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Ji C, Tao Y, Li X, Wang J, Chen J, Aniagu S, Jiang Y, Chen T. AHR-mediated m 6A RNA methylation contributes to PM 2.5-induced cardiac malformations in zebrafish larvae. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131749. [PMID: 37270964 DOI: 10.1016/j.jhazmat.2023.131749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/11/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
A growing body of evidence indicates that ambient fine particle matter (PM2.5) exposure inhibits heart development, but the underlying mechanisms remain elusive. We hypothesized that m6A RNA methylation plays an important role in the cardiac developmental toxicity of PM2.5. In this study, we demonstrated that extractable organic matter (EOM) from PM2.5 significantly decreased global m6A RNA methylation levels in the heart of zebrafish larvae, which were restored by the methyl donor, betaine. Betaine also attenuated EOM-induced ROS overgeneration, mitochondrial damage, apoptosis and heart defects. Furthermore, we found that the aryl hydrocarbon receptor (AHR), which was activated by EOM, directly repressed the transcription of methyltransferases mettl14 and mettl3. EOM also induced genome-wide m6A RNA methylation changes, which led us to focus more on the aberrant m6A methylation changes that were subsequently alleviated by the AHR inhibitor, CH223191. In addition, we found that the expression levels of traf4a and bbc3, two apoptosis related genes, were upregulated by EOM but restored to control levels by the forced expression of mettl14. Moreover, knockdown of either traf4a or bbc3 attenuated EOM-induced ROS overproduction and apoptosis. In conclusion, our results indicate that PM2.5 induces m6A RNA methylation changes via AHR-mediated mettl14 downregulation, which upregulates traf4a and bbc3, leading to apoptosis and cardiac malformations.
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Affiliation(s)
- Cheng Ji
- Suzhou Medical College, Soochow University, Suzhou, China
| | - Yizhou Tao
- Suzhou Medical College, Soochow University, Suzhou, China
| | - Xiaoxiao Li
- Suzhou Medical College, Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Jin Wang
- Suzhou Medical College, Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Jin Chen
- Suzhou Medical College, Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Stanley Aniagu
- Toxicology, Risk Assessment, and Research Division, Texas Commission on Environmental Quality, 12015 Park 35 Cir, Austin, TX, USA
| | - Yan Jiang
- Suzhou Medical College, Soochow University, Suzhou, China.
| | - Tao Chen
- Suzhou Medical College, Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.
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2
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Brandes RP, Gilsbach R. Is It in the EPIgenome?: Epigenetics Marks at Birth Are Associated With Arterial Stiffness in Children. Hypertension 2021; 78:801-803. [PMID: 34379434 DOI: 10.1161/hypertensionaha.121.17777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Ralf P Brandes
- Institute for Cardiovascular Physiology, Faculty of Medicine, Goethe-University Frankfurt, Germany. DZHK - German Center for Cardiovascular Research, Partner site Rhine-Main
| | - Ralf Gilsbach
- Institute for Cardiovascular Physiology, Faculty of Medicine, Goethe-University Frankfurt, Germany. DZHK - German Center for Cardiovascular Research, Partner site Rhine-Main
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3
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Progress towards improving homing and engraftment of hematopoietic stem cells for clinical transplantation. Curr Opin Hematol 2020; 26:266-272. [PMID: 31045644 DOI: 10.1097/moh.0000000000000510] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Hematopoietic cell transplantation (HCT) is a life-saving treatment for a variety of hematological and nonhematological disorders. Successful clinical outcomes after transplantation rely on adequate hematopoietic stem cell (HSC) numbers, and the homing and subsequent short-term and long-term engraftment of these cells in the bone marrow. Enhancing the homing capability of HSCs has the potential for high impact on improving HCT and patient survival. RECENT FINDINGS There are a number of ways to enhance HSC engraftment. Neutralizing negative epigenetic regulation by histone deacetylase 5 (HDAC5) increases surface CXCR4 expression and promotes human HSC homing and engraftment in immune-deficient NSG (NOD.Cg-Prkdc IL2rgt/Sz) mice. Short-term treatment of cells with glucocorticoids, pharmacological stabilization of hypoxia-inducible factor (HIF)-1α, increasing membrane lipid raft aggregation, and inhibition of dipeptidyl peptidase 4 (DPP4) facilitates HSC homing and engraftment. Added to these procedures, modulating the mitochondria permeability transition pore (MPTP) to mitigate ambient air-induced extra physiological oxygen stress/shock (EPHOSS) by hypoxic harvest and processing, or using cyclosporine A during air collection increases functional HSC numbers and improves HSC engraftment. SUMMARY A better understanding of the regulation of human HSC homing mediated by various signaling pathways will facilitate development of more efficient means to enhance HCT efficacy.
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Bahado-Singh RO, Vishweswaraiah S, Aydas B, Yilmaz A, Saiyed NM, Mishra NK, Guda C, Radhakrishna U. Precision cardiovascular medicine: artificial intelligence and epigenetics for the pathogenesis and prediction of coarctation in neonates. J Matern Fetal Neonatal Med 2020; 35:457-464. [PMID: 32019381 DOI: 10.1080/14767058.2020.1722995] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Advances in omics and computational Artificial Intelligence (AI) have been said to be key to meeting the objectives of precision cardiovascular medicine. The focus of precision medicine includes a better assessment of disease risk and understanding of disease mechanisms. Our objective was to determine whether significant epigenetic changes occur in isolated, non-syndromic CoA. Further, we evaluated the AI analysis of DNA methylation for the prediction of CoA.Methods: Genome-wide DNA methylation analysis of newborn blood DNA was performed in 24 isolated, non-syndromic CoA cases and 16 controls using the Illumina HumanMethylation450 BeadChip arrays. Cytosine nucleotide (CpG) methylation changes in CoA in each of 450,000 CpG loci were determined. Ingenuity pathway analysis (IPA) was performed to identify molecular and disease pathways that were epigenetically dysregulated. Using methylation data, six artificial intelligence (AI) platforms including deep learning (DL) was used for CoA detection.Results: We identified significant (FDR p-value ≤ .05) methylation changes in 65 different CpG sites located in 75 genes in CoA subjects. DL achieved an AUC (95% CI) = 0.97 (0.80-1) with 95% sensitivity and 98% specificity. Gene ontology (GO) analysis yielded epigenetic alterations in important cardiovascular developmental genes and biological processes: abnormal morphology of cardiovascular system, left ventricular dysfunction, heart conduction disorder, thrombus formation, and coronary artery disease.Conclusion: In an exploratory study we report the use of AI and epigenomics to achieve important objectives of precision cardiovascular medicine. Accurate prediction of CoA was achieved using a newborn blood spot. Further, we provided evidence of a significant epigenetic etiology in isolated CoA development.
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Affiliation(s)
- Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Buket Aydas
- Department of Mathematics & Computer Science, Albion College, Albion, Michigan, USA
| | - Ali Yilmaz
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
| | - Nazia M Saiyed
- Nirma Institute of Science, Nirma University, Ahmedabad, India
| | - Nitish K Mishra
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology & Anatomy College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan, USA
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5
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Jiang Y, Li J, Ren F, Ji C, Aniagu S, Chen T. PM2.5-induced extensive DNA methylation changes in the heart of zebrafish embryos and the protective effect of folic acid. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113331. [PMID: 31614245 DOI: 10.1016/j.envpol.2019.113331] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/29/2019] [Accepted: 09/29/2019] [Indexed: 06/10/2023]
Abstract
We previously found that folic acid (FA) attenuated cardiac defects in zebrafish embryos exposed to extractable organic matter (EOM) from PM2.5, but the underlining mechanisms remain to be elucidated. Since DNA methylation is crucial to cardiac development, we hypothesized that EOM-induced aberrant DNA methylation changes could be diminished by FA supplementation. In this study, zebrafish embryos were exposed to EOM in the absence or presence of FA. Genomic-wide DNA methylation analysis identified both DNA hypo- and hyper-methylation changes in CCGG sites in zebrafish embryos exposed to EOM, which were attenuated by FA supplementation. We identified a total of 316 genes with extensive DNA methylation changes in EOM samples but little or no DNA methylation changes in EOM plus FA samples. The genes were involved in critical cellular processes and signaling pathways important for embryo development. In addition, the EOM-decreased SAM/SAH ratio was counteracted by FA supplementation. Furthermore, FA attenuated the EOM-induced changes in the expression of genes involved in the regulation of DNA methylation and in folate biosynthesis. In conclusion, our data suggest that FA supplementation protected zebrafish embryos from the cardiac developmental toxicity of PM2.5 by alleviating EOM-induced DNA methylation changes.
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Affiliation(s)
- Yan Jiang
- Medical College of Soochow University, Suzhou, China
| | - Jianxiang Li
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Fei Ren
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China
| | - Cheng Ji
- Medical College of Soochow University, Suzhou, China
| | - Stanley Aniagu
- Toxicology, Risk Assessment and Research Division, Texas Commission on Environmental Quality, 12015 Park 35 Cir, Austin, TX, USA
| | - Tao Chen
- Medical College of Soochow University, Suzhou, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, China.
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CaM kinase II regulates cardiac hemoglobin expression through histone phosphorylation upon sympathetic activation. Proc Natl Acad Sci U S A 2019; 116:22282-22287. [PMID: 31619570 DOI: 10.1073/pnas.1816521116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Sympathetic activation of β-adrenoreceptors (β-AR) represents a hallmark in the development of heart failure (HF). However, little is known about the underlying mechanisms of gene regulation. In human ventricular myocardium from patients with end-stage HF, we found high levels of phosphorylated histone 3 at serine-28 (H3S28p). H3S28p was increased by inhibition of the catecholamine-sensitive protein phosphatase 1 and decreased by β-blocker pretreatment. By a series of in vitro and in vivo experiments, we show that the β-AR downstream protein kinase CaM kinase II (CaMKII) directly binds and phosphorylates H3S28. Whereas, in CaMKII-deficient myocytes, acute catecholaminergic stimulation resulted in some degree of H3S28p, sustained catecholaminergic stimulation almost entirely failed to induce H3S28p. Genome-wide analysis of CaMKII-mediated H3S28p in response to chronic β-AR stress by chromatin immunoprecipitation followed by massive genomic sequencing led to the identification of CaMKII-dependent H3S28p target genes. Forty percent of differentially H3S28p-enriched genomic regions were associated with differential, mostly increased expression of the nearest genes, pointing to CaMKII-dependent H3S28p as an activating histone mark. Remarkably, the adult hemoglobin genes showed an H3S28p enrichment close to their transcriptional start or end sites, which was associated with increased messenger RNA and protein expression. In summary, we demonstrate that chronic β-AR activation leads to CaMKII-mediated H3S28p in cardiomyocytes. Thus, H3S28p-dependent changes may play an unexpected role for cardiac hemoglobin regulation in the context of sympathetic activation. These data also imply that CaMKII may be a yet unrecognized stress-responsive regulator of hematopoesis.
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7
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Pasipoularides A. Clinical-pathological correlations of BAV and the attendant thoracic aortopathies. Part 1: Pluridisciplinary perspective on their hemodynamics and morphomechanics. J Mol Cell Cardiol 2019; 133:223-232. [PMID: 31150733 DOI: 10.1016/j.yjmcc.2019.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/10/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Clinical BAV manifestations pertain to faulty aortic valve (AOV) function, the associated aortopathy, and other complications such as endocarditis, thrombosis and thromboembolism. BAV arises during valvulogenesis when 2 of the 3 leaflets/cusps of the AOV are fused together. Ensuing asymmetric BAV morphologies alter downstream ejection jet flow-trajectories. Based on BAV morphologies, ejection-flows exhibit different wall-impingement and scouring patterns in the proximal aorta, with excessive hydrodynamic wall-shear that correlates closely with mural vascular smooth muscle cell and extracellular matrix disruptions, revealing hemodynamic participation in the pathogenesis of BAV-associated aortopathies. Since the embryologic regions implicated in both BAV and aortopathies derive from neural crest cells and second heart field cells, there may exist a common multifactorial/polygenic embryological basis linking the abnormalities. The use of Electronic Health Records - encompassing integrated NGS variant panels and phenotypic data - in clinical studies could speed-up comprehensive understanding of multifactorial genetic-phenotypic and environmental factor interactions. This Survey represents the first in a 2-article pluridisciplinary work. Taken in toto, the series covers hemodynamic/morphomechanical and environmental (milieu intérieur) aspects in Part 1, and molecular, genetic and associated epigenetic aspects in Part 2. Together, Parts 1-2 should serve as a reference-milestone and driver for further pluridisciplinary research and its urgent translations in the clinical setting.
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Affiliation(s)
- Ares Pasipoularides
- Duke/NSF Center for Emerging Cardiovascular Technologies, Emeritus Faculty of Surgery and of Biomedical Engineering, Duke University School of Medicine and Graduate School, Durham, NC, USA.
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Segers VFM, Gevaert AB, Boen JRA, Van Craenenbroeck EM, De Keulenaer GW. Epigenetic regulation of intercellular communication in the heart. Am J Physiol Heart Circ Physiol 2019; 316:H1417-H1425. [DOI: 10.1152/ajpheart.00038.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The myocardium is a highly structured tissue consisting of different cell types including cardiomyocytes, endothelial cells, fibroblasts, smooth muscle cells, inflammatory cells, and stem cells. Microvascular endothelial cells are the most abundant cell type in the myocardium and play crucial roles during cardiac development, in normal adult myocardium, and during myocardial diseases such as heart failure. In the last decade, epigenetic changes have been described regulating cellular function in almost every cell type in the organism. Here, we review recent evidence on different epigenetic changes that regulate intercellular communication in normal myocardium and during myocardial diseases, including cardiac remodeling. Epigenetic changes influence many intercellular communication signaling systems, including the nitric oxide, angiotensin, and endothelin signaling systems. In this review, we go beyond discussing classic endothelial function (for instance nitric oxide secretion) and will discuss epigenetic regulation of intercellular communication.
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Affiliation(s)
- Vincent F. M. Segers
- Laboratory of Physiopharmacology, University of Antwerp, Antwerp, Belgium
- Department of Cardiology, University Hospital Antwerp, Edegem, Belgium
| | - Andreas B. Gevaert
- Laboratory of Physiopharmacology, University of Antwerp, Antwerp, Belgium
- Department of Cardiology, University Hospital Antwerp, Edegem, Belgium
- Research Group Cardiovascular Diseases, GENCOR Department, University of Antwerp, Antwerp, Belgium
| | - Jente R. A. Boen
- Laboratory of Physiopharmacology, University of Antwerp, Antwerp, Belgium
- Research Group Cardiovascular Diseases, GENCOR Department, University of Antwerp, Antwerp, Belgium
| | - Emeline M. Van Craenenbroeck
- Department of Cardiology, University Hospital Antwerp, Edegem, Belgium
- Research Group Cardiovascular Diseases, GENCOR Department, University of Antwerp, Antwerp, Belgium
| | - Gilles W. De Keulenaer
- Laboratory of Physiopharmacology, University of Antwerp, Antwerp, Belgium
- Department of Cardiology, Ziekenhuisnetwerk Antwerpen, Hospital, Antwerp, Belgium
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9
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Abstract
Spatiotemporal gene expression during cardiac development is a highly regulated process. Activation of key signaling pathways involved in electrophysiological programming, such as Notch and Wnt signaling, occurs in early cardiovascular development and these pathways are reactivated during pathologic remodeling. Direct targets of these signaling pathways have also been associated with inherited arrhythmias such as Brugada syndrome and arrhythmogenic cardiomyopathy. In addition, evidence is emerging from animal models that reactivation of Notch and Wnt signaling during cardiac pathology may predispose to acquired arrhythmias, underscoring the importance of elucidating the transcriptional and epigenetic effects on cardiac gene regulation. Here, we highlight specific examples where gene expression dictates electrophysiological properties in both normal and diseased hearts.
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10
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Zhang RR, Cai K, Liu L, Yang Q, Zhang P, Gui YH, Wang F. A regulatory variant in TBX2 promoter is related to the decreased susceptibility of congenital heart disease in the Han Chinese population. Mol Genet Genomic Med 2018; 7:e00530. [PMID: 30525309 PMCID: PMC6393683 DOI: 10.1002/mgg3.530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/30/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Background Tbx2 plays a vital role in the cardiac cushion development. In this study, we aimed to determine the relationship between common genetic variants in the promoter region of TBX2 gene and the risk of congenital heart disease (CHD). Methods Blood samples of 516 CHD patients and 587 control subjects were enrolled. Sanger sequencing and SNaPshot analysis were performed for genotyping in our case–control cohort. Luciferase and electrophoretic mobility shift assay (EMSA) were conducted to uncover the potential modulatory mechanism of the related variants. Results Variant rs4455026(c.‐1028G>C) in TBX2 promoter region was found to be associated with significantly lower CHD susceptibility. The risk of CHD in C allele carriers (GC and CC genotypes) decreased by 30% compared to the wild‐type GG genotype subjects (OR = 0.70, 95% CI = 0.55–0.89, p = 0.0038). It was revealed that G to C variation resulted in a decrease in the transcriptional activity of luciferase gene, and a potential change in binding affinity with certain nucleoproteins in EMSA data. Conclusion The minor C allele of rs4455026 in TBX2 promoter region was related with lower CHD susceptibility in the Han Chinese population via repressing its transcriptional activity.
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Affiliation(s)
- Ran-Ran Zhang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China.,Department of Pediatrics, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ke Cai
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Lian Liu
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Qian Yang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Yong-Hao Gui
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
| | - Feng Wang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai, China
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Menon V, Lincoln J. The Genetic Regulation of Aortic Valve Development and Calcific Disease. Front Cardiovasc Med 2018; 5:162. [PMID: 30460247 PMCID: PMC6232166 DOI: 10.3389/fcvm.2018.00162] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/19/2018] [Indexed: 12/19/2022] Open
Abstract
Heart valves are dynamic, highly organized structures required for unidirectional blood flow through the heart. Over an average lifetime, the valve leaflets or cusps open and close over a billion times, however in over 5 million Americans, leaflet function fails due to biomechanical insufficiency in response to wear-and-tear or pathological stimulus. Calcific aortic valve disease (CAVD) is the most common valve pathology and leads to stiffening of the cusp and narrowing of the aortic orifice leading to stenosis and insufficiency. At the cellular level, CAVD is characterized by valve endothelial cell dysfunction and osteoblast-like differentiation of valve interstitial cells. These processes are associated with dysregulation of several molecular pathways important for valve development including Notch, Sox9, Tgfβ, Bmp, Wnt, as well as additional epigenetic regulators. In this review, we discuss the multifactorial mechanisms that contribute to CAVD pathogenesis and the potential of targeting these for the development of novel, alternative therapeutics beyond surgical intervention.
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Affiliation(s)
- Vinal Menon
- Center for Cardiovascular Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States
| | - Joy Lincoln
- Center for Cardiovascular Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,The Heart Center, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, Ohio State University, Columbus, OH, United States
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12
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Hauser AT, Robaa D, Jung M. Epigenetic small molecule modulators of histone and DNA methylation. Curr Opin Chem Biol 2018; 45:73-85. [PMID: 29579619 DOI: 10.1016/j.cbpa.2018.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 12/14/2022]
Abstract
DNA and histone methylation belong to the key regulatory components in the epigenetic machinery, and dysregulations of these processes have been associated with various human diseases. Small molecule modulators of these epigenetic targets are highly valuable both as chemical probes to study the biological roles of the target proteins, and as potential therapeutics. Indeed, recent years have seen the discovery of chemical modulators of several epigenetic targets, some of which are already marketed drugs or undergoing clinical trials. In this review, we will focus on small molecule modulators of DNA and histone methylation.
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Affiliation(s)
- Alexander-Thomas Hauser
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany.
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13
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Luise C, Robaa D. Application of Virtual Screening Approaches for the Identification of Small Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1. Methods Mol Biol 2018; 1824:347-370. [PMID: 30039418 DOI: 10.1007/978-1-4939-8630-9_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Computer-based approaches represent a powerful tool which helps to identify and optimize lead structures in the process of drug discovery. Computer-aided drug design techniques (CADD) encompass a large variety of methods which are subdivided into structure-based (SBDD) and ligand-based drug design (LBDD) methods. Several approaches have been successfully used over the last three decades in different fields. Indeed also in the field of epigenetics, virtual screening (VS) studies and structure-based approaches have been applied to identify novel chemical modulators of epigenetic targets as well as to predict the binding mode of active ligands and to study the protein dynamics.In this chapter, an iterative VS approach using both SBDD and LBDD methods, which was successful in identifying Spindlin1 inhibitors, will be described. All protocol steps, starting from structure-based pharmacophore modeling, protein and database preparation along with docking and similarity search, will be explained in details.
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Affiliation(s)
- Chiara Luise
- Department of Pharmaceutical Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany.
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14
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Stingone JA, Luben TJ, Carmichael SL, Aylsworth AS, Botto LD, Correa A, Gilboa SM, Langlois PH, Nembhard WN, Richmond-Bryant J, Shaw GM, Olshan AF. Maternal Exposure to Nitrogen Dioxide, Intake of Methyl Nutrients, and Congenital Heart Defects in Offspring. Am J Epidemiol 2017; 186:719-729. [PMID: 28520847 PMCID: PMC5610640 DOI: 10.1093/aje/kwx139] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 10/12/2016] [Accepted: 10/25/2016] [Indexed: 01/06/2023] Open
Abstract
Nutrients that regulate methylation processes may modify susceptibility to the effects of air pollutants. Data from the National Birth Defects Prevention Study (United States, 1997-2006) were used to estimate associations between maternal exposure to nitrogen dioxide (NO2), dietary intake of methyl nutrients, and the odds of congenital heart defects in offspring. NO2 concentrations, a marker of traffic-related air pollution, averaged across postconception weeks 2-8, were assigned to 6,160 nondiabetic mothers of cases and controls using inverse distance-squared weighting of air monitors within 50 km of maternal residences. Intakes of choline, folate, methionine, and vitamins B6 and B12 were assessed using a food frequency questionnaire. Hierarchical regression models, which accounted for similarities across defects, were constructed, and relative excess risks due to interaction were calculated. Relative to women with the lowest NO2 exposure and high methionine intake, women with the highest NO2 exposure and lowest methionine intake had the greatest odds of offspring with a perimembranous ventricular septal defect (odds ratio = 3.23, 95% confidence interval: 1.74, 6.01; relative excess risk due to interaction = 2.15, 95% confidence interval: 0.39, 3.92). Considerable departure from additivity was not observed for other defects. These results provide modest evidence of interaction between nutrition and NO2 exposure during pregnancy.
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15
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Abstract
The presence of local renin angiotensin aldosterone systems (RAAS) in the cardiovascular and renal tissues and their influence in cardiovascular and renal diseases are described. The fundamental role of ACE/Ang II/AT1 receptor axis activation as well the counterregulatory role of ACE2/Ang (1-7)/Mas receptor activation on cardiovascular and renal physiology and pathology are emphasized. The presence of a local RAS and its influence on hypertension is discussed, and finally, the hypothesis that epigenetic factors change the RAAS in utero and induce the expression of renin or Ang II inside the cells of the cardiovascular system is presented.
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Affiliation(s)
- Walmor C De Mello
- Department of Pharmacology, School of Medicine, Medical Sciences Campus, UPR, San Juan, PR 00936, USA.
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16
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Exercise Training and Epigenetic Regulation: Multilevel Modification and Regulation of Gene Expression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1000:281-322. [PMID: 29098627 DOI: 10.1007/978-981-10-4304-8_16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Exercise training elicits acute and adaptive long term changes in human physiology that mediate the improvement of performance and health state. The responses are integrative and orchestrated by several mechanisms, as gene expression. Gene expression is essential to construct the adaptation of the biological system to exercise training, since there are molecular processes mediating oxidative and non-oxidative metabolism, angiogenesis, cardiac and skeletal myofiber hypertrophy, and other processes that leads to a greater physiological status. Epigenetic is the field that studies about gene expression changes heritable by meiosis and mitosis, by changes in chromatin and DNA conformation, but not in DNA sequence, that studies the regulation on gene expression that is independent of genotype. The field approaches mechanisms of DNA and chromatin conformational changes that inhibit or increase gene expression and determine tissue specific pattern. The three major studied epigenetic mechanisms are DNA methylation, Histone modification, and regulation of noncoding RNA-associated genes. This review elucidates these mechanisms, focusing on the relationship between them and their relationship with exercise training, physical performance and the enhancement of health status. On this chapter, we clarified the relationship of epigenetic modulations and their intimal relationship with acute and chronic effect of exercise training, concentrating our effort on skeletal muscle, heart and vascular responses, that are the most responsive systems against to exercise training and play crucial role on physical performance and improvement of health state.
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Kranzhöfer DK, Gilsbach R, Grüning BA, Backofen R, Nührenberg TG, Hein L. 5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation. PLoS One 2016; 11:e0166575. [PMID: 27851806 PMCID: PMC5112848 DOI: 10.1371/journal.pone.0166575] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/31/2016] [Indexed: 01/17/2023] Open
Abstract
Background Cardiomyocytes undergo major changes in DNA methylation during maturation and transition to a non-proliferative state after birth. 5’-hydroxylation of methylated cytosines (5hmC) is not only involved in DNA loss of CpG methylation but is also thought to be an epigenetic mark with unique distribution and functions. Here, we sought to get insight into the dynamics of 5’-hydroxymethylcytosine in newborn and adult cardiomyocytes. Methods Cardiomyocyte nuclei from newborn and adult C57BL/6 mice were purified by flow cytometric sorting. 5hmC-containing DNA was captured by selective chemical labeling, followed by deep sequencing. Sequencing reads of library replicates were mapped independently (n = 3 for newborn, n = 2 for adult mice) and merged for further analysis steps. 5hmC coverage was normalized to read length and the total number of mapped reads (RPKM). MethylC-Seq, ChIP-Seq and RNA-Seq data sets of newborn and adult cardiomyocytes served to elucidate specific features of 5hmC at gene bodies and around low methylated regions (LMRs) representing regulatory genomic regions with enhancer function. Results 163,544 and 315,220 5hmC peaks were identified in P1 and adult cardiomyocytes, respectively. Of these peaks, 66,641 were common between P1 and adult cardiomyocytes with more than 50% reciprocal overlap. P1 and adult 5hmC peaks were overrepresented in genic features such as exons, introns, 3’- and 5’-untranslated regions (UTRs), promotors and transcription end sites (TES). During cardiomyocyte maturation, 5hmC was found to be enriched at sites of subsequent DNA loss of CpG methylation such as gene bodies of upregulated genes (i.e. Atp2a2, Tnni3, Mb, Pdk4). Additionally, centers of postnatally established enhancers were premarked by 5hmC before DNA loss of CpG methylation. Conclusions Simultaneous analysis of 5hmC-Seq, MethylC-Seq, RNA-Seq and ChIP-Seq data at two defined time points of cardiomyocyte maturation demonstrates that 5hmC is positively associated with gene expression and decorates sites of subsequent DNA loss of CpG methylation.
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Affiliation(s)
- David K. Kranzhöfer
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ralf Gilsbach
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Björn A. Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Thomas G. Nührenberg
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- University Heart Center Freiburg • Bad Krozingen, Department for Cardiology und Angiology II, Bad Krozingen, Germany
- * E-mail: (TN); (LH)
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- * E-mail: (TN); (LH)
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Robaa D, Wagner T, Luise C, Carlino L, McMillan J, Flaig R, Schüle R, Jung M, Sippl W. Identification and Structure-Activity Relationship Studies of Small-Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1. ChemMedChem 2016; 11:2327-2338. [DOI: 10.1002/cmdc.201600362] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/22/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Dina Robaa
- Institute of Pharmacy; Martin Luther University of Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Tobias Wagner
- Institute of Pharmaceutical Sciences; University of Freiburg; 79104 Freiburg Germany
| | - Chiara Luise
- Institute of Pharmacy; Martin Luther University of Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Luca Carlino
- Institute of Pharmacy; Martin Luther University of Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Joel McMillan
- Department of Urology and Center for Clinical Research; University of Freiburg Medical Center; 79106 Freiburg Germany
- Diamond Light Source Ltd.; Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Ralf Flaig
- Diamond Light Source Ltd.; Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Roland Schüle
- Department of Urology and Center for Clinical Research; University of Freiburg Medical Center; 79106 Freiburg Germany
- German Cancer Research Center (DKFZ); Heidelberg Germany
- German Cancer Consortium (DKTK); Freiburg Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences; University of Freiburg; 79104 Freiburg Germany
- German Cancer Research Center (DKFZ); Heidelberg Germany
- German Cancer Consortium (DKTK); Freiburg Germany
| | - Wolfgang Sippl
- Institute of Pharmacy; Martin Luther University of Halle-Wittenberg; Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
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Lother A, Hein L. Pharmacology of heart failure: From basic science to novel therapies. Pharmacol Ther 2016; 166:136-49. [PMID: 27456554 DOI: 10.1016/j.pharmthera.2016.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/08/2016] [Indexed: 01/10/2023]
Abstract
Chronic heart failure is one of the leading causes for hospitalization in the United States and Europe, and is accompanied by high mortality. Current pharmacological therapy of chronic heart failure with reduced ejection fraction is largely based on compounds that inhibit the detrimental action of the adrenergic and the renin-angiotensin-aldosterone systems on the heart. More than one decade after spironolactone, two novel therapeutic principles have been added to the very recently released guidelines on heart failure therapy: the HCN-channel inhibitor ivabradine and the combined angiotensin and neprilysin inhibitor valsartan/sacubitril. New compounds that are in phase II or III clinical evaluation include novel non-steroidal mineralocorticoid receptor antagonists, guanylate cyclase activators or myosine activators. A variety of novel candidate targets have been identified and the availability of gene transfer has just begun to accelerate translation from basic science to clinical application. This review provides an overview of current pharmacology and pharmacotherapy in chronic heart failure at three stages: the updated clinical guidelines of the American Heart Association and the European Society of Cardiology, new drugs which are in clinical development, and finally innovative drug targets and their mechanisms in heart failure which are emerging from preclinical studies will be discussed.
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Affiliation(s)
- Achim Lother
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Heart Center, Department of Cardiology and Angiology I, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
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Exchange of chemical signals between cardiac cells. Fundamental role on cell communication and metabolic cooperation. Exp Cell Res 2016; 346:130-6. [PMID: 27237090 DOI: 10.1016/j.yexcr.2016.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 01/14/2023]
Abstract
The exchange of chemical signals between cardiac cells and its relevance for cell communication and metabolic cooperation was reviewed. The role of gap junctions on the transfer of chemical information was discussed as well as the different factors involved in its regulation including changes in cell volume, high glucose, activation of the renin angiotensin aldosterone system including the intracrine effect of renin and angiotensin II on chemical coupling and cardiac energetics. Finally, the possible role of epigenetic changes of the renin angiotensin aldosterone system (RAAS) on the expression of components of the RAAS was discussed. The evidence available leads to the conception of the heart as a metabolic syncytium in which glucose as well nucleotides and hormones can flow from cell-to-cell though gap junctions, providing a new vision of how alterations in metabolic cooperation can induce cardiac diseases. These findings represent a stimulus for future research in this important area of cardiac physiology and pathology.
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Abstract
Cardiac transcription factors orchestrate the complex cellular and molecular events required to produce a functioning heart. Misregulation of the cardiac transcription program leads to embryonic developmental defects and is associated with human congenital heart diseases. Recent studies have expanded our understanding of the regulation of cardiac gene expression at an additional layer, involving the coordination of epigenetic and transcriptional regulators. In this review, we highlight and discuss discoveries made possible by the genetic and embryological tools available in the zebrafish model organism, with a focus on the novel functions of cardiac transcription factors and epigenetic and transcriptional regulatory proteins during cardiogenesis.
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Wang L, Ma L, Pang S, Huang J, Yan B. Sequence Variants of SIRT6 Gene Promoter in Myocardial Infarction. Genet Test Mol Biomarkers 2016; 20:185-90. [PMID: 26886147 DOI: 10.1089/gtmb.2015.0188] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
AIMS Coronary artery disease (CAD), including myocardial infarction (MI), is a common complex disease caused by atherosclerosis. Although more than 50 genetic variants have been associated with CAD, these loci collectively account for only 10% of CAD cases. Genetic variants of low and rare frequencies have been proposed as the main causes of CAD. SIRT6, one of the highly conserved NAD-dependent class III deacetylases, has been implicated in cardiovascular diseases. Considering the important roles that SIRT6 plays in the cardiovascular system, inflammation, and lipid and cholesterol metabolism, genetic variants were hypothesized to contribute to MI development. METHODS The promoter regions of the SIRT6 gene were genetically analyzed in large cohorts of MI patients (n = 371) and ethnically-matched controls (n = 383). RESULTS A total of 15 DNA sequence variants (DSVs) were identified, including seven single-nucleotide polymorphisms (SNPs). Two novel heterozygous DSVs, g.4183823G>C and g.4183742G>A, were identified in two MI patients but in none of the controls. Two SNPs, g.4183685T>C (rs4359565) and g.4182942C>A (rs3760905), were found in MI patients with significantly higher frequencies compared with controls. CONCLUSIONS These DSVs identified in MI patients may alter the transcriptional activity of the SIRT6 gene promoter and alter SIRT6 levels which might contribute to the risk of MI.
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Affiliation(s)
- Lekun Wang
- 1 College of Clinical Medicine, Jining Medical University , Jining, China
| | - Ling Ma
- 2 Division of Cardiology, Affiliated Hospital of Jining Medical University, Jining Medical University , Jining, China
| | - Shuchao Pang
- 3 Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Affiliated Hospital of Jining Medical University, Jining Medical University , Jining, China
| | - Jian Huang
- 3 Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Affiliated Hospital of Jining Medical University, Jining Medical University , Jining, China
| | - Bo Yan
- 3 Shandong Provincial Key Laboratory of Cardiac Disease Diagnosis and Treatment, Affiliated Hospital of Jining Medical University, Jining Medical University , Jining, China .,4 Shandong Provincial Sino-US Cooperation Research Center for Translational Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University , Jining, China
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Stenzig J, Hirt MN, Löser A, Bartholdt LM, Hensel JT, Werner TR, Riemenschneider M, Indenbirken D, Guenther T, Müller C, Hübner N, Stoll M, Eschenhagen T. DNA methylation in an engineered heart tissue model of cardiac hypertrophy: common signatures and effects of DNA methylation inhibitors. Basic Res Cardiol 2015; 111:9. [DOI: 10.1007/s00395-015-0528-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/09/2015] [Indexed: 12/11/2022]
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Bahado-Singh RO, Zaffra R, Albayarak S, Chelliah A, Bolinjkar R, Turkoglu O, Radhakrishna U. Epigenetic markers for newborn congenital heart defect (CHD). J Matern Fetal Neonatal Med 2015; 29:1881-7. [PMID: 26429603 DOI: 10.3109/14767058.2015.1069811] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Our objective was to determine whether there were significant differences in genome-wide DNA methylation in newborns with major congenital heart defect (CHD) compared to controls. We also evaluated methylation of cytosines in CpG motifs for the detection of these CHDs. METHODS Genome-wide DNA methylation analysis was performed on DNA from 60 newborns with various CHDs, including hypoplastic left heart syndrome, ventricular septal deficit, atrial septal defect, pulmonary stenosis, coarctation of the aorta and Tetralogy of Fallot, and 32 controls. RESULTS Highly significant differences in cytosine methylation were seen in a large number of genes throughout the genome for all CHD categories. Gene ontology analysis of CHD overall indicated over-represented biological processes involving cell development and differentiation, and anatomical structure morphogenesis. Methylation of individual cytosines in CpG motifs had high diagnostic accuracy for the detection of CHD. For example, for coarctation one predictive model based on levels of particular cytosine nucleotides achieved a sensitivity of 100% and specificity of 93.8% (AUC = 0.974, p < 0.00001). CONCLUSION Profound differences in cytosine methylation were observed in hundreds of genes in newborns with different types of CHD. There appears to be the potential for development of accurate genetic biomarkers for CHD detection in newborns.
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Affiliation(s)
- Ray O Bahado-Singh
- a Department of Obstetrics and Gynecology , William Beaumont School of Medicine, Oakland University , Royal Oak , MI , USA and
| | - Rita Zaffra
- b Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Samet Albayarak
- b Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Anushka Chelliah
- b Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Rashmi Bolinjkar
- b Department of Obstetrics and Gynecology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Onur Turkoglu
- a Department of Obstetrics and Gynecology , William Beaumont School of Medicine, Oakland University , Royal Oak , MI , USA and
| | - Uppala Radhakrishna
- a Department of Obstetrics and Gynecology , William Beaumont School of Medicine, Oakland University , Royal Oak , MI , USA and
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Martinez SR, Gay MS, Zhang L. Epigenetic mechanisms in heart development and disease. Drug Discov Today 2015; 20:799-811. [PMID: 25572405 PMCID: PMC4492921 DOI: 10.1016/j.drudis.2014.12.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/05/2014] [Accepted: 12/29/2014] [Indexed: 12/11/2022]
Abstract
Suboptimal intrauterine development has been linked to predisposition to cardiovascular disease in adulthood, a concept termed 'developmental origins of health and disease'. Although the exact mechanisms underlying this developmental programming are unknown, a growing body of evidence supports the involvement of epigenetic regulation. Epigenetic mechanisms such as DNA methylation, histone modifications and micro-RNA confer added levels of gene regulation without altering DNA sequences. These modifications are relatively stable signals, offering possible insight into the mechanisms underlying developmental origins of health and disease. This review will discuss the role of epigenetic mechanisms in heart development as well as aberrant epigenetic regulation contributing to cardiovascular disease. Additionally, we will address recent advances targeting epigenetic mechanisms as potential therapeutic approaches to cardiovascular disease.
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Affiliation(s)
- Shannalee R Martinez
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Maresha S Gay
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Lubo Zhang
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA.
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Manea SA, Constantin A, Manda G, Sasson S, Manea A. Regulation of Nox enzymes expression in vascular pathophysiology: Focusing on transcription factors and epigenetic mechanisms. Redox Biol 2015; 5:358-366. [PMID: 26133261 PMCID: PMC4501559 DOI: 10.1016/j.redox.2015.06.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 02/06/2023] Open
Abstract
NADPH oxidases (Nox) represent a family of hetero-oligomeric enzymes whose exclusive biological function is the generation of reactive oxygen species (ROS). Nox-derived ROS are essential modulators of signal transduction pathways that control key physiological activities such as cell growth, proliferation, migration, differentiation, and apoptosis, immune responses, and biochemical pathways. Enhanced formation of Nox-derived ROS, which is generally associated with the up-regulation of different Nox subtypes, has been established in various pathologies, namely cardiovascular diseases, diabetes, obesity, cancer, and neurodegeneration. The detrimental effects of Nox-derived ROS are related to alterations in cell signalling and/or direct irreversible oxidative damage of nucleic acids, proteins, carbohydrates, and lipids. Thus, understanding of transcriptional regulation mechanisms of Nox enzymes have been extensively investigated in an attempt to find ways to counteract the excessive formation of Nox-derived ROS in various pathological states. Despite the numerous existing data, the molecular pathways responsible for Nox up-regulation are not completely understood. This review article summarizes some of the recent advances and concepts related to the regulation of Nox expression in the vascular pathophysiology. It highlights the role of transcription factors and epigenetic mechanisms in this process. Identification of the signalling molecules involved in Nox up-regulation, which is associated with the onset and development of cardiovascular dysfunction may contribute to the development of novel strategies for the treatment of cardiovascular diseases. Nox is a unique class of enzymes whose sole function is the generation of ROS. Nox-derived ROS play a major role in cell physiology. Enhanced expression and activation of Nox has been reported in numerous pathologies. Nox expression is regulated via complex transcription factor-epigenetic mechanisms. Understanding of Nox regulation is essential to counteract ROS-induced cell damage.
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Affiliation(s)
- Simona-Adriana Manea
- Institute of Cellular Biology and Pathology "Nicolae Simionescu" of the Romanian Academy, 8, B.P. Hasdeu Street, 050568 Bucharest, Romania
| | - Alina Constantin
- Institute of Cellular Biology and Pathology "Nicolae Simionescu" of the Romanian Academy, 8, B.P. Hasdeu Street, 050568 Bucharest, Romania
| | - Gina Manda
- "Victor Babes" National Institute of Pathology, Bucharest, Romania
| | - Shlomo Sasson
- The Institute for Drug Research, Department of Pharmacology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Adrian Manea
- Institute of Cellular Biology and Pathology "Nicolae Simionescu" of the Romanian Academy, 8, B.P. Hasdeu Street, 050568 Bucharest, Romania.
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Preissl S, Schwaderer M, Raulf A, Hesse M, Grüning BA, Köbele C, Backofen R, Fleischmann BK, Hein L, Gilsbach R. Deciphering the Epigenetic Code of Cardiac Myocyte Transcription. Circ Res 2015; 117:413-23. [PMID: 26105955 DOI: 10.1161/circresaha.115.306337] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/23/2015] [Indexed: 12/22/2022]
Abstract
RATIONALE Epigenetic mechanisms are crucial for cell identity and transcriptional control. The heart consists of different cell types, including cardiac myocytes, endothelial cells, fibroblasts, and others. Therefore, cell type-specific analysis is needed to gain mechanistic insight into the regulation of gene expression in cardiac myocytes. Although cytosolic mRNA represents steady-state levels, nuclear mRNA more closely reflects transcriptional activity. To unravel epigenetic mechanisms of transcriptional control, cell type-specific analysis of nuclear mRNA and epigenetic modifications is crucial. OBJECTIVE The aim was to purify cardiac myocyte nuclei from hearts of different species by magnetic- or fluorescent-assisted sorting and to determine the nuclear and cellular RNA expression profiles and epigenetic marks in a cardiac myocyte-specific manner. METHODS AND RESULTS Frozen cardiac tissue samples were used to isolate cardiac myocyte nuclei. High sorting purity was confirmed for cardiac myocyte nuclei isolated from mice, rats, and humans. Deep sequencing of nuclear RNA revealed a major fraction of nascent, unspliced RNA in contrast to results obtained from purified cardiac myocytes. Cardiac myocyte nuclear and cellular RNA expression profiles showed differences, especially for metabolic genes. Genome-wide maps of the transcriptional elongation mark H3K36me3 were generated by chromatin-immunoprecipitation. Transcriptome and epigenetic data confirmed the high degree of cardiac myocyte-specificity of our protocol. An integrative analysis of nuclear mRNA and histone mark occurrence indicated a major impact of the chromatin state on transcriptional activity in cardiac myocytes. CONCLUSIONS This study establishes cardiac myocyte-specific sorting of nuclei as a universal method to investigate epigenetic and transcriptional processes in cardiac myocytes of different origins. These data sets provide novel insight into cardiac myocyte transcription.
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Affiliation(s)
- Sebastian Preissl
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.)
| | - Martin Schwaderer
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.)
| | - Alexandra Raulf
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.)
| | - Michael Hesse
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.)
| | - Björn A Grüning
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.)
| | - Claudia Köbele
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.)
| | - Rolf Backofen
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.)
| | - Bernd K Fleischmann
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.)
| | - Lutz Hein
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
| | - Ralf Gilsbach
- From the Institute of Experimental and Clinical Pharmacology and Toxicology (S.P., M.S., C.K., L.H., R.G.), and Bioinformatics Group, Department of Computer Science (B.A.G., R.B.), University of Freiburg, Freiburg, Germany; Institute of Physiology I, Life and Brain Center, University of Bonn, Bonn, Germany (A.R., M.H., B.K.F.); Pharma Center Bonn, Bonn, Germany (B.K.F.); and BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany (L.H.).
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Abstract
The heart is the first organ to form during embryonic development. Given the complex nature of cardiac differentiation and morphogenesis, it is not surprising that some form of congenital heart disease is present in ≈1 percent of newborns. The molecular determinants of heart development have received much attention over the past several decades. This has been driven in large part by an interest in understanding the causes of congenital heart disease coupled with the potential of using knowledge from developmental biology to generate functional cells and tissues that could be used for regenerative medicine purposes. In this review, we highlight the critical signaling pathways and transcription factor networks that regulate cardiomyocyte lineage specification in both in vivo and in vitro models. Special focus will be given to epigenetic regulators that drive the commitment of cardiomyogenic cells from nascent mesoderm and their differentiation into chamber-specific myocytes, as well as regulation of myocardial trabeculation.
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Affiliation(s)
- Sharon L Paige
- From the Division of Pediatric Cardiology and Department of Pediatrics (S.L.P., S.M.W.), Cardiovascular Institute (K.P., A.X., S.M.W.), Division of Cardiovascular Medicine, Department of Medicine, Institute for Stem Cell Biology and Institute for Stem Cell Biology and Regenerative Medicine Regenerative Medicine, Child Health Research Institute (S.M.W.), Stanford University School of Medicine, CA
| | - Karolina Plonowska
- From the Division of Pediatric Cardiology and Department of Pediatrics (S.L.P., S.M.W.), Cardiovascular Institute (K.P., A.X., S.M.W.), Division of Cardiovascular Medicine, Department of Medicine, Institute for Stem Cell Biology and Institute for Stem Cell Biology and Regenerative Medicine Regenerative Medicine, Child Health Research Institute (S.M.W.), Stanford University School of Medicine, CA
| | - Adele Xu
- From the Division of Pediatric Cardiology and Department of Pediatrics (S.L.P., S.M.W.), Cardiovascular Institute (K.P., A.X., S.M.W.), Division of Cardiovascular Medicine, Department of Medicine, Institute for Stem Cell Biology and Institute for Stem Cell Biology and Regenerative Medicine Regenerative Medicine, Child Health Research Institute (S.M.W.), Stanford University School of Medicine, CA
| | - Sean M Wu
- From the Division of Pediatric Cardiology and Department of Pediatrics (S.L.P., S.M.W.), Cardiovascular Institute (K.P., A.X., S.M.W.), Division of Cardiovascular Medicine, Department of Medicine, Institute for Stem Cell Biology and Institute for Stem Cell Biology and Regenerative Medicine Regenerative Medicine, Child Health Research Institute (S.M.W.), Stanford University School of Medicine, CA.
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29
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De Mello WC. Chemical Communication between Heart Cells is Disrupted by Intracellular Renin and Angiotensin II: Implications for Heart Development and Disease. Front Endocrinol (Lausanne) 2015; 6:72. [PMID: 26042086 PMCID: PMC4437035 DOI: 10.3389/fendo.2015.00072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 04/22/2015] [Indexed: 12/11/2022] Open
Abstract
HighlightsIntracellular renin and angiotensin disrupts chemical communication in heart.Epigenetic modification of renin angiotensin aldosterone system (RAAS) and heart disease.Intracrine renin angiotensin and metabolic cooperation.Gap junction, intracellular renin and angiotensin, cellular patterns, and heart development. The finding that intracellular renin and angiotensin II (Ang II) disrupts chemical communication and impairs metabolic cooperation between cardiomyocytes induced by aldosterone, hyperglycemia, and pathological conditions like myocardial ischemia is discussed. The hypothesis is presented that epigenetic changes of the renin angiotensin aldosterone system (RAAS) are responsible for cardiovascular abnormalities, including the expression of RAAS components inside cardiac myocytes (intracrine RAAS) with serious consequences including inhibition of electrical and chemical communication in the heart, resulting in metabolic disarrangement and cardiac arrhythmias. Moreover, the inhibition of gap junctional communication induced by intracellular Ang II or renin can contribute to the selection of cellular patterns during heart development.
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Affiliation(s)
- Walmor C. De Mello
- School of Medicine, University of Puerto Rico, San Juan, PR, USA
- *Correspondence: Walmor C. De Mello, School of Medicine, UPR, Medical Sciences Campus, San Juan, PR 00936, USA,
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30
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Shang X, Su J, Wan Q, Su J. CpA/CpG methylation of CiMDA5 possesses tight association with the resistance against GCRV and negatively regulates mRNA expression in grass carp, Ctenopharyngodon idella. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 48:86-94. [PMID: 25260715 DOI: 10.1016/j.dci.2014.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/19/2014] [Accepted: 09/19/2014] [Indexed: 06/03/2023]
Abstract
Melanoma differentiation-associated gene 5 (MDA5) plays a crucial role in recognizing intracellular viral infection, activating the interferon regulatory factor pathways as well as inducing antiviral response. While the antiviral regulatory mechanism of MDA5 remains unclear. In the present study, CiMDA5 (Ctenopharyngodon idella MDA5) against grass carp reovirus (GCRV) would be initially revealed from the perspective of DNA methylation, a pivotal epigenetic modification. Two CpG islands (CGIs) were predicted located in the first exon of CiMDA5, of which the first CpG island was 427 bp in length possessed 29 candidate CpG loci and 34 CpA loci, and the second one was 130 bp in length involving 7 CpG loci as well as 10 CpA loci. By bisulfite sequencing PCR (BSP), the methylation statuses were detected in spleen of 70 individuals divided into resistant/susceptible groups post challenge experiment, and the resistance-association analysis was performed with Chi-square test. Quantitative real-time RT-PCR (qRT-PCR) was carried out to explore the relationship between DNA methylation and gene expression in CiMDA5. Results indicated that the methylation levels of CpA/CpG sites at +200, +202, +204, +207 nt, which consisted of a putative densely methylated element (DME), were significantly higher in the susceptible group than those in the resistant group. Meanwhile, the average transcription of CiMDA5 was down-regulated in the susceptible individuals compared with the resistant individuals. Evidently, the DNA methylation may be the negative modulator of CiMDA5 antiviral expression. Collectively, the methylation levels of CiMDA5 demonstrated the tight association with the resistance against GCRV and the negative-regulated roles in mRNA expression. This study first discovered the resistance-associated gene modulated by DNA methylation in teleost, preliminary revealed the underlying regulatory mechanism of CiMDA5 transcription against GCRV as well as laid a theoretical foundation on molecular nosogenesis of hemorrhagic diseases in C. idella.
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Affiliation(s)
- Xueying Shang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianguo Su
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Quanyuan Wan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Juanjuan Su
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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