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Tatman PD, Kao DP, Chatfield KC, Carroll IA, Wagner JA, Jonas ER, Sucharov CC, Port JD, Lowes BD, Minobe WA, Huebler SP, Karimpour-Fard A, Rodriguez EM, Liggett SB, Bristow MR. An extensive β1-adrenergic receptor gene signaling network regulates molecular remodeling in dilated cardiomyopathies. JCI Insight 2023; 8:e169720. [PMID: 37606047 PMCID: PMC10543724 DOI: 10.1172/jci.insight.169720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/11/2023] [Indexed: 08/23/2023] Open
Abstract
We investigated the extent, biologic characterization, phenotypic specificity, and possible regulation of a β1-adrenergic receptor-linked (β1-AR-linked) gene signaling network (β1-GSN) involved in left ventricular (LV) eccentric pathologic remodeling. A 430-member β1-GSN was identified by mRNA expression in transgenic mice overexpressing human β1-ARs or from literature curation, which exhibited opposite directional behavior in interventricular septum endomyocardial biopsies taken from patients with beta-blocker-treated, reverse remodeled dilated cardiomyopathies. With reverse remodeling, the major biologic categories and percentage of the dominant directional change were as follows: metabolic (19.3%, 81% upregulated); gene regulation (14.9%, 78% upregulated); extracellular matrix/fibrosis (9.1%, 92% downregulated); and cell homeostasis (13.3%, 60% upregulated). Regarding the comparison of β1-GSN categories with expression from 19,243 nonnetwork genes, phenotypic selection for major β1-GSN categories was exhibited for LV end systolic volume (contractility measure), ejection fraction (remodeling index), and pulmonary wedge pressure (wall tension surrogate), beginning at 3 months and persisting to study completion at 12 months. In addition, 121 lncRNAs were identified as possibly involved in cis-acting regulation of β1-GSN members. We conclude that an extensive 430-member gene network downstream from the β1-AR is involved in pathologic ventricular remodeling, with metabolic genes as the most prevalent category.
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Affiliation(s)
| | - David P. Kao
- Division of Cardiology, Department of Medicine, and
- Colorado Center for Personalized Medicine University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kathryn C. Chatfield
- Division of Cardiology, Department of Medicine, and
- Department of Pediatric Cardiology, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Ian A. Carroll
- Division of Cardiology, Department of Medicine, and
- ARCA biopharma, Westminster, Colorado, USA
| | | | | | | | | | - Brian D. Lowes
- Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | | | | | - Anis Karimpour-Fard
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Stephen B. Liggett
- Departments of Medicine and Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Michael R. Bristow
- Division of Cardiology, Department of Medicine, and
- ARCA biopharma, Westminster, Colorado, USA
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2
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Gromova T, Gehred ND, Vondriska TM. Single-cell transcriptomes in the heart: when every epigenome counts. Cardiovasc Res 2023; 119:64-78. [PMID: 35325060 PMCID: PMC10233279 DOI: 10.1093/cvr/cvac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The response of an organ to stimuli emerges from the actions of individual cells. Recent cardiac single-cell RNA-sequencing studies of development, injury, and reprogramming have uncovered heterogeneous populations even among previously well-defined cell types, raising questions about what level of experimental resolution corresponds to disease-relevant, tissue-level phenotypes. In this review, we explore the biological meaning behind this cellular heterogeneity by undertaking an exhaustive analysis of single-cell transcriptomics in the heart (including a comprehensive, annotated compendium of studies published to date) and evaluating new models for the cardiac function that have emerged from these studies (including discussion and schematics that depict new hypotheses in the field). We evaluate the evidence to support the biological actions of newly identified cell populations and debate questions related to the role of cell-to-cell variability in development and disease. Finally, we present emerging epigenomic approaches that, when combined with single-cell RNA-sequencing, can resolve basic mechanisms of gene regulation and variability in cell phenotype.
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Affiliation(s)
- Tatiana Gromova
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natalie D Gehred
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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3
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Kraus L, Beavens B. The Current Therapeutic Role of Chromatin Remodeling for the Prognosis and Treatment of Heart Failure. Biomedicines 2023; 11:biomedicines11020579. [PMID: 36831115 PMCID: PMC9953583 DOI: 10.3390/biomedicines11020579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Cardiovascular diseases are a major cause of death globally, with no cure to date. Many interventions have been studied and suggested, of which epigenetics and chromatin remodeling have been the most promising. Over the last decade, major advancements have been made in the field of chromatin remodeling, particularly for the treatment of heart failure, because of innovations in bioinformatics and gene therapy. Specifically, understanding changes to the chromatin architecture have been shown to alter cardiac disease progression via variations in genomic sequencing, targeting cardiac genes, using RNA molecules, and utilizing chromatin remodeler complexes. By understanding these chromatin remodeling mechanisms in an injured heart, treatments for heart failure have been suggested through individualized pharmaceutical interventions as well as biomarkers for major disease states. By understanding the current roles of chromatin remodeling in heart failure, a potential therapeutic approach may be discovered in the future.
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Early adaptive chromatin remodeling events precede pathologic phenotypes and are reinforced in the failing heart. J Mol Cell Cardiol 2021; 160:73-86. [PMID: 34273410 PMCID: PMC9181638 DOI: 10.1016/j.yjmcc.2021.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022]
Abstract
The temporal nature of chromatin structural changes underpinning pathologic transcription are poorly understood. We measured chromatin accessibility and DNA methylation to study the contribution of chromatin remodeling at different stages of cardiac hypertrophy and failure. ATAC-seq and reduced representation bisulfite sequencing were performed in cardiac myocytes after transverse aortic constriction (TAC) or depletion of the chromatin structural protein CTCF. Early compensation to pressure overload showed changes in chromatin accessibility and DNA methylation preferentially localized to intergenic and intronic regions. Most methylation and accessibility changes observed in enhancers and promoters at the late phase (3 weeks after TAC) were established at an earlier time point (3 days after TAC), before heart failure manifests. Enhancers were paired with genes based on chromatin conformation capture data: while enhancer accessibility generally correlated with changes in gene expression, this feature, nor DNA methylation, was alone sufficient to predict transcription of all enhancer interacting genes. Enrichment of transcription factors and active histone marks at these regions suggests that enhancer activity coordinates with other epigenetic factors to determine gene transcription. In support of this hypothesis, ChIP-qPCR demonstrated increased enhancer and promoter occupancy of GATA4 and NKX2.5 at Itga9 and Nppa, respectively, concomitant with increased transcription of these genes in the diseased heart. Lastly, we demonstrate that accessibility and DNA methylation are imperfect predictors of chromatin structure at the scale of A/B compartmentalization-rather, accessibility, DNA methylation, transcription factors and other histone marks work within these domains to determine gene expression. These studies establish that chromatin reorganization during early compensation after pathologic stimuli is maintained into the later decompensatory phases of heart failure. The findings reveal the rules for how local chromatin features govern gene expression in the context of global genomic structure and identify chromatin remodeling events for therapeutic targeting in disease.
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Ijaz T, Burke MA. BET Protein-Mediated Transcriptional Regulation in Heart Failure. Int J Mol Sci 2021; 22:6059. [PMID: 34199719 PMCID: PMC8199980 DOI: 10.3390/ijms22116059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
Heart failure is a complex disease process with underlying aberrations in neurohormonal systems that promote dysregulated cellular signaling and gene transcription. Over the past 10 years, the advent of small-molecule inhibitors that target transcriptional machinery has demonstrated the importance of the bromodomain and extraterminal (BET) family of epigenetic reader proteins in regulating gene transcription in multiple mouse models of cardiomyopathy. BETs bind to acetylated histone tails and transcription factors to integrate disparate stress signaling networks into a defined gene expression program. Under myocardial stress, BRD4, a BET family member, is recruited to superenhancers and promoter regions of inflammatory and profibrotic genes to promote transcription elongation. Whole-transcriptome analysis of BET-dependent gene networks suggests a major role of nuclear-factor kappa b and transforming growth factor-beta in the development of cardiac fibrosis and systolic dysfunction. Recent investigations also suggest a prominent role of BRD4 in maintaining cardiomyocyte mitochondrial respiration under basal conditions. In this review, we summarize the data from preclinical heart failure studies that explore the role of BET-regulated transcriptional mechanisms and delve into landmark studies that define BET bromodomain-independent processes involved in cardiac homeostasis.
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Affiliation(s)
| | - Michael A. Burke
- Division of Cardiology, Department of Internal Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
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The poly(ADP-ribosyl)ation of BRD4 mediated by PARP1 promoted pathological cardiac hypertrophy. Acta Pharm Sin B 2021; 11:1286-1299. [PMID: 34094834 PMCID: PMC8148063 DOI: 10.1016/j.apsb.2020.12.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/18/2020] [Accepted: 10/13/2020] [Indexed: 12/02/2022] Open
Abstract
The bromodomain and extraterminal (BET) family member BRD4 is pivotal in the pathogenesis of cardiac hypertrophy. BRD4 induces hypertrophic gene expression by binding to the acetylated chromatin, facilitating the phosphorylation of RNA polymerases II (Pol II) and leading to transcription elongation. The present study identified a novel post-translational modification of BRD4: poly(ADP-ribosyl)ation (PARylation), that was mediated by poly(ADP-ribose)polymerase-1 (PARP1) in cardiac hypertrophy. BRD4 silencing or BET inhibitors JQ1 and MS417 prevented cardiac hypertrophic responses induced by isoproterenol (ISO), whereas overexpression of BRD4 promoted cardiac hypertrophy, confirming the critical role of BRD4 in pathological cardiac hypertrophy. PARP1 was activated in ISO-induced cardiac hypertrophy and facilitated the development of cardiac hypertrophy. BRD4 was involved in the prohypertrophic effect of PARP1, as implied by the observations that BRD4 inhibition or silencing reversed PARP1-induced hypertrophic responses, and that BRD4 overexpression suppressed the anti-hypertrophic effect of PARP1 inhibitors. Interactions of BRD4 and PARP1 were observed by co-immunoprecipitation and immunofluorescence. PARylation of BRD4 induced by PARP1 was investigated by PARylation assays. In response to hypertrophic stimuli like ISO, PARylation level of BRD4 was elevated, along with enhanced interactions between BRD4 and PARP1. By investigating the PARylation of truncation mutants of BRD4, the C-terminal domain (CTD) was identified as the PARylation modification sites of BRD4. PARylation of BRD4 facilitated its binding to the transcription start sites (TSS) of hypertrophic genes, resulting in enhanced phosphorylation of RNA Pol II and transcription activation of hypertrophic genes. The present findings suggest that strategies targeting inhibition of PARP1-BRD4 might have therapeutic potential for pathological cardiac hypertrophy.
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Key Words
- ANP, atrial natriuretic peptide
- BET, bromodomain and extraterminal domain
- BNP, brain natriuretic polypeptide
- BRD4
- BW, body weight
- CDK9, cyclin-dependent kinase 9
- Cardiac hypertrophy
- EF, ejection fraction
- FBS, fetal bovine serum
- FS, fractional shortening
- HATs, histone acetyltransferases
- HDACs, histone deacetylases
- HE, hematoxylin-eosin
- HW, heart weight
- Hypertrophic genes
- IF, immunofluorescence
- ISO, isoproterenol
- Isoproterenol
- LVAW, left ventricular anterior wall thickness
- LVID, left ventricular internal diameter
- LVPW, left ventricular posterior wall thickness
- NC, negative control
- NRCMs, neonatal rat cardiomyocytes
- NS, normal saline
- PARP1
- PARP1, poly(ADP-ribose)polymerase-1
- PARylation
- PBS, phosphate buffer solution
- PSR, picrosirius red
- RNA Pol II
- RNA Pol II, RNA polymerases II
- SD, Sprague–Dawley
- TL, tibia length
- TSS, transcription start sites
- Transcription activation
- WGA, wheat germ agglutinin
- co-IP, co-immunoprecipitation
- siRNA, small-interfering RNA
- β-AR, β-adrenergic receptor
- β-MHC, β-myosin heavy chain
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Li L, Xie W, Gui Y, Zheng XL. Bromodomain-containing protein 4 and its role in cardiovascular diseases. J Cell Physiol 2020; 236:4829-4840. [PMID: 33345363 DOI: 10.1002/jcp.30225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022]
Abstract
Bromodomain-containing protein 4 (BRD4), a chromatin-binding protein, is involved in the development of various tumors. Recent evidence suggests that BRD4 also plays a significant role in cardiovascular diseases, such as ischemic heart disease, hypertension, and cardiac hypertrophy. This review summarizes the roles of BRD4 as a potential regulator of various pathophysiological processes in cardiovascular diseases, implicating that BRD4 may be a new therapeutic target for cardiovascular diseases in the future.
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Affiliation(s)
- Liang Li
- Department of Pathophysiology, Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, China.,Department of Biochemistry and Molecular Biology, Libin Cardiovascular Institute, Cumming School of Medicine, The University of Calgary, Calgary, Alberta, Canada
| | - Wei Xie
- Department of Biochemistry and Molecular Biology, Libin Cardiovascular Institute, Cumming School of Medicine, The University of Calgary, Calgary, Alberta, Canada.,Department of Anatomy, Clinical Anatomy & Reproductive Medicine Application Institute, University of South China, Hengyang, Hunan, China
| | - Yu Gui
- Department of Biochemistry and Molecular Biology, Libin Cardiovascular Institute, Cumming School of Medicine, The University of Calgary, Calgary, Alberta, Canada
| | - Xi-Long Zheng
- Department of Biochemistry and Molecular Biology, Libin Cardiovascular Institute, Cumming School of Medicine, The University of Calgary, Calgary, Alberta, Canada
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8
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Epigenetic Targets for Oligonucleotide Therapies of Pulmonary Arterial Hypertension. Int J Mol Sci 2020; 21:ijms21239222. [PMID: 33287230 PMCID: PMC7731052 DOI: 10.3390/ijms21239222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 01/13/2023] Open
Abstract
Arterial wall remodeling underlies increased pulmonary vascular resistance and right heart failure in pulmonary arterial hypertension (PAH). None of the established vasodilator drug therapies for PAH prevents or reverse established arterial wall thickening, stiffening, and hypercontractility. Therefore, new approaches are needed to achieve long-acting prevention and reversal of occlusive pulmonary vascular remodeling. Several promising new drug classes are emerging from a better understanding of pulmonary vascular gene expression programs. In this review, potential epigenetic targets for small molecules and oligonucleotides will be described. Most are in preclinical studies aimed at modifying the growth of vascular wall cells in vitro or normalizing vascular remodeling in PAH animal models. Initial success with lung-directed delivery of oligonucleotides targeting microRNAs suggests other epigenetic mechanisms might also be suitable drug targets. Those targets include DNA methylation, proteins of the chromatin remodeling machinery, and long noncoding RNAs, all of which act as epigenetic regulators of vascular wall structure and function. The progress in testing small molecules and oligonucleotide-based drugs in PAH models is summarized.
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Li X, Liao J, Jiang Z, Liu X, Chen S, He X, Zhu L, Duan X, Xu Z, Qi B, Guo X, Tong R, Shi J. A concise review of recent advances in anti-heart failure targets and its small molecules inhibitors in recent years. Eur J Med Chem 2020; 186:111852. [PMID: 31759729 DOI: 10.1016/j.ejmech.2019.111852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 11/30/2022]
Abstract
Heart failure is a disease with high mortality and the risk of heart failure increases in magnitude with age. The patients of heart failure is increasing year by year. Hence, Pharmaceutical researchers have to develop new drugs with better pharmacological effects to coping with this phenomenon. In this article, we reviewed the small molecule compounds for heart failure that have been marketed in recent years or are promising to enter clinical research. We also reviewed the SAR (structure activity relationship) of these molecules, such as renin inhibitors, ROMK inhibitors, a kind of new diuretics, and some dual-targets inhibitors. These small molecules proven to be beneficial effect on heart failure patients. Which may provide ideas for the design of novel anti-heart failure therapeutic drugs.
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Affiliation(s)
- Xingxing Li
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China
| | - Jing Liao
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China; Pediatric Department Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, People's Republic of China, Chengdu, 610072, China
| | - Zhongliang Jiang
- Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Xinyu Liu
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China
| | - Shan Chen
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China
| | - Xia He
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China; Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Individual Key Laboratory, Chengdu, People's Republic of China, Chengdu, 610072, China
| | - Ling Zhu
- Eastern Hospital, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, 610072, China
| | - Xingmei Duan
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China; Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Individual Key Laboratory, Chengdu, People's Republic of China, Chengdu, 610072, China
| | - Zhuyu Xu
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China
| | - Baowen Qi
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Xiaoqiang Guo
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Rongsheng Tong
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China; Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Individual Key Laboratory, Chengdu, People's Republic of China, Chengdu, 610072, China.
| | - Jianyou Shi
- School of Medicine, University of Electronic Science and Technology of China, Sichuan Provincial People's Hospital, Chengdu, 610054, China; Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Individual Key Laboratory, Chengdu, People's Republic of China, Chengdu, 610072, China.
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10
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A Genomic Approach to Characterize the Vulnerable Patient – a Clinical Update. JOURNAL OF INTERDISCIPLINARY MEDICINE 2019. [DOI: 10.2478/jim-2019-0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Atherosclerosis is the elemental precondition for any cardiovascular disease and the predominant cause of ischemic heart disease that often leads to myocardial infarction. Systemic risk factors play an important role in the starting and progression of atherosclerosis. The complexity of the disease is caused by its multifactorial origin. Besides the traditional risk factors, genetic predisposition is also a strong risk factor. Many studies have intensively researched cardioprotective drugs, which can relieve myocardial ischemia and reperfusion injury, thereby reducing infarct size. A better understanding of abnormal epigenetic pathways in the myocardial pathology may result in new treatment options. Individualized therapy based on genome sequencing is important for an effective future medical treatment. Studies based on multiomics help to better understand the pathophysiological mechanism of several diseases at a molecular level. Epigenomic, transcriptomic, proteomic, and metabolomic research may be essential in detecting the pathological phenotype of myocardial ischemia and ischemic heart failure.
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11
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Transcriptome Analysis of Hypertrophic Heart Tissues from Murine Transverse Aortic Constriction and Human Aortic Stenosis Reveals Key Genes and Transcription Factors Involved in Cardiac Remodeling Induced by Mechanical Stress. DISEASE MARKERS 2019; 2019:5058313. [PMID: 31772688 PMCID: PMC6854968 DOI: 10.1155/2019/5058313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/20/2019] [Accepted: 09/17/2019] [Indexed: 11/18/2022]
Abstract
Background Mechanical stress-induced cardiac remodeling that results in heart failure is characterized by transcriptional reprogramming of gene expression. However, a systematic study of genomic changes involved in this process has not been performed to date. To investigate the genomic changes and underlying mechanism of cardiac remodeling, we collected and analyzed DNA microarray data for murine transverse aortic constriction (TAC) and human aortic stenosis (AS) from the Gene Expression Omnibus database and the European Bioinformatics Institute. Methods and Results The differential expression genes (DEGs) across the datasets were merged. The Venn diagrams showed that the number of intersections for early and late cardiac remodeling was 74 and 16, respectively. Gene ontology and protein–protein interaction network analysis showed that metabolic changes, cell differentiation and growth, cell cycling, and collagen fibril organization accounted for a great portion of the DEGs in the TAC model, while in AS patients' immune system signaling and cytokine signaling displayed the most significant changes. The intersections between the TAC model and AS patients were few. Nevertheless, the DEGs of the two species shared some common regulatory transcription factors (TFs), including SP1, CEBPB, PPARG, and NFKB1, when the heart was challenged by applied mechanical stress. Conclusions This study unravels the complex transcriptome profiles of the heart tissues and highlighting the candidate genes involved in cardiac remodeling induced by mechanical stress may usher in a new era of precision diagnostics and treatment in patients with cardiac remodeling.
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12
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Abstract
Supplemental Digital Content is available in the text. If unifying principles could be revealed for how the same genome encodes different eukaryotic cells and for how genetic variability and environmental input are integrated to impact cardiovascular health, grand challenges in basic cell biology and translational medicine may succumb to experimental dissection. A rich body of work in model systems has implicated chromatin-modifying enzymes, DNA methylation, noncoding RNAs, and other transcriptome-shaping factors in adult health and in the development, progression, and mitigation of cardiovascular disease. Meanwhile, deployment of epigenomic tools, powered by next-generation sequencing technologies in cardiovascular models and human populations, has enabled description of epigenomic landscapes underpinning cellular function in the cardiovascular system. This essay aims to unpack the conceptual framework in which epigenomes are studied and to stimulate discussion on how principles of chromatin function may inform investigations of cardiovascular disease and the development of new therapies.
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Affiliation(s)
- Manuel Rosa-Garrido
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles
| | - Douglas J Chapski
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles
| | - Thomas M Vondriska
- From the Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles.
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13
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Lu D, Wang J, Li J, Guan F, Zhang X, Dong W, Liu N, Gao S, Zhang L. Meox1 accelerates myocardial hypertrophic decompensation through Gata4. Cardiovasc Res 2019; 114:300-311. [PMID: 29155983 DOI: 10.1093/cvr/cvx222] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
Aims Pathological hypertrophy is the result of gene network regulation, which ultimately leads to adverse cardiac remodelling and heart failure (HF) and is accompanied by the reactivation of a 'foetal gene programme'. The Mesenchyme homeobox 1 (Meox1) gene is one of the foetal programme genes. Meox1 may play a role in embryonic development, but its regulation of pathological hypertrophy is not known. Therefore, this study investigated the effect of Meox1 on pathological hypertrophy, including familial and pressure overload-induced hypertrophy, and its potential mechanism of action. Methods and results Meox1 expression was markedly down-regulated in the wild-type adult mouse heart with age, and expression was up-regulated in heart tissues from familial dilated cardiomyopathy (FDCM) mice of the cTnTR141W strain, familial hypertrophic cardiomyopathy (FHCM) mice of the cTnTR92Q strain, pressure overload-induced HF mice, and hypertrophic cardiomyopathy (HCM) patients. Echocardiography, histopathology, and hypertrophic molecular markers consistently demonstrated that Meox1 overexpression exacerbated the phenotypes in FHCM and in mice with thoracic aorta constriction (TAC), and that Meox1 knockdown improved the pathological changes. Gata4 was identified as a potential downstream target of Meox1 using digital gene expression (DGE) profiling, real-time PCR, and bioinformatics analysis. Promoter activity data and chromatin immunoprecipitation (ChIP) and Gata4 knockdown analyses indicated that Meox1 acted via activation of Gata4 transcription. Conclusion Meox1 accelerated decompensation via the downstream target Gata4, at least in part directly. Meox1 and other foetal programme genes form a highly interconnected network, which offers multiple therapeutic entry points to dampen the aberrant expression of foetal genes and pathological hypertrophy.
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Affiliation(s)
- Dan Lu
- Key Laboratory of Human Disease Comparative Medicine, NHFPC, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Building 5, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Jizheng Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 Beilishilu, Beijing 100037, China
| | - Jing Li
- Key Laboratory of Human Disease Comparative Medicine, NHFPC, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Building 5, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Feifei Guan
- Key Laboratory of Human Disease Comparative Medicine, NHFPC, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Building 5, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Xu Zhang
- Key Laboratory of Human Disease Comparative Medicine, NHFPC, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Building 5, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Wei Dong
- Key Laboratory of Human Disease Comparative Medicine, NHFPC, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Building 5, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Ning Liu
- Key Laboratory of Human Disease Comparative Medicine, NHFPC, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Building 5, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Shan Gao
- Key Laboratory of Human Disease Comparative Medicine, NHFPC, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Building 5, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
| | - Lianfeng Zhang
- Key Laboratory of Human Disease Comparative Medicine, NHFPC, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Building 5, Panjiayuan Nanli, Chaoyang District, Beijing 100021, China
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14
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Epigenetic therapies in heart failure. J Mol Cell Cardiol 2019; 130:197-204. [PMID: 30991033 DOI: 10.1016/j.yjmcc.2019.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/20/2022]
Abstract
Heart failure (HF) is a dominant cause of morbidity and mortality in the developed world, with available pharmacotherapies limited by high rates of residual mortality and a failure to directly target the changes in cell state that drive adverse cardiac remodeling. Pathologic cardiac remodeling is driven by stress-activated cardiac signaling cascades that converge on defined components of the chromatin regulatory apparatus in the nucleus, triggering broad shifts in transcription and cell state. Thus, studies focusing on how cytosolic signaling pathways couple to the nuclear gene control machinery has been an area of therapeutic interest in HF. In this review, we discuss current concepts pertaining to the role of chromatin regulators in HF pathogenesis, with a focus on specific proteins and RNA-containing macromolecular complexes that have shown promise as druggable targets in the experimental setting.
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15
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Chapski DJ, Rosa-Garrido M, Hua N, Alber F, Vondriska TM. Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation. Front Cardiovasc Med 2019; 5:186. [PMID: 30697540 PMCID: PMC6341059 DOI: 10.3389/fcvm.2018.00186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/10/2018] [Indexed: 11/13/2022] Open
Abstract
Packaging of the genome in the nucleus is a non-random process that is thought to directly contribute to cell type-specific transcriptomes, although this hypothesis remains untested. Epigenome architecture, as assayed by chromatin conformation capture techniques, such as Hi-C, has recently been described in the mammalian cardiac myocyte and found to be remodeled in the setting of heart failure. In the present study, we sought to determine whether the structural features of the epigenome are conserved between different cell types by investigating Hi-C and RNA-seq data from heart and liver. Investigation of genes with enriched expression in heart or liver revealed nuanced interaction paradigms between organs: first, the log2 ratios of heart:liver (or liver:heart) intrachromosomal interactions are higher in organ-specific gene sets (p = 0.009), suggesting that organ-specific genes have specialized chromatin structural features. Despite similar number of total interactions between cell types, intrachromosomal interaction profiles in heart but not liver demonstrate that genes forming promoter-to-transcription-end-site loops in the cardiac nucleus tend to be involved in cardiac-related pathways. The same analysis revealed an analogous organ-specific interaction profile for liver-specific loop genes. Investigation of A/B compartmentalization (marker of chromatin accessibility) revealed that in the heart, 66.7% of cardiac-specific genes are in compartment A, while 66.1% of liver-specific genes are found in compartment B, suggesting that there exists a cardiac chromatin topology that allows for expression of cardiac genes. Analyses of interchromosomal interactions revealed a relationship between interchromosomal interaction count and organ-specific gene localization (p = 2.2 × 10-16) and that, for both organs, regions of active or inactive chromatin tend to segregate in 3D space (i.e., active with active, inactive with inactive). 3D models of topologically associating domains (TADs) suggest that TADs tend to interact with regions of similar compartmentalization across chromosomes, revealing trans structural interactions contributing to genomic compartmentalization at distinct structural scales. These models reveal discordant nuclear compaction strategies, with heart packaging compartment A genes preferentially toward the center of the nucleus and liver exhibiting preferential arrangement toward the periphery. Taken together, our data suggest that intra- and interchromosomal chromatin architecture plays a role in orchestrating tissue-specific gene expression.
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Affiliation(s)
- Douglas J Chapski
- Departments of Anesthesiology, Physiology and Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Manuel Rosa-Garrido
- Departments of Anesthesiology, Physiology and Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Nan Hua
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Frank Alber
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Thomas M Vondriska
- Departments of Anesthesiology, Physiology and Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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16
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McKinsey TA, Vondriska TM, Wang Y. Epigenomic regulation of heart failure: integrating histone marks, long noncoding RNAs, and chromatin architecture. F1000Res 2018; 7. [PMID: 30416708 PMCID: PMC6206605 DOI: 10.12688/f1000research.15797.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/16/2018] [Indexed: 12/25/2022] Open
Abstract
Epigenetic processes are known to have powerful roles in organ development across biology. It has recently been found that some of the chromatin modulatory machinery essential for proper development plays a previously unappreciated role in the pathogenesis of cardiac disease in adults. Investigations using genetic and pharmacologic gain- and loss-of-function approaches have interrogated the function of distinct epigenetic regulators, while the increased deployment of the suite of next-generation sequencing technologies have fundamentally altered our understanding of the genomic targets of these chromatin modifiers. Here, we review recent developments in basic and translational research that have provided tantalizing clues that may be used to unlock the therapeutic potential of the epigenome in heart failure. Additionally, we provide a hypothesis to explain how signal-induced crosstalk between histone tail modifications and long non-coding RNAs triggers chromatin architectural remodeling and culminates in cardiac hypertrophy and fibrosis.
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Affiliation(s)
- Timothy A McKinsey
- Department of Medicine, Division of Cardiology and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas M Vondriska
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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17
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Perrino C, Barabási AL, Condorelli G, Davidson SM, De Windt L, Dimmeler S, Engel FB, Hausenloy DJ, Hill JA, Van Laake LW, Lecour S, Leor J, Madonna R, Mayr M, Prunier F, Sluijter JPG, Schulz R, Thum T, Ytrehus K, Ferdinandy P. Epigenomic and transcriptomic approaches in the post-genomic era: path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heart. Cardiovasc Res 2018; 113:725-736. [PMID: 28460026 PMCID: PMC5437366 DOI: 10.1093/cvr/cvx070] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/27/2017] [Indexed: 01/19/2023] Open
Abstract
Despite advances in myocardial reperfusion therapies, acute myocardial ischaemia/reperfusion injury and consequent ischaemic heart failure represent the number one cause of morbidity and mortality in industrialized societies. Although different therapeutic interventions have been shown beneficial in preclinical settings, an effective cardioprotective or regenerative therapy has yet to be successfully introduced in the clinical arena. Given the complex pathophysiology of the ischaemic heart, large scale, unbiased, global approaches capable of identifying multiple branches of the signalling networks activated in the ischaemic/reperfused heart might be more successful in the search for novel diagnostic or therapeutic targets. High-throughput techniques allow high-resolution, genome-wide investigation of genetic variants, epigenetic modifications, and associated gene expression profiles. Platforms such as proteomics and metabolomics (not described here in detail) also offer simultaneous readouts of hundreds of proteins and metabolites. Isolated omics analyses usually provide Big Data requiring large data storage, advanced computational resources and complex bioinformatics tools. The possibility of integrating different omics approaches gives new hope to better understand the molecular circuitry activated by myocardial ischaemia, putting it in the context of the human ‘diseasome’. Since modifications of cardiac gene expression have been consistently linked to pathophysiology of the ischaemic heart, the integration of epigenomic and transcriptomic data seems a promising approach to identify crucial disease networks. Thus, the scope of this Position Paper will be to highlight potentials and limitations of these approaches, and to provide recommendations to optimize the search for novel diagnostic or therapeutic targets for acute ischaemia/reperfusion injury and ischaemic heart failure in the post-genomic era.
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Affiliation(s)
- Cinzia Perrino
- Department of Advanced Biomedical Sciences, Federico II University, Via Pansini 5, 80131 Naples, Italy
| | - Albert-Laszló Barabási
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, USA.,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Network Science, Central European University, Budapest, Hungary.,Department of Medicine, and Division of Network Medicine, Brigham and Womens Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Gianluigi Condorelli
- Department of Cardiovascular Medicine, Humanitas Research Hospital and Humanitas University, Rozzano, Italy.,Institute of Genetic and Biomedical Research, National Research Council of Italy, Rozzano, Milan, Italy
| | - Sean Michael Davidson
- The Hatter Cardiovascular Institute, Institute of Cardiovascular Science, University College London, London, UK
| | - Leon De Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, University Frankfurt, Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), RheinMain, Germany
| | - Felix Benedikt Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Derek John Hausenloy
- The Hatter Cardiovascular Institute, University College London, London, UK.,The National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, UK.,Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, Singapore.,National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore.,Yong Loo Lin School of Medicine, National University Singapore, Singapore.,Barts Heart Centre, St Bartholomew's Hospital, London, UK
| | - Joseph Addison Hill
- Departments of Medicine (Cardiology) and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Linda Wilhelmina Van Laake
- Division of Heart and Lungs, Hubrecht Institute, University Medical Center Utrecht, Utrecht, The Netherlands.,UMC Utrecht Regenerative Medicine Center and Hubrecht Institute, Utrecht, The Netherlands
| | - Sandrine Lecour
- Hatter Cardiovascular Research Institute, University of Cape Town, Cape Town, South Africa
| | - Jonathan Leor
- Neufeld Cardiac Research Institute, Tel-Aviv University, Tel-Aviv, Israel.,Tamman Cardiovascular Research Institute, Sheba Medical Center; Sheba Center for Regenerative Medicine, Stem Cell, and Tissue Engineering, Tel Hashomer, Israel
| | - Rosalinda Madonna
- Center of Aging Sciences and Translational Medicine - CESI-MeT, "G. d'Annunzio" University, Chieti, Italy; Institute of Cardiology, Department of Neurosciences, Imaging, and Clinical Sciences, "G. d'Annunzio" University, Chieti, Italy.,The Texas Heart Institute and Center for Cardiovascular Biology and Atherosclerosis Research, Department of Internal Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Fabrice Prunier
- Department of Cardiology, Institut MITOVASC, University of Angers, University Hospital of Angers, Angers, France
| | - Joost Petrus Geradus Sluijter
- Cardiology and UMC Utrecht Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rainer Schulz
- Institute of Physiology, Justus Liebig University Giessen, Giessen, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Kirsti Ytrehus
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.,Cardiovascular Research Group, Department of Biochemistry, University of Szeged, Szeged, Hungary.,Pharmahungary Group, Szeged, Hungary
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18
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Sun Y, Xie Y, Du L, Sun J, Liu Z. Inhibition of BRD4 attenuates cardiomyocyte apoptosis via NF-κB pathway in a rat model of myocardial infarction. Cardiovasc Ther 2018; 36. [PMID: 29352508 DOI: 10.1111/1755-5922.12320] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/24/2017] [Accepted: 01/15/2018] [Indexed: 11/28/2022] Open
Affiliation(s)
- Yiping Sun
- Department of Cardiac Surgery; the Affiliated Zhongshan Hospital of Fudan University; Xuhui Shanghai China
| | - Ying Xie
- Department of Physiology and Pathophysiology; School of Basic Medical Science; Tianjin Medical University; Heping Tianjin China
| | - Luping Du
- Department of Physiology and Pathophysiology; School of Basic Medical Science; Tianjin Medical University; Heping Tianjin China
| | - Jingwu Sun
- Department of Cardiology; the Affiliated Hospital of Binzhou Medical University; Binzhou Shandong China
| | - Zhiqiang Liu
- Department of Physiology and Pathophysiology; School of Basic Medical Science; Tianjin Medical University; Heping Tianjin China
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19
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Rosa-Garrido M, Chapski DJ, Schmitt AD, Kimball TH, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih TT, Soehalim E, Liem D, Ping P, Galjart NJ, Ren S, Wang Y, Ren B, Vondriska TM. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure. Circulation 2017; 136:1613-1625. [PMID: 28802249 PMCID: PMC5648689 DOI: 10.1161/circulationaha.117.029430] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/31/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. METHODS To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. RESULTS Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. CONCLUSIONS These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy.
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Affiliation(s)
- Manuel Rosa-Garrido
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Douglas J Chapski
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Anthony D Schmitt
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Todd H Kimball
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Elaheh Karbassi
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Emma Monte
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Enrique Balderas
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Matteo Pellegrini
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Tsai-Ting Shih
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Elizabeth Soehalim
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - David Liem
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Peipei Ping
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Niels J Galjart
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Shuxun Ren
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Yibin Wang
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Bing Ren
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Thomas M Vondriska
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.).
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20
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Affiliation(s)
- Douglas L Mann
- From Center for Cardiovascular Research, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO.
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21
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Abstract
Fibrosis is defined as excess deposition of extracellular matrix, resulting in tissue scarring and organ dysfunction. It is estimated that 45% of deaths in the developed world are due to fibrosis-induced organ failure. Despite the well-accepted role of fibrosis in the pathogenesis of numerous diseases, there are only two US Food and Drug Administration–approved anti-fibrotic therapies, both of which are currently restricted to the treatment of pulmonary fibrosis. Thus, organ fibrosis represents a massive unmet medical need. Here, we review recent findings suggesting that an epigenetic regulatory protein, BRD4, is a nodal effector of organ fibrosis, and we highlight the potential of small-molecule BRD4 inhibitors for the treatment of diverse fibrotic diseases.
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Affiliation(s)
- Matthew S Stratton
- Department of Medicine, Division of Cardiology and Consortium for Fibrosis Research & Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Saptarsi M Haldar
- Gladstone Institutes and Department of Medicine, Division of Cardiology, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Timothy A McKinsey
- Department of Medicine, Division of Cardiology and Consortium for Fibrosis Research & Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
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22
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Duan Q, McMahon S, Anand P, Shah H, Thomas S, Salunga HT, Huang Y, Zhang R, Sahadevan A, Lemieux ME, Brown JD, Srivastava D, Bradner JE, McKinsey TA, Haldar SM. BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure. Sci Transl Med 2017; 9:eaah5084. [PMID: 28515341 PMCID: PMC5544253 DOI: 10.1126/scitranslmed.aah5084] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 01/18/2017] [Accepted: 03/30/2017] [Indexed: 12/13/2022]
Abstract
Despite current standard of care, the average 5-year mortality after an initial diagnosis of heart failure (HF) is about 40%, reflecting an urgent need for new therapeutic approaches. Previous studies demonstrated that the epigenetic reader protein bromodomain-containing protein 4 (BRD4), an emerging therapeutic target in cancer, functions as a critical coactivator of pathologic gene transactivation during cardiomyocyte hypertrophy. However, the therapeutic relevance of these findings to human disease remained unknown. We demonstrate that treatment with the BET bromodomain inhibitor JQ1 has therapeutic effects during severe, preestablished HF from prolonged pressure overload, as well as after a massive anterior myocardial infarction in mice. Furthermore, JQ1 potently blocks agonist-induced hypertrophy in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). Integrated transcriptomic analyses across animal models and human iPSC-CMs reveal that BET inhibition preferentially blocks transactivation of a common pathologic gene regulatory program that is robustly enriched for NFκB and TGF-β signaling networks, typified by innate inflammatory and profibrotic myocardial genes. As predicted by these specific transcriptional mechanisms, we found that JQ1 does not suppress physiological cardiac hypertrophy in a mouse swimming model. These findings establish that pharmacologically targeting innate inflammatory and profibrotic myocardial signaling networks at the level of chromatin is effective in animal models and human cardiomyocytes, providing the critical rationale for further development of BET inhibitors and other epigenomic medicines for HF.
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Affiliation(s)
- Qiming Duan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Priti Anand
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Hirsh Shah
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Sean Thomas
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Hazel T Salunga
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Yu Huang
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Rongli Zhang
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Aarathi Sahadevan
- Institute for Transformative Molecular Medicine and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | | | - Jonathan D Brown
- Division of Cardiovascular Medicine, Department of Medicine, and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- Division of Cardiology, Department of Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA 94158, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Timothy A McKinsey
- Division of Cardiology, Department of Medicine, Consortium for Fibrosis Research & Translation, University of Colorado, Anschutz Medical Campus, Denver, CO 80204, USA
| | - Saptarsi M Haldar
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.
- Division of Cardiology, Department of Medicine, and Cardiovascular Research Institute, University of California San Francisco School of Medicine, San Francisco, CA 94158, USA
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23
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Yang Y, Zhao L, Xu B, Yang L, Zhang J, Zhang H, Zhou J. Design, synthesis and biological evaluation of dihydroquinoxalinone derivatives as BRD4 inhibitors. Bioorg Chem 2016; 68:236-44. [DOI: 10.1016/j.bioorg.2016.08.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 12/01/2022]
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24
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The potential of targeting epigenetic regulators for the treatment of fibrotic cardiac diseases. Future Med Chem 2016; 8:1533-6. [PMID: 27556930 DOI: 10.4155/fmc-2016-0144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Stratton MS, Lin CY, Anand P, Tatman PD, Ferguson BS, Wickers ST, Ambardekar AV, Sucharov CC, Bradner JE, Haldar SM, McKinsey TA. Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers Is Suppressed by a MicroRNA. Cell Rep 2016; 16:1366-1378. [PMID: 27425608 PMCID: PMC4972677 DOI: 10.1016/j.celrep.2016.06.074] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 05/04/2016] [Accepted: 06/16/2016] [Indexed: 12/20/2022] Open
Abstract
BRD4 governs pathological cardiac gene expression by binding acetylated chromatin, resulting in enhanced RNA polymerase II (Pol II) phosphorylation and transcription elongation. Here, we describe a signal-dependent mechanism for the regulation of BRD4 in cardiomyocytes. BRD4 expression is suppressed by microRNA-9 (miR-9), which targets the 3' UTR of the Brd4 transcript. In response to stress stimuli, miR-9 is downregulated, leading to derepression of BRD4 and enrichment of BRD4 at long-range super-enhancers (SEs) associated with pathological cardiac genes. A miR-9 mimic represses stimulus-dependent targeting of BRD4 to SEs and blunts Pol II phosphorylation at proximal transcription start sites, without affecting BRD4 binding to SEs that control constitutively expressed cardiac genes. These findings suggest that dynamic enrichment of BRD4 at SEs genome-wide serves a crucial role in the control of stress-induced cardiac gene expression and define a miR-dependent signaling mechanism for the regulation of chromatin state and Pol II phosphorylation.
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Affiliation(s)
- Matthew S Stratton
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Priti Anand
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Philip D Tatman
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Medical Scientist Training Program, University of Colorado Denver, Aurora, CO 80045, USA
| | - Bradley S Ferguson
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Sean T Wickers
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Amrut V Ambardekar
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Carmen C Sucharov
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Saptarsi M Haldar
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Division of Cardiology, Department of Medicine and Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, CA 94143, USA
| | - Timothy A McKinsey
- Division of Cardiology, Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA; Medical Scientist Training Program, University of Colorado Denver, Aurora, CO 80045, USA.
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Abstract
Epigenetic regulatory mechanisms play key roles in cardiac development, differentiation, homeostasis, response to stress and injury, and disease. Human heart failure (HF) epigenetic regulatory mechanisms have not been deciphered to date. This 2-part review distills the rapidly evolving research focused on human HF epigenetic regulatory mechanisms. Part I, which was published in the September/October issue, focused on epigenetic regulatory mechanisms involving RNA, specifically the role of short, intermediate, and long noncoding RNAs (lncRNAs) and endogenous competing RNA regulatory networks. Part II, now in the November/December issue, focuses on the epigenetic regulatory mechanisms involving DNA, including DNA methylation, histone modifications, and chromatin conformational changes. Part II concludes with 2 examples of well-studied integrated epigenetic regulatory mechanisms: the structural and functional roles of the Mediator complex in regulating transcription and the epigenetic networked "cross-talk" regulating atrial natriuretic peptide and brain natriuretic peptide promoter activation.
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Suzuki H, Katanasaka Y, Sunagawa Y, Miyazaki Y, Funamoto M, Wada H, Hasegawa K, Morimoto T. Tyrosine phosphorylation of RACK1 triggers cardiomyocyte hypertrophy by regulating the interaction between p300 and GATA4. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1544-57. [PMID: 27208796 DOI: 10.1016/j.bbadis.2016.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 04/28/2016] [Accepted: 05/11/2016] [Indexed: 01/05/2023]
Abstract
The zinc finger protein GATA4 is a transcription factor involved in cardiomyocyte hypertrophy. It forms a functional complex with the intrinsic histone acetyltransferase (HAT) p300. The HAT activity of p300 is required for the acetylation and transcriptional activity of GATA4, as well as for cardiomyocyte hypertrophy and the development of heart failure. In the present study, we have identified Receptor for Activated Protein Kinase C1 (RACK1) as a novel GATA4-binding protein using tandem affinity purification and mass spectrometry analyses. We found that exogenous RACK1 repressed phenylephrine (PE)-induced hypertrophic responses, such as myofibrillar organization, increased cell size, and hypertrophy-associated gene transcription, in cultured cardiomyocytes. RACK1 physically interacted with GATA4 and the overexpression of RACK1 reduced PE-induced formation of the p300/GATA4 complex and the acetylation and DNA binding activity of GATA4. In response to hypertrophic stimulation in cultured cardiomyocytes and in the hearts of hypertensive heart disease model rats, the tyrosine phosphorylation of RACK1 was increased, and the binding between GATA4 and RACK1 was reduced. In addition, the tyrosine phosphorylation of RACK1 was required for the disruption of the RACK1/GATA4 complex and for the formation of the p300/GATA4 complex. These findings demonstrate that RACK1 is involved in p300/GATA4-dependent hypertrophic responses in cardiomyocytes and is a promising therapeutic target for heart failure.
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Affiliation(s)
- Hidetoshi Suzuki
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yasufumi Katanasaka
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan; Division of Translational Research, Clinical Research Institute, Kyoto Medical Center, National Hospital Organization, Kyoto, Japan; Shizuoka General Hospital, Shizuoka, Japan
| | - Yoichi Sunagawa
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan; Division of Translational Research, Clinical Research Institute, Kyoto Medical Center, National Hospital Organization, Kyoto, Japan; Shizuoka General Hospital, Shizuoka, Japan
| | - Yusuke Miyazaki
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Masafumi Funamoto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hiromichi Wada
- Division of Translational Research, Clinical Research Institute, Kyoto Medical Center, National Hospital Organization, Kyoto, Japan
| | - Koji Hasegawa
- Division of Translational Research, Clinical Research Institute, Kyoto Medical Center, National Hospital Organization, Kyoto, Japan
| | - Tatsuya Morimoto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan; Division of Translational Research, Clinical Research Institute, Kyoto Medical Center, National Hospital Organization, Kyoto, Japan; Shizuoka General Hospital, Shizuoka, Japan.
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Ghoshal A, Yugandhar D, Srivastava AK. BET inhibitors in cancer therapeutics: a patent review. Expert Opin Ther Pat 2016; 26:505-22. [PMID: 26924192 DOI: 10.1517/13543776.2016.1159299] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Inhibition of Bromodomain and Extra Terminal (BET) proteins is an emerging approach for developing advanced cancer therapeutics. In 2015, at least thirty patents have been published for developing cancer chemotherapeutics by targeting BET. Currently there are seven small molecule BET inhibitors in various stages of clinical trials for the development of anti-cancer drugs. AREAS COVERED Important patents focusing on development of BET inhibitors as potential cancer therapeutics published in 2015 have been covered. The reports are presented together with a review of the related structural chemical space. This review mainly focuses on the therapeutic applications, chemical class and structural modifications along with the molecules currently in clinical trials. EXPERT OPINION BET sub-family proteins are one of the emerging targets to develop anti-cancer agents. Although many research groups have demonstrated the rationality of BET inhibition to combat cancer, a detailed molecular study needs to be performed to investigate the affected biological pathways. Selectivity among BET proteins should be kept in mind while developing BET inhibitors. In-silico molecular modelling studies can also provide valuable information for designing selective BET inhibitors towards anti-cancer drug discovery and development.
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Affiliation(s)
- Anirban Ghoshal
- a Medicinal Chemistry and Pharmacology Division , CSIR - Indian Institute of Chemical Technology , Hyderabad , India
| | - D Yugandhar
- a Medicinal Chemistry and Pharmacology Division , CSIR - Indian Institute of Chemical Technology , Hyderabad , India.,b Chemical Science Division, Academy of Scientific & Innovative Research (AcSIR) , New Delhi , India
| | - Ajay Kumar Srivastava
- a Medicinal Chemistry and Pharmacology Division , CSIR - Indian Institute of Chemical Technology , Hyderabad , India.,b Chemical Science Division, Academy of Scientific & Innovative Research (AcSIR) , New Delhi , India
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Yu LM, Xu Y. Epigenetic regulation in cardiac fibrosis. World J Cardiol 2015; 7:784-791. [PMID: 26635926 PMCID: PMC4660473 DOI: 10.4330/wjc.v7.i11.784] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/16/2015] [Accepted: 09/28/2015] [Indexed: 02/06/2023] Open
Abstract
Cardiac fibrosis represents an adoptive response in the heart exposed to various stress cues. While resolution of the fibrogenic response heralds normalization of heart function, persistent fibrogenesis is usually associated with progressive loss of heart function and eventually heart failure. Cardiac fibrosis is regulated by a myriad of factors that converge on the transcription of genes encoding extracellular matrix proteins, a process the epigenetic machinery plays a pivotal role. In this mini-review, we summarize recent advances regarding the epigenetic regulation of cardiac fibrosis focusing on the role of histone and DNA modifications and non-coding RNAs.
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Sun Y, Huang J, Song K. BET protein inhibition mitigates acute myocardial infarction damage in rats via the TLR4/TRAF6/NF-κB pathway. Exp Ther Med 2015; 10:2319-2324. [PMID: 26668635 DOI: 10.3892/etm.2015.2789] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 09/07/2015] [Indexed: 01/04/2023] Open
Abstract
Acute myocardial infarction (AMI) is among the most serious cardiovascular diseases and is a leading cause of mortality in developed countries. Previous studies have indicated the central role played by the bromodomain (BRD) proteins, which belong to the BRD and extra-terminal (BET) family, in gene control during heart failure pathogenesis. In addition, BET inhibition has been shown to suppress cardiomyocyte hypertrophy. However, the role of BET proteins in myocardial infarction remains unclear. The present study aimed to investigate whether BETs inhibition mitigates AMI, and explore the molecular mechanism underlying this effect. A rat model of acute myocardial infarction was established, and rats were divided into the sham, AMI and AMI + JQ1 groups. JQ1, a well-known selective BRD inhibitor, was used to suppress BET domain family activity. The mRNA and protein expression levels of BRD2, BRD3 and BRD4 were evaluated using quantitative polymerase chain reaction and western blot analysis, respectively. In addition, the expression levels of markers of cardiac damage were determined using commercial kits. The results indicated that BRD2 and BRD4 mRNA and protein expression levels were significantly increased in the AMI group compared with those in the sham group. In addition, BET inhibition decreased AMI damage in vivo by reversing cardiac function injury, decreasing serum lactate dehydrogenase and creatine kinase-MB isozyme activity, in addition to decreasing the expression levels of high-sensitivity C-reactive protein and interleukin-6. Furthermore, the results suggested that Toll-like receptor 4 (TLR4) signaling was activated by the increased expression of TLR4, TNF receptor-associated factor 6 (TRAF6) and nuclear factor (NF)-κB during AMI. However, JQ1 treatment suppressed TLR4 signaling activation. In conclusion, the present results demonstrated that the inhibition of BET family proteins suppresses AMI, and that this effect was partially mediated by the inhibition of TLR4/TRAF6/NF-κB signaling.
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Affiliation(s)
- Yangli Sun
- Department of Cardiovascular Internal Medicine, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan 450007, P.R. China
| | - Jie Huang
- Department of Cardiovascular Internal Medicine, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan 450007, P.R. China
| | - Kunpeng Song
- Department of Cardiovascular Internal Medicine, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan 450007, P.R. China
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Czubryt MP. Going the distance: Epigenetic regulation of endothelial endothelin-1 controls cardiac hypertrophy. J Mol Cell Cardiol 2015; 82:60-2. [DOI: 10.1016/j.yjmcc.2015.02.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 01/08/2023]
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Stratton MS, McKinsey TA. Acetyl-lysine erasers and readers in the control of pulmonary hypertension and right ventricular hypertrophy. Biochem Cell Biol 2014; 93:149-57. [PMID: 25707943 DOI: 10.1139/bcb-2014-0119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Acetylation of lysine residues within nucleosomal histone tails provides a crucial mechanism for epigenetic control of gene expression. Acetyl groups are coupled to lysine residues by histone acetyltransferases (HATs) and removed by histone deacetylases (HDACs), which are also commonly referred to as "writers" and "erasers", respectively. In addition to altering the electrostatic properties of histones, lysine acetylation often creates docking sites for bromodomain-containing "reader" proteins. This review focuses on epigenetic control of pulmonary hypertension (PH) and associated right ventricular (RV) cardiac hypertrophy and failure. Effects of small molecule HDAC inhibitors in pre-clinical models of PH are highlighted. Furthermore, we describe the recently discovered role of bromodomain and extraterminal (BET) reader proteins in the control of cardiac hypertrophy, and provide evidence suggesting that one member of this family, BRD4, contributes to the pathogenesis of RV failure. Together, the data suggest intriguing potential for pharmacological epigenetic therapies for the treatment of PH and right-sided heart failure.
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Affiliation(s)
- Matthew S Stratton
- Department of Medicine, Division of Cardiology, University of Colorado Denver, 12700 E. 19th Ave, Aurora, CO 80045-0508, USA
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34
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Comer BS, Ba M, Singer CA, Gerthoffer WT. Epigenetic targets for novel therapies of lung diseases. Pharmacol Ther 2014; 147:91-110. [PMID: 25448041 DOI: 10.1016/j.pharmthera.2014.11.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 11/06/2014] [Indexed: 12/13/2022]
Abstract
In spite of substantial advances in defining the immunobiology and function of structural cells in lung diseases there is still insufficient knowledge to develop fundamentally new classes of drugs to treat many lung diseases. For example, there is a compelling need for new therapeutic approaches to address severe persistent asthma that is insensitive to inhaled corticosteroids. Although the prevalence of steroid-resistant asthma is 5-10%, severe asthmatics require a disproportionate level of health care spending and constitute a majority of fatal asthma episodes. None of the established drug therapies including long-acting beta agonists or inhaled corticosteroids reverse established airway remodeling. Obstructive airways remodeling in patients with chronic obstructive pulmonary disease (COPD), restrictive remodeling in idiopathic pulmonary fibrosis (IPF) and occlusive vascular remodeling in pulmonary hypertension are similarly unresponsive to current drug therapy. Therefore, drugs are needed to achieve long-acting suppression and reversal of pathological airway and vascular remodeling. Novel drug classes are emerging from advances in epigenetics. Novel mechanisms are emerging by which cells adapt to environmental cues, which include changes in DNA methylation, histone modifications and regulation of transcription and translation by noncoding RNAs. In this review we will summarize current epigenetic approaches being applied to preclinical drug development addressing important therapeutic challenges in lung diseases. These challenges are being addressed by advances in lung delivery of oligonucleotides and small molecules that modify the histone code, DNA methylation patterns and miRNA function.
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Affiliation(s)
- Brian S Comer
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Mariam Ba
- Department of Pharmacology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - Cherie A Singer
- Department of Pharmacology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - William T Gerthoffer
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA.
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