinic, Rochester MN
| | - Eric W. Klee
- From the Division of Cardiovascular Diseases (K.S., A.K.D., I.J.K.) and Biomedical Statistics and Informatics, Departments of Health Sciences Research and Laboratory Medicine and Pathology (E.W.K.), Mayo Clinic, Rochester MN
| | - Angela K. Dalenberg
- From the Division of Cardiovascular Diseases (K.S., A.K.D., I.J.K.) and Biomedical Statistics and Informatics, Departments of Health Sciences Research and Laboratory Medicine and Pathology (E.W.K.), Mayo Clinic, Rochester MN
| | - Iftikhar J. Kullo
- From the Division of Cardiovascular Diseases (K.S., A.K.D., I.J.K.) and Biomedical Statistics and Informatics, Departments of Health Sciences Research and Laboratory Medicine and Pathology (E.W.K.), Mayo Clinic, Rochester MN
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68
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Garnatz AS, Gao Z, Broman M, Martens S, Earley JU, Svensson EC. FOG-2 mediated recruitment of the NuRD complex regulates cardiomyocyte proliferation during heart development. Dev Biol 2014; 395:50-61. [PMID: 25196150 DOI: 10.1016/j.ydbio.2014.08.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 08/05/2014] [Accepted: 08/26/2014] [Indexed: 12/21/2022]
Abstract
FOG-2 is a multi-zinc finger protein that binds the transcriptional activator GATA4 and modulates GATA4-mediated regulation of target genes during heart development. Our previous work has demonstrated that the Nucleosome Remodeling and Deacetylase (NuRD) complex physically interacts with FOG-2 and is necessary for FOG-2 mediated repression of GATA4 activity in vitro. However, the relevance of this interaction for FOG-2 function in vivo has remained unclear. In this report, we demonstrate the importance of FOG-2/NuRD interaction through the generation and characterization of mice homozygous for a mutation in FOG-2 that disrupts NuRD binding (FOG-2(R3K5A)). These mice exhibit a perinatal lethality and have multiple cardiac malformations, including ventricular and atrial septal defects and a thin ventricular myocardium. To investigate the etiology of the thin myocardium, we measured the rate of cardiomyocyte proliferation in wild-type and FOG-2(R3K5A) developing hearts. We found cardiomyocyte proliferation was reduced by 31±8% in FOG-2(R3K5A) mice. Gene expression analysis indicated that the cell cycle inhibitor Cdkn1a (p21(cip1)) is up-regulated 2.0±0.2-fold in FOG-2(R3K5A) hearts. In addition, we demonstrate that FOG-2 can directly repress the activity of the Cdkn1a gene promoter, suggesting a model by which FOG-2/NuRD promotes ventricular wall thickening by repression of this cell cycle inhibitor. Consistent with this notion, the genetic ablation of Cdkn1a in FOG-2(R3K5A) mice leads to an improvement in left ventricular function and a partial rescue of left ventricular wall thickness. Taken together, our results define a novel mechanism in which FOG-2/NuRD interaction is required for cardiomyocyte proliferation by directly down-regulating the cell cycle inhibitor Cdkn1a during heart development.
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Affiliation(s)
- Audrey S Garnatz
- Committee on Development, Regeneration, and Stem Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Zhiguang Gao
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Broman
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Spencer Martens
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Judy U Earley
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Eric C Svensson
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; Committee on Development, Regeneration, and Stem Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
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69
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Mitić T, Caporali A, Floris I, Meloni M, Marchetti M, Urrutia R, Angelini GD, Emanueli C. EZH2 modulates angiogenesis in vitro and in a mouse model of limb ischemia. Mol Ther 2014; 23:32-42. [PMID: 25189741 PMCID: PMC4426795 DOI: 10.1038/mt.2014.163] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/23/2014] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms may regulate the expression of pro-angiogenic genes, thus affecting reparative angiogenesis in ischemic limbs. The enhancer of zest homolog-2 (EZH2) induces thtrimethylation of lysine 27 on histone H3 (H3K27me3), which represses gene transcription. We explored (i) if EZH2 expression is regulated by hypoxia and ischemia; (ii) the impact of EZH2 on the expression of two pro-angiogenic genes: eNOS and BDNF; (iii) the functional effect of EZH2 inhibition on cultured endothelial cells (ECs); (iv) the therapeutic potential of EZH2 inhibition in a mouse model of limb ischemia (LI). EZH2 expression was increased in cultured ECs exposed to hypoxia (control: normoxia) and in ECs extracted from mouse ischemic limb muscles (control: absence of ischemia). EZH2 increased the H3K27me3 abundance onto regulatory regions of eNOS and BDNF promoters. In vitro RNA silencing or pharmacological inhibition by 3-deazaneplanocin (DZNep) of EZH2 increased eNOS and BDNF mRNA and protein levels and enhanced functional capacities (migration, angiogenesis) of ECs under either normoxia or hypoxia. In mice with experimentally induced LI, DZNep increased angiogenesis in ischaemic muscles, the circulating levels of pro-angiogenic hematopoietic cells and blood flow recovery. Targeting EZH2 for inhibition may open new therapeutic avenues for patients with limb ischemia.
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Affiliation(s)
- Tijana Mitić
- Bristol Heart Institute, School of Clinical Sciences, University of Bristol, England, UK
| | - Andrea Caporali
- 1] Bristol Heart Institute, School of Clinical Sciences, University of Bristol, England, UK [2] Center for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Scotland, UK
| | - Ilaria Floris
- Bristol Heart Institute, School of Clinical Sciences, University of Bristol, England, UK
| | - Marco Meloni
- Bristol Heart Institute, School of Clinical Sciences, University of Bristol, England, UK
| | - Micol Marchetti
- Bristol Heart Institute, School of Clinical Sciences, University of Bristol, England, UK
| | - Raul Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Mayo Clinic, Rochester, Minnesota, USA
| | - Gianni D Angelini
- 1] Bristol Heart Institute, School of Clinical Sciences, University of Bristol, England, UK [2] National Heart and Lung Institute, Hammersmith Campus, Imperial College of London, London, England, UK
| | - Costanza Emanueli
- 1] Bristol Heart Institute, School of Clinical Sciences, University of Bristol, England, UK [2] National Heart and Lung Institute, Hammersmith Campus, Imperial College of London, London, England, UK
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70
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Billerey C, Boussaha M, Esquerré D, Rebours E, Djari A, Meersseman C, Klopp C, Gautheret D, Rocha D. Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics 2014; 15:499. [PMID: 24948191 PMCID: PMC4073507 DOI: 10.1186/1471-2164-15-499] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/13/2014] [Indexed: 01/24/2023] Open
Abstract
Background The advent of large-scale gene expression technologies has helped to reveal in eukaryotic cells, the existence of thousands of non-coding transcripts, whose function and significance remain mostly poorly understood. Among these non-coding transcripts, long non-coding RNAs (lncRNAs) are the least well-studied but are emerging as key regulators of diverse cellular processes. In the present study, we performed a survey in bovine Longissimus thoraci of lincRNAs (long intergenic non-coding RNAs not overlapping protein-coding transcripts). To our knowledge, this represents the first such study in bovine muscle. Results To identify lincRNAs, we used paired-end RNA sequencing (RNA-Seq) to explore the transcriptomes of Longissimus thoraci from nine Limousin bull calves. Approximately 14–45 million paired-end reads were obtained per library. A total of 30,548 different transcripts were identified. Using a computational pipeline, we defined a stringent set of 584 different lincRNAs with 418 lincRNAs found in all nine muscle samples. Bovine lincRNAs share characteristics seen in their mammalian counterparts: relatively short transcript and gene lengths, low exon number and significantly lower expression, compared to protein-encoding genes. As for the first time, our study identified lincRNAs from nine different samples from the same tissue, it is possible to analyse the inter-individual variability of the gene expression level of the identified lincRNAs. Interestingly, there was a significant difference when we compared the expression variation of the 418 lincRNAs with the 10,775 known selected protein-encoding genes found in all muscle samples. In addition, we found 2,083 pairs of lincRNA/protein-encoding genes showing a highly significant correlated expression. Fourteen lincRNAs were selected and 13 were validated by RT-PCR. Some of the lincRNAs expressed in muscle are located within quantitative trait loci for meat quality traits. Conclusions Our study provides a glimpse into the lincRNA content of bovine muscle and will facilitate future experimental studies to unravel the function of these molecules. It may prove useful to elucidate their effect on mechanisms underlying the genetic variability of meat quality traits. This catalog will complement the list of lincRNAs already discovered in cattle and therefore will help to better annotate the bovine genome. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-499) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Dominique Rocha
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France.
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71
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Epigenetics in cardiac development, function, and disease. Cell Tissue Res 2014; 356:585-600. [DOI: 10.1007/s00441-014-1887-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/02/2014] [Indexed: 12/13/2022]
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72
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Mathiyalagan P, Keating ST, Du XJ, El-Osta A. Chromatin modifications remodel cardiac gene expression. Cardiovasc Res 2014; 103:7-16. [PMID: 24812277 DOI: 10.1093/cvr/cvu122] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Signalling and transcriptional control involve precise programmes of gene activation and suppression necessary for cardiovascular physiology. Deep sequencing of DNA-bound transcription factors reveals a remarkable complexity of co-activators or co-repressors that serve to alter chromatin modification and regulate gene expression. The regulated complexes characterized by genome-wide mapping implicate the recruitment and exchange of proteins with specific enzymatic activities that include roles for histone acetylation and methylation in key developmental programmes of the heart. As for transcriptional changes in response to pathological stress, co-regulatory complexes are also differentially utilized to regulate genes in cardiac disease. Members of the histone deacetylase (HDAC) family catalyse the removal of acetyl groups from proteins whose pharmacological inhibition has profound effects preventing heart failure. HDACs interact with a complex co-regulatory network of transcription factors, chromatin-remodelling complexes, and specific histone modifiers to regulate gene expression in the heart. For example, the histone methyltransferase (HMT), enhancer of zeste homolog 2 (Ezh2), is regulated by HDAC inhibition and associated with pathological cardiac hypertrophy. The challenge now is to target the activity of enzymes involved in protein modification to prevent or reverse the expression of genes implicated with cardiac hypertrophy. In this review, we discuss the role of HDACs and HMTs with a focus on chromatin modification and gene function as well as the clinical treatment of heart failure.
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Affiliation(s)
- Prabhu Mathiyalagan
- Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Samuel T Keating
- Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
| | - Xiao-Jun Du
- Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
| | - Assam El-Osta
- Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
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Elevated methylation of the RXRA promoter region may be responsible for its downregulated expression in the myocardium of patients with TOF. Pediatr Res 2014; 75:588-94. [PMID: 24513686 DOI: 10.1038/pr.2014.17] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 11/21/2013] [Indexed: 11/08/2022]
Abstract
BACKGROUND As an important component of retinoid acid signaling pathway, the retinoid X receptor α (RXRA) is considered to play an important role in the pathogenesis of tetralogy of Fallot (TOF). METHODS The expression level of RXRA mRNA and the methylation status of the RXRA promoter region in 26 patients with TOF and 6 controls were detected using real-time PCR and bisulfite-specific PCR and cloning-based sequencing, respectively. Dual-luciferase reporter assays, combined with in vitro methylation assay, were performed to determine the transcriptional regulatory activity of unmethylated and methylated CpG regions in the RXRA promoter. RESULTS The mRNA expression of RXRA in the right ventricular outflow tract (RVOT) myocardium was significantly decreased in patients with TOF compared with that in the controls. The methylation status of region -1453 to -1000 containing CpG sites 1-23 in the RXRA promoter region was higher in patients with TOF than that in the controls. This region contained several transcription factor sites. In addition, dual-luciferase reporter assays combined with methylation assay in vitro showed that this region had transcriptional regulatory activity, which can be depressed by the methylation of this region. CONCLUSION The elevated methylation at RXRA promoter may be responsible for the downregulated mRNA expression in RVOT myocardium of patients with TOF.
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74
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Watson CJ, Collier P, Tea I, Neary R, Watson JA, Robinson C, Phelan D, Ledwidge MT, McDonald KM, McCann A, Sharaf O, Baugh JA. Hypoxia-induced epigenetic modifications are associated with cardiac tissue fibrosis and the development of a myofibroblast-like phenotype. Hum Mol Genet 2014; 23:2176-88. [PMID: 24301681 DOI: 10.1093/hmg/ddt614] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Ischemia caused by coronary artery disease and myocardial infarction leads to aberrant ventricular remodeling and cardiac fibrosis. This occurs partly through accumulation of gene expression changes in resident fibroblasts, resulting in an overactive fibrotic phenotype. Long-term adaptation to a hypoxic insult is likely to require significant modification of chromatin structure in order to maintain the fibrotic phenotype. Epigenetic changes may play an important role in modulating hypoxia-induced fibrosis within the heart. Therefore, the aim of the study was to investigate the potential pro-fibrotic impact of hypoxia on cardiac fibroblasts and determine whether alterations in DNA methylation could play a role in this process. This study found that within human cardiac tissue, the degree of hypoxia was associated with increased expression of collagen 1 and alpha-smooth muscle actin (ASMA). In addition, human cardiac fibroblast cells exposed to prolonged 1% hypoxia resulted in a pro-fibrotic state. These hypoxia-induced pro-fibrotic changes were associated with global DNA hypermethylation and increased expression of the DNA methyltransferase (DNMT) enzymes DNMT1 and DNMT3B. Expression of these methylating enzymes was shown to be regulated by hypoxia-inducible factor (HIF)-1α. Using siRNA to block DNMT3B expression significantly reduced collagen 1 and ASMA expression. In addition, application of the DNMT inhibitor 5-aza-2'-deoxycytidine suppressed the pro-fibrotic effects of TGFβ. Epigenetic modifications and changes in the epigenetic machinery identified in cardiac fibroblasts during prolonged hypoxia may contribute to the pro-fibrotic nature of the ischemic milieu. Targeting up-regulated expression of DNMTs in ischemic heart disease may prove to be a valuable therapeutic approach.
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Affiliation(s)
- Chris J Watson
- School of Medicine & Medical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Bernstein D. Introduction to the series: challenges and opportunities in pediatric heart failure and transplantation. Circulation 2014; 129:112-4. [PMID: 24396014 DOI: 10.1161/circulationaha.113.006102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Daniel Bernstein
- Department of Pediatrics and the Stanford Cardiovascular Institute, Stanford University, Stanford, CA
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76
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Bevilacqua A, Willis MS, Bultman SJ. SWI/SNF chromatin-remodeling complexes in cardiovascular development and disease. Cardiovasc Pathol 2014; 23:85-91. [PMID: 24183004 PMCID: PMC3946279 DOI: 10.1016/j.carpath.2013.09.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 12/19/2022] Open
Abstract
Our understanding of congenital heart defects has been recently advanced by whole exome sequencing projects, which have identified de novo mutations in many genes encoding epigenetic regulators. Notably, multiple subunits of switching defective/sucrose non-fermenting (SWI/SNF) chromatin-remodeling complexes have been identified as strong candidates underlying these defects because they physically and functionally interact with cardiogenic transcription factors critical to cardiac development, such as TBX5, GATA-4, and NKX2-5. While these studies indicate a critical role of SWI/SNF complexes in cardiac development and congenital heart disease, many exciting new discoveries have identified their critical role in the adult heart in both physiological and pathological conditions involving multiple cell types in the heart, including cardiomyocytes, vascular endothelial cells, pericytes, and neural crest cells. This review summarizes the role of SWI/SNF chromatin-remodeling complexes in cardiac development, congenital heart disease, cardiac hypertrophy, and vascular endothelial cell survival. Although the clinical relevance of SWI/SNF mutations has traditionally been focused primarily on their role in tumor suppression, these recent studies illustrate their critical role in the heart whereby they regulate cell proliferation, differentiation, and apoptosis of cardiac derived cell lines.
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Affiliation(s)
- Ariana Bevilacqua
- Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Monte S Willis
- Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA.
| | - Scott J Bultman
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA.
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Karppinen S, Rapila R, Mäkikallio K, Hänninen SL, Rysä J, Vuolteenaho O, Tavi P. Endothelin-1 signalling controls early embryonic heart rate in vitro and in vivo. Acta Physiol (Oxf) 2014; 210:369-80. [PMID: 24325624 DOI: 10.1111/apha.12194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 04/10/2013] [Accepted: 01/11/2013] [Indexed: 12/13/2022]
Abstract
AIM Spontaneous activity of embryonic cardiomyocytes originates from sarcoplasmic reticulum (SR) Ca(2+) release during early cardiogenesis. However, the regulation of heart rate during embryonic development is still not clear. The aim of this study was to determine how endothelin-1 (ET-1) affects the heart rate of embryonic mice, as well as the pathway through which it exerts its effects. METHODS The effects of ET-1 and ET-1 receptor inhibition on cardiac contraction were studied using confocal Ca(2+) imaging of isolated mouse embryonic ventricular cardiomyocytes and ultrasonographic examination of embryonic cardiac contractions in utero. In addition, the amount of ET-1 peptide and ET receptor a (ETa) and b (ETb) mRNA levels were measured during different stages of development of the cardiac muscle. RESULTS High ET-1 concentration and expression of both ETa and ETb receptors was observed in early cardiac tissue. ET-1 was found to increase the frequency of spontaneous Ca(2+) oscillations in E10.5 embryonic cardiomyocytes in vitro. Non-specific inhibition of ET receptors with tezosentan caused arrhythmia and bradycardia in isolated embryonic cardiomyocytes and in whole embryonic hearts both in vitro (E10.5) and in utero (E12.5). ET-1-mediated stimulation of early heart rate was found to occur via ETb receptors and subsequent inositol trisphosphate receptor activation and increased SR Ca(2+) leak. CONCLUSION Endothelin-1 is required to maintain a sufficient heart rate, as well as to prevent arrhythmia during early development of the mouse heart. This is achieved through ETb receptor, which stimulates Ca(2+) leak through IP3 receptors.
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Affiliation(s)
- S. Karppinen
- Department of Biotechnology and Molecular Medicine; A.I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio Finland
| | - R. Rapila
- Department of Biotechnology and Molecular Medicine; A.I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio Finland
| | - K. Mäkikallio
- Department of Obstetrics and Gynecology; University of Oulu; Oulu Finland
| | - S. L. Hänninen
- Department of Physiology; Institute of Biomedicine; University of Oulu; Oulu Finland
| | - J. Rysä
- Department of Pharmacology and Toxicology; Institute of Biomedicine; University of Oulu; Oulu Finland
| | - O. Vuolteenaho
- Department of Physiology; Institute of Biomedicine; University of Oulu; Oulu Finland
| | - P. Tavi
- Department of Biotechnology and Molecular Medicine; A.I. Virtanen Institute for Molecular Sciences; University of Eastern Finland; Kuopio Finland
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78
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Mathiyalagan P, Okabe J, Chang L, Su Y, Du XJ, El-Osta A. The primary microRNA-208b interacts with Polycomb-group protein, Ezh2, to regulate gene expression in the heart. Nucleic Acids Res 2014; 42:790-803. [PMID: 24137001 PMCID: PMC3902903 DOI: 10.1093/nar/gkt896] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 09/12/2013] [Accepted: 09/12/2013] [Indexed: 12/12/2022] Open
Abstract
The Polycomb-group protein, Ezh2, is required for epigenetic gene silencing in the adult heart by unknown mechanism. We investigated the role of Ezh2 and non-coding RNAs in a mouse model of pressure overload using transverse aortic constriction (TAC) attenuated by the prototypical histone deacetylase inhibitor, trichostatin A (TSA). Chromatin immunoprecipitation of TAC and TAC+TSA hearts suggests interaction of Ezh2 and primary microRNA-208b (pri-miR-208b) in the regulation of hypertrophic gene expression. RNAi silencing of pri-miR-208b and Ezh2 validate pri-miR-208b-mediated transcriptional silencing of genes implicated in cardiac hypertrophy including the suppression of the bi-directional promoter (bdP) of the cardiac myosin heavy chain genes. In TAC mouse heart, TSA attenuated Ezh2 binding to bdP and restored antisense β-MHC and α-MHC gene expression. RNA-chromatin immunoprecipitation experiments in TAC hearts also show increased pri-miR-208b dependent-chromatin binding. These results are the first description by which primary miR interactions serve to integrate chromatin modifications and the transcriptional response to distinct signaling cues in the heart. These studies provide a framework for MHC expression and regulation of genes implicated in pathological remodeling of ventricular hypertrophy.
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Affiliation(s)
- Prabhu Mathiyalagan
- Epigenetics in Human Health and Disease Laboratory, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Experimental Cardiology, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia and Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
| | - Jun Okabe
- Epigenetics in Human Health and Disease Laboratory, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Experimental Cardiology, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia and Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
| | - Lisa Chang
- Epigenetics in Human Health and Disease Laboratory, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Experimental Cardiology, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia and Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
| | - Yidan Su
- Epigenetics in Human Health and Disease Laboratory, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Experimental Cardiology, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia and Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
| | - Xiao-Jun Du
- Epigenetics in Human Health and Disease Laboratory, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Experimental Cardiology, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia and Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Experimental Cardiology, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia and Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
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79
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Monte E, Mouillesseaux K, Chen H, Kimball T, Ren S, Wang Y, Chen JN, Vondriska TM, Franklin S. Systems proteomics of cardiac chromatin identifies nucleolin as a regulator of growth and cellular plasticity in cardiomyocytes. Am J Physiol Heart Circ Physiol 2013; 305:H1624-38. [PMID: 24077883 PMCID: PMC3882469 DOI: 10.1152/ajpheart.00529.2013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/10/2013] [Indexed: 11/22/2022]
Abstract
Myocyte hypertrophy antecedent to heart failure involves changes in global gene expression, although the preceding mechanisms to coordinate DNA accessibility on a genomic scale are unknown. Chromatin-associated proteins alter chromatin structure by changing their association with DNA, thereby altering the gene expression profile. Little is known about the global changes in chromatin subproteomes that accompany heart failure, and the mechanisms by which these proteins alter chromatin structure. The present study tests the fundamental hypothesis that cardiac growth and plasticity in the setting of disease recapitulates conserved developmental chromatin remodeling events. We used quantitative proteomics to identify chromatin-associated proteins extracted via detergent and to quantify changes in their abundance during disease. Our study identified 321 proteins in this subproteome, demonstrating it to have modest conservation (37%) with that revealed using strong acid. Of these proteins, 176 exhibited altered expression during cardiac hypertrophy and failure; we conducted extensive functional characterization of one of these proteins, Nucleolin. Morpholino-based knockdown of nucleolin nearly abolished protein expression but surprisingly had little impact on gross morphological development. However, hearts of fish lacking Nucleolin displayed severe developmental impairment, abnormal chamber patterning and functional deficits, ostensibly due to defects in cardiac looping and myocyte differentiation. The mechanisms underlying these defects involve perturbed bone morphogenetic protein 4 expression, decreased rRNA transcription, and a shift to more heterochromatic chromatin. This study reports the quantitative analysis of a new chromatin subproteome in the normal and diseased mouse heart. Validation studies in the complementary model system of zebrafish examine the role of Nucleolin to orchestrate genomic reprogramming events shared between development and disease.
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Affiliation(s)
- Emma Monte
- Department of Anesthesiology, University of California, Los Angeles, Los Angeles, California
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80
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Papait R, Kunderfranco P, Stirparo GG, Latronico MVG, Condorelli G. Long noncoding RNA: a new player of heart failure? J Cardiovasc Transl Res 2013; 6:876-83. [PMID: 23835777 PMCID: PMC3838575 DOI: 10.1007/s12265-013-9488-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/14/2013] [Indexed: 01/10/2023]
Abstract
One the most important discoveries of the post-genomic era is that a large fraction of the genome transcribes a heterogeneous population of noncoding RNAs (ncRNA). ncRNAs shorter than 200 nucleotides are usually identified as short/small ncRNAs--examples include PIWI-interacting RNAs, small interfering RNAs, and microRNAs (miRNAs)--whereas those longer than 200 nucleotides are classified as long ncRNAs (lncRNAs). These molecules are emerging as important regulators of cellular process, such as development, differentiation, and metabolism. Not surprisingly, ncRNAs are involved also in human diseases, such as cancer and metabolic and neuronal disorders. Although the role of miRNAs is being largely investigated in cardiovascular biology, little is known about other classes of ncRNA in this field. However, recent reports have started to reveal the importance of lncRNA in heart development and suggest also an involvement in heart failure. Here, we will discuss these reports and the therapeutic potential of lncRNA for heart failure.
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Affiliation(s)
- Roberto Papait
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, MI 20098 Italy
- Institute of Genetics and Biomedical Research, National Research Council of Italy (CNR), Rozzano, MI 20098 Italy
| | - Paolo Kunderfranco
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, MI 20098 Italy
| | - Giuliano Giuseppe Stirparo
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, MI 20098 Italy
- University of Milan, Milan, 20100 Italy
| | | | - Gianluigi Condorelli
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, MI 20098 Italy
- University of Milan, Milan, 20100 Italy
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81
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Recent advances in cardiovascular development. Circ Res 2013; 113:e102-5. [PMID: 24201114 DOI: 10.1161/circresaha.113.302820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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82
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Mathiyalagan P, Keating ST, Du XJ, El-Osta A. Interplay of chromatin modifications and non-coding RNAs in the heart. Epigenetics 2013; 9:101-12. [PMID: 24247090 DOI: 10.4161/epi.26405] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Precisely regulated patterns of gene expression are dependent on the binding of transcription factors and chromatin-associated determinants referred to as co-activators and co-repressors. These regulatory components function with the core transcriptional machinery to serve in critical activities to alter chromatin modification and regulate gene expression. While we are beginning to understand that cell-type specific patterns of gene expression are necessary to achieve selective cardiovascular developmental programs, we still do not know the molecular machineries that localize these determinants in the heart. With clear implications for the epigenetic control of gene expression signatures, the ENCODE (Encyclopedia of DNA Elements) Project Consortium determined that about 90% of the human genome is transcribed while only 1-2% of transcripts encode proteins. Emerging evidence suggests that non-coding RNA (ncRNA) serves as a signal for decoding chromatin modifications and provides a potential molecular basis for cell type-specific and promoter-specific patterns of gene expression. The discovery of the histone methyltransferase enzyme EZH2 in the regulation of gene expression patterns implicated in cardiac hypertrophy suggests a novel role for chromatin-associated ncRNAs and is the focus of this article.
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Affiliation(s)
- Prabhu Mathiyalagan
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia
| | - Samuel T Keating
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia
| | - Xiao-Jun Du
- Experimental Cardiology Laboratory; Baker IDI Heart and Diabetes Institute; Melbourne, VIC Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia; Epigenomics Profiling Facility; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia; Department of Pathology; The University of Melbourne; Melbourne, VIC Australia; Faculty of Medicine; Monash University; Melbourne, VIC Australia
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83
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Luna-Zurita L, Bruneau BG. Chromatin modulators as facilitating factors in cellular reprogramming. Curr Opin Genet Dev 2013; 23:556-61. [PMID: 23993229 DOI: 10.1016/j.gde.2013.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 10/26/2022]
Abstract
In the last few years, cellular reprogramming has emerged as a means to alter cellular identity and generate diverse cell types for disease modeling, drug testing, and potential therapeutic use. Since each cell type is a result of a specific gene expression profile finely regulated by the activity of a repertoire of transcription factors (TFs), reprogramming approaches have, thus far, been relatively inefficient and based largely on the forced expression of selective cell type-specific TFs. TFs function within the confines of chromatin, and the chromatin states can in turn be modulated by TF activity. Therefore, the knowledge of how chromatin remodeling factors alter chromatin structure, control TF activity and gene expression has led to an improved reprogramming efficiency and extended the number of cellular types that can be generated by cellular reprogramming. Here we review recent insights into the role and mechanisms by which chromatin remodeling, histone modifications, and DNA methylation contribute to cellular differentiation and reprogramming.
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Affiliation(s)
- Luis Luna-Zurita
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
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84
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Fang F, Chen D, Yu L, Dai X, Yang Y, Tian W, Cheng X, Xu H, Weng X, Fang M, Zhou J, Gao Y, Chen Q, Xu Y. Proinflammatory stimuli engage Brahma related gene 1 and Brahma in endothelial injury. Circ Res 2013; 113:986-96. [PMID: 23963727 DOI: 10.1161/circresaha.113.301296] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RATIONALE Endothelial dysfunction inflicted by inflammation is found in a host of cardiovascular pathologies. One hallmark event in this process is the aggregation and adhesion of leukocyte to the vessel wall mediated by the upregulation of adhesion molecules (CAM) in endothelial cells at the transcriptional level. The epigenetic modulator(s) of CAM transactivation and its underlying pathophysiological relevance remain poorly defined. OBJECTIVE Our goal was to determine the involvement of Brahma related gene 1 (Brg1) and Brahma (Brm) in CAM transactivation and its relevance in the pathogenesis of atherosclerosis. METHODS AND RESULTS In the present study, we report that proinflammatory stimuli augmented the expression of Brg1 and Brm in vitro in cultured endothelial cells and in vivo in arteries isolated from rodents. Overexpression of Brg1 and Brm promoted while knockdown of Brg1 and Brm abrogated transactivation of adhesion molecules and leukocyte adhesion induced by inflammatory signals. Brg1 and Brm interacted with and were recruited to the CAM promoters by nuclear factor κB/p65. Conversely, depletion of Brg1 and Brm disrupted the kinetics of p65 binding on CAM promoters and crippled CAM activation. Silencing of Brg1 and Brm also altered key epigenetic changes associated with CAM transactivation. Of intrigue, 17β-estradiol antagonized both the expression and activity of Brg1/Brm. Most importantly, endothelial-targeted elimination of Brg1/Brm conferred atheroprotective effects to Apoe(-/-) mice on a Western diet. CONCLUSIONS Our data suggest that Brg1 and Brm integrate various proinflammatory cues into CAM transactivation and endothelial malfunction and, as such, may serve as potential therapeutic targets in treating inflammation-related cardiovascular diseases.
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Affiliation(s)
- Fei Fang
- From the State Key Laboratory of Reproductive Medicine, and Atherosclerosis Research Center, Provincial Key Laboratory of Cardiovascular Disease; and Department of Pathophysiology, Nanjing Medical University, Nanjing, China
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85
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Epigenetics: a new mechanism of regulation of heart failure? Basic Res Cardiol 2013; 108:361. [PMID: 23740219 PMCID: PMC3709081 DOI: 10.1007/s00395-013-0361-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 03/01/2013] [Accepted: 03/13/2013] [Indexed: 01/04/2023]
Abstract
Heart failure is a syndrome resulting from a complex genetic predisposition and multiple environmental factors, and is a leading cause of morbidity and mortality. It is frequently accompanied by changes in heart mass, size, and shape, a process known as pathological cardiac remodeling. At the molecular level, these changes are preceded and accompanied by a specific gene expression program characterized by expression of certain ‘fetal’ genes. This re-expression of fetal genes in the adult heart contributes to the development of the syndrome. Therefore, counteracting the gene expression changes occurring in heart failure could be a therapeutic approach for this pathology. One mechanism of gene expression regulation that has gained importance is epigenetics. This review gives an overview of the roles of some epigenetic mechanisms, such as DNA methylation, histone modifications, ATP-dependent chromatin remodeling, and microRNA-dependent mechanisms, in heart failure.
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86
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Corsten-Janssen N, Kerstjens-Frederikse WS, du Marchie Sarvaas GJ, Baardman ME, Bakker MK, Bergman JE, Hove HD, Heimdal KR, Rustad CF, Hennekam RC, Hofstra RM, Hoefsloot LH, Van Ravenswaaij-Arts CM, Kapusta L. The Cardiac Phenotype in Patients With a
CHD7
Mutation. ACTA ACUST UNITED AC 2013; 6:248-54. [DOI: 10.1161/circgenetics.113.000054] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Loss-of-function mutations in
CHD7
cause Coloboma, Heart Disease, Atresia of Choanae, Retardation of Growth and/or Development, Genital Hypoplasia, and Ear Abnormalities With or Without Deafness (CHARGE) syndrome, a variable combination of multiple congenital malformations including heart defects. Heart defects are reported in 70% to 92% of patients with a
CHD7
mutation, but most studies are small and do not provide a detailed classification of the defects. We present the first, detailed, descriptive study on the cardiac phenotype of 299 patients with a
CHD7
mutation and discuss the role of CHD7 in cardiac development.
Methods and Results—
We collected information on congenital heart defects in 299 patients with a pathogenic
CHD7
mutation, of whom 220 (74%) had a congenital heart defect. Detailed information on the heart defects was available for 202 of these patients. We classified the heart defects based on embryonic cardiac development and compared the distribution to 1007 equally classified nonsyndromic heart defects of patients registered by EUROCAT, a European Registry of Congenital Anomalies. Heart defects are highly variable in patients with
CHD7
mutations, but atrioventricular septal defects and conotruncal heart defects are over-represented. Sex did not have an effect on the presence of heart defects, but truncating
CHD7
mutations resulted in a heart defect significantly more often than missense or splice-site mutations (χ
2
,
P
<0.001).
Conclusions—
CHD7 plays an important role in cardiac development, given that we found a wide range of heart defects in 74% of a large cohort of patients with a CHD7 mutation. Conotruncal defects and atrioventricular septal defects are over-represented in patients with
CHD7
mutations compared with patients with nonsyndromic heart defects.
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Affiliation(s)
- Nicole Corsten-Janssen
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Wilhelmina S. Kerstjens-Frederikse
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Gideon J. du Marchie Sarvaas
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Maria E. Baardman
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Marian K. Bakker
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Jorieke E.H. Bergman
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Hanne D. Hove
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Ketil R. Heimdal
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Cecilie F. Rustad
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Raoul C.M. Hennekam
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Robert M.W. Hofstra
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Lies H. Hoefsloot
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Conny M.A. Van Ravenswaaij-Arts
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
| | - Livia Kapusta
- From the Department of Genetics (N.C.-J., W.S.K.-F., M.E.B., M.K.B., J.E.H.B., C.M.A.V.R.-A.) and Center for Congenital Heart Diseases (G.J.d.M.S.), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark (H.D.H.); Department of Medical Genetics, Oslo University Hospital, Oslo, Norway (K.R.H., C.F.R.); Department of Pediatrics and Genetics, Academic Medical Center, University of Amsterdam,
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Xiong Y, Li W, Shang C, Chen RM, Han P, Yang J, Stankunas K, Wu B, Pan M, Zhou B, Longaker MT, Chang CP. Brg1 governs a positive feedback circuit in the hair follicle for tissue regeneration and repair. Dev Cell 2013; 25:169-81. [PMID: 23602386 DOI: 10.1016/j.devcel.2013.03.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 01/29/2013] [Accepted: 03/25/2013] [Indexed: 11/24/2022]
Abstract
Hair follicle stem cells (bulge cells) are essential for hair regeneration and early epidermal repair after wounding. Here we show that Brg1, a key enzyme in the chromatin-remodeling machinery, is dynamically expressed in bulge cells to control tissue regeneration and repair. In mice, sonic hedgehog (Shh) signals Gli to activate Brg1 in bulge cells to begin hair regeneration, whereas Brg1 recruits NF-κB to activate Shh in matrix cells to sustain hair growth. Such reciprocal Brg1-Shh interaction is essential for hair regeneration. Moreover, Brg1 is indispensable for maintaining the bulge cell reservoir. Without Brg1, bulge cells are depleted over time, partly through the ectopic expression of the cell-cycle inhibitor p27(Kip1). Also, bulge Brg1 is activated by skin injury to facilitate early epidermal repair. Our studies demonstrate a molecular circuit that integrates chromatin remodeling (Brg1), transcriptional regulation (NF-κB, Gli), and intercellular signaling (Shh) to control bulge stem cells during tissue regeneration.
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Affiliation(s)
- Yiqin Xiong
- Department of Medicine, Division of Cardiovascular Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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88
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Abstract
Congenital heart disease (CHD) is the most common congenital anomaly in newborn babies. Cardiac malformations have been produced in multiple experimental animal models, by perturbing selected molecules that function in the developmental pathways involved in myocyte specification, differentiation, or cardiac morphogenesis. In contrast, the precise genetic, epigenetic, or environmental basis for these perturbations in humans remains poorly understood. Over the past few decades, researchers have tried to bridge this knowledge gap through conventional genome-wide analyses of rare Mendelian CHD families, and by sequencing candidate genes in CHD cohorts. Although yielding few, usually highly penetrant, disease gene mutations, these discoveries provided 3 notable insights. First, human CHD mutations impact a heterogeneous set of molecules that orchestrate cardiac development. Second, CHD mutations often alter gene/protein dosage. Third, identical pathogenic CHD mutations cause a variety of distinct malformations, implying that higher order interactions account for particular CHD phenotypes. The advent of contemporary genomic technologies including single nucleotide polymorphism arrays, next-generation sequencing, and copy number variant platforms are accelerating the discovery of genetic causes of CHD. Importantly, these approaches enable study of sporadic cases, the most common presentation of CHD. Emerging results from ongoing genomic efforts have validated earlier observations learned from the monogenic CHD families. In this review, we explore how continued use of these technologies and integration of systems biology is expected to expand our understanding of the genetic architecture of CHD.
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Affiliation(s)
- Akl C Fahed
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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89
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Circulation Research
Thematic Synopsis: Cardiovascular Development. Circ Res 2013. [DOI: 10.1161/circresaha.113.301305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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90
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Rosa-Garrido M, Karbassi E, Monte E, Vondriska TM. Regulation of chromatin structure in the cardiovascular system. Circ J 2013; 77:1389-98. [PMID: 23575346 DOI: 10.1253/circj.cj-13-0176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
It has been appreciated for some time that cardiovascular disease involves large-scale transcriptional changes in various cell types. What has become increasingly clear only in the past few years, however, is the role of chromatin remodeling in cardiovascular phenotypes in normal physiology, as well as in development and disease. This review summarizes the state of the chromatin field in terms of distinct mechanisms to regulate chromatin structure in vivo, identifying when these modes of regulation have been demonstrated in cardiovascular tissues. We describe areas in which a better understanding of chromatin structure is leading to new insights into the fundamental biology of cardiovascular disease.
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Affiliation(s)
- Manuel Rosa-Garrido
- Department of Anesthesiology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
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91
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Kloos W, Katus HA, Meder B. Genetic cardiomyopathies. Lessons learned from humans, mice, and zebrafish. Herz 2013; 37:612-7. [PMID: 22767018 DOI: 10.1007/s00059-012-3651-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dilated cardiomyopathy (DCM) is a multifactorial disease of the heart muscle and a leading cause of congestive heart failure. Human genetic studies and the establishment of suitable animal models such as mice and zebrafish have already revealed parts of its genetic etiology. With the next generation of genomic sequencing technologies (NGS) on the rise, the comprehensive genetic dissection of DCM patients will reveal clinically relevant information, novel causes, and modifiers of this complex disorder. The recent exploration of the epigenome as another mechanism of cardiac gene regulation will further elucidate unexplained variations observed in the correlation between the patient's genotype and phenotype. Some of these intriguing advances being made in basic genetic research will soon find their way into clinical practice for more individualized treatment of cardiomyopathy patients.
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Affiliation(s)
- W Kloos
- Abteilung Innere Medizin III, Kardiologie, Angiologie und Pulmologie, Universitätsklinik Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Gemany
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92
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Brg1 governs distinct pathways to direct multiple aspects of mammalian neural crest cell development. Proc Natl Acad Sci U S A 2013; 110:1738-43. [PMID: 23319608 DOI: 10.1073/pnas.1218072110] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Development of the cerebral vessels, pharyngeal arch arteries (PAAs). and cardiac outflow tract (OFT) requires multipotent neural crest cells (NCCs) that migrate from the neural tube to target tissue destinations. Little is known about how mammalian NCC development is orchestrated by gene programming at the chromatin level, however. Here we show that Brahma-related gene 1 (Brg1), an ATPase subunit of the Brg1/Brahma-associated factor (BAF) chromatin-remodeling complex, is required in NCCs to direct cardiovascular development. Mouse embryos lacking Brg1 in NCCs display immature cerebral vessels, aberrant PAA patterning, and shortened OFT. Brg1 suppresses an apoptosis factor, Apoptosis signal-regulating kinase 1 (Ask1), and a cell cycle inhibitor, p21(cip1), to inhibit apoptosis and promote proliferation of NCCs, thereby maintaining a multipotent cell reservoir at the neural crest. Brg1 also supports Myosin heavy chain 11 (Myh11) expression to allow NCCs to develop into mature vascular smooth muscle cells of cerebral vessels. Within NCCs, Brg1 partners with chromatin remodeler Chromodomain-helicase-DNA-binding protein 7 (Chd7) on the PlexinA2 promoter to activate PlexinA2, which encodes a receptor for semaphorin to guide NCCs into the OFT. Our findings reveal an important role for Brg1 and its downstream pathways in the survival, differentiation, and migration of the multipotent NCCs critical for mammalian cardiovascular development.
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93
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Almeida C, Nagarajan D, Tian J, Leal SW, Wheeler K, Munley M, Blackstock W, Zhao W. The role of alveolar epithelium in radiation-induced lung injury. PLoS One 2013; 8:e53628. [PMID: 23326473 PMCID: PMC3543315 DOI: 10.1371/journal.pone.0053628] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/30/2012] [Indexed: 11/19/2022] Open
Abstract
Pneumonitis and fibrosis are major lung complications of irradiating thoracic malignancies. In the current study, we determined the effect of thoracic irradiation on the lungs of FVB/N mice. Survival data showed a dose-dependent increase in morbidity following thoracic irradiation with single (11–13 Gy) and fractionated doses (24–36 Gy) of 137Cs γ-rays. Histological examination showed a thickening of vessel walls, accumulation of inflammatory cells, collagen deposition, and regional fibrosis in the lungs 14 weeks after a single 12 Gy dose and a fractionated 30 Gy dose; this damage was also seen 5 months after a fractionated 24 Gy dose. After both single and fractionated doses, i] aquaporin-5 was markedly decreased, ii] E-cadherin was reduced and iii] prosurfactant Protein C (pro-SP-c), the number of pro-SP-c+ cells and vimentin expression were increased in the lungs. Immunofluorescence analysis revealed co-localization of pro-SP-c and α-smooth muscle actin in the alveoli after a single dose of 12 Gy. These data suggest that, i] the FVB/N mouse strain is sensitive to thoracic radiation ii] aquaporin-5, E-cadherin, and pro-SP-c may serve as sensitive indicators of radiation-induced lung injury; and iii] the epithelial-to-mesenchymal transition may play an important role in the development of radiation-induced lung fibrosis.
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Affiliation(s)
- Celine Almeida
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Brain Tumor Center of Wake Forest University, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Devipriya Nagarajan
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Brain Tumor Center of Wake Forest University, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jian Tian
- Radiation Research Laboratories, Department of Radiation Medicine, Loma Linda University and Medical Center, Loma Linda, California, United States of America
| | - Sofia Walder Leal
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Brain Tumor Center of Wake Forest University, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Kenneth Wheeler
- Department of Radiology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Brain Tumor Center of Wake Forest University, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Michael Munley
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - William Blackstock
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Weiling Zhao
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- Brain Tumor Center of Wake Forest University, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- * E-mail:
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94
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Lin CJ, Lin CY, Chen CH, Zhou B, Chang CP. Partitioning the heart: mechanisms of cardiac septation and valve development. Development 2012; 139:3277-99. [PMID: 22912411 DOI: 10.1242/dev.063495] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Heart malformations are common congenital defects in humans. Many congenital heart defects involve anomalies in cardiac septation or valve development, and understanding the developmental mechanisms that underlie the formation of cardiac septal and valvular tissues thus has important implications for the diagnosis, prevention and treatment of congenital heart disease. The development of heart septa and valves involves multiple types of progenitor cells that arise either within or outside the heart. Here, we review the morphogenetic events and genetic networks that regulate spatiotemporal interactions between the cells that give rise to septal and valvular tissues and hence partition the heart.
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Affiliation(s)
- Chien-Jung Lin
- Division of Cardiovascular Medicine, Department of Medicine, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
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95
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Circulation Research
Thematic Synopsis. Circ Res 2012; 111:e205-29. [DOI: 10.1161/circresaha.112.280941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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96
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Cao D, Wang C, Tang R, Chen H, Zhang Z, Tatsuguchi M, Wang DZ. Acetylation of myocardin is required for the activation of cardiac and smooth muscle genes. J Biol Chem 2012; 287:38495-504. [PMID: 23007391 DOI: 10.1074/jbc.m112.353649] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myocardin belongs to the SAF-A/B, Acinus, PIAS (SAP) domain family of transcription factors and is specifically expressed in cardiac and smooth muscle. Myocardin functions as a transcriptional coactivator of SRF and is sufficient and necessary for smooth muscle gene expression. We have previously found that myocardin induces the acetylation of nucleosomal histones surrounding SRF-binding sites in the control regions of cardiac and smooth muscle genes through recruiting chromatin-modifying enzyme p300, yet no studies have determined whether myocardin itself is similarly modified. In this study, we show that myocardin is a direct target for p300-mediated acetylation. p300 acetylates lysine residues at the N terminus of the myocardin protein. Interestingly, a direct interaction between p300 and myocardin, which is mediated by the C terminus of myocardin, is required for the acetylation event. Acetylation of myocardin by p300 enhances the association of myocardin and SRF as well as the formation of the myocardin-SRF-CArG box ternary complex. Conversely, acetylation of myocardin decreases the binding of histone deacetylase 5 (HDAC5) to myocardin. Acetylation of myocardin is required for myocardin to activate smooth muscle genes. Our study demonstrates that acetylation plays a key role in modulating myocardin function in controlling cardiac and smooth muscle gene expression.
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Affiliation(s)
- Dongsun Cao
- Department of Cardiology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA
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97
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Ware SM, Jefferies JL. New Genetic Insights into Congenital Heart Disease. JOURNAL OF CLINICAL & EXPERIMENTAL CARDIOLOGY 2012; S8:003. [PMID: 22822471 PMCID: PMC3401115 DOI: 10.4172/2155-9880.s8-003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
There has been remarkable progress in understanding the genetic basis of cardiovascular malformations. Chromosome microarray analysis has provided a new tool to understand the genetic basis of syndromic cardiovascular malformations resulting from microdeletion or microduplication of genetic material, allowing the delineation of new syndromes. Improvements in sequencing technology have led to increasingly comprehensive testing for aortopathy, cardiomyopathy, single gene syndromic disorders, and Mendelian-inherited congenital heart disease. Understanding the genetic etiology for these disorders has improved their clinical recognition and management and led to new guidelines for treatment and family-based diagnosis and surveillance. These new discoveries have also expanded our understanding of the contribution of genetic variation, susceptibility alleles, and epigenetics to isolated congenital heart disease. This review summarizes the current understanding of the genetic basis of syndromic and non-syndromic congenital heart disease and highlights new diagnostic and management recommendations.
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Affiliation(s)
- Stephanie M. Ware
- The Heart Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, MLC 7020, Cincinnati, OH 45229-3039, USA
| | - John Lynn Jefferies
- The Heart Institute, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, MLC 7020, Cincinnati, OH 45229-3039, USA
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98
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Histone deacetylase is required for the activation of Wnt/β-catenin signaling crucial for heart valve formation in zebrafish embryos. Biochem Biophys Res Commun 2012; 423:140-6. [PMID: 22634317 DOI: 10.1016/j.bbrc.2012.05.098] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 05/17/2012] [Indexed: 12/16/2022]
Abstract
During vertebrate heart valve formation, Wnt/β-catenin signaling induces BMP signals in atrioventricular canal (AVC) myocardial cells and underlying AVC endocardial cells then undergo endothelial-mesenchymal transdifferentiation (EMT) by receiving this BMP signals. Histone deacetylases (HDACs) have been implicated in numerous developmental processes by regulating gene expression. However, their specific roles in controlling heart valve development are largely unexplored. To investigate the role of HDACs in vertebrate heart valve formation, we treated zebrafish embryos with trichostatin A (TSA), an inhibitor of class I and II HDACs, from 36 to 48 h post-fertilization (hpf) during which heart looping and valve formation occur. Following TSA treatment, abnormal linear heart tube development was observed. In these embryos, expression of AVC myocardial bmp4 and AVC endocardial notch1b genes was markedly reduced with subsequent failure of EMT in the AVC endocardial cells. However, LiCl-mediated activation of Wnt/β-catenin signaling was able to rescue defective heart tube formation, bmp4 and notch1b expression, and EMT in the AVC region. Taken together, our results demonstrated that HDAC activity plays a pivotal role in vertebrate heart tube formation by activating Wnt/β-catenin signaling which induces bmp4 expression in AVC myocardial cells.
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99
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Chromatin-remodeling complex specificity and embryonic vascular development. Cell Mol Life Sci 2012; 69:3921-31. [PMID: 22618247 DOI: 10.1007/s00018-012-1023-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/12/2012] [Accepted: 05/02/2012] [Indexed: 12/27/2022]
Abstract
Vascular development is a dynamic process that relies on the coordinated expression of numerous genes, but the factors that regulate gene expression during blood vessel development are not well defined. ATP-dependent chromatin-remodeling complexes are gaining attention for their specific temporal and spatial effects on gene expression during vascular development. Genetic mutations in chromatin-remodeling complex subunits are revealing roles for the complexes in vascular signaling pathways at discrete developmental time points. Phenotypic analysis of these models at various stages of vascular development will continue to expand our understanding of how chromatin remodeling impacts new blood vessel growth. Such research could also provide novel therapeutic targets for the treatment of vascular pathologies.
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100
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Wang QT. Epigenetic regulation of cardiac development and function by polycomb group and trithorax group proteins. Dev Dyn 2012; 241:1021-33. [PMID: 22514007 DOI: 10.1002/dvdy.23796] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2012] [Indexed: 12/29/2022] Open
Abstract
Heart disease is a leading cause of death and disability in developed countries. Heart disease includes a broad range of diseases that affect the development and/or function of the cardiovascular system. Some of these diseases, such as congenital heart defects, are present at birth. Others develop over time and may be influenced by both genetic and environmental factors. Many of the known heart diseases are associated with abnormal expression of genes. Understanding the factors and mechanisms that regulate gene expression in the heart is essential for the detection, treatment, and prevention of heart diseases. Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are special families of chromatin factors that regulate developmental gene expression in many tissues and organs. Accumulating evidence suggests that these proteins are important regulators of development and function of the heart as well. A better understanding of their roles and functional mechanisms will translate into new opportunities for combating heart disease.
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Affiliation(s)
- Q Tian Wang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
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