1
|
Akanyibah FA, Zhu Y, Wan A, Ocansey DKW, Xia Y, Fang AN, Mao F. Effects of DNA methylation and its application in inflammatory bowel disease (Review). Int J Mol Med 2024; 53:55. [PMID: 38695222 DOI: 10.3892/ijmm.2024.5379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is marked by persistent inflammation, and its development and progression are linked to environmental, genetic, immune system and gut microbial factors. DNA methylation (DNAm), as one of the protein modifications, is a crucial epigenetic process used by cells to control gene transcription. DNAm is one of the most common areas that has drawn increasing attention recently, with studies revealing that the interleukin (IL)‑23/IL‑12, wingless‑related integration site, IL‑6‑associated signal transducer and activator of transcription 3, suppressor of cytokine signaling 3 and apoptosis signaling pathways are involved in DNAm and in the pathogenesis of IBD. It has emerged that DNAm‑associated genes are involved in perpetuating the persistent inflammation that characterizes a number of diseases, including IBD, providing a novel therapeutic strategy for exploring their treatment. The present review discusses DNAm‑associated genes in the pathogenesis of IBD and summarizes their application as possible diagnostic, prognostic and therapeutic biomarkers in IBD. This may provide a reference for the particular form of IBD and its related methylation genes, aiding in clinical decision‑making and encouraging therapeutic alternatives.
Collapse
Affiliation(s)
- Francis Atim Akanyibah
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| | - Yi Zhu
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, P.R. China
| | - Aijun Wan
- Zhenjiang College, Zhenjiang, Jiangsu 212028, P.R. China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - An-Ning Fang
- Basic Medical School, Anhui Medical College, Hefei, Anhui 230061, P.R. China
| | - Fei Mao
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, P.R. China
| |
Collapse
|
2
|
Russell-Hallinan A, Cappa O, Kerrigan L, Tonry C, Edgar K, Glezeva N, Ledwidge M, McDonald K, Collier P, Simpson DA, Watson CJ. Single-Cell RNA Sequencing Reveals Cardiac Fibroblast-Specific Transcriptomic Changes in Dilated Cardiomyopathy. Cells 2024; 13:752. [PMID: 38727290 PMCID: PMC11083662 DOI: 10.3390/cells13090752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Dilated cardiomyopathy (DCM) is the most common cause of heart failure, with a complex aetiology involving multiple cell types. We aimed to detect cell-specific transcriptomic alterations in DCM through analysis that leveraged recent advancements in single-cell analytical tools. Single-cell RNA sequencing (scRNA-seq) data from human DCM cardiac tissue were subjected to an updated bioinformatic workflow in which unsupervised clustering was paired with reference label transfer to more comprehensively annotate the dataset. Differential gene expression was detected primarily in the cardiac fibroblast population. Bulk RNA sequencing was performed on an independent cohort of human cardiac tissue and compared with scRNA-seq gene alterations to generate a stratified list of higher-confidence, fibroblast-specific expression candidates for further validation. Concordant gene dysregulation was confirmed in TGFβ-induced fibroblasts. Functional assessment of gene candidates showed that AEBP1 may play a significant role in fibroblast activation. This unbiased approach enabled improved resolution of cardiac cell-type-specific transcriptomic alterations in DCM.
Collapse
Affiliation(s)
- Adam Russell-Hallinan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (A.R.-H.); (C.T.); (K.E.); (D.A.S.)
| | - Oisín Cappa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (A.R.-H.); (C.T.); (K.E.); (D.A.S.)
| | - Lauren Kerrigan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (A.R.-H.); (C.T.); (K.E.); (D.A.S.)
| | - Claire Tonry
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (A.R.-H.); (C.T.); (K.E.); (D.A.S.)
| | - Kevin Edgar
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (A.R.-H.); (C.T.); (K.E.); (D.A.S.)
| | - Nadezhda Glezeva
- School of Medicine, UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland; (N.G.); (K.M.)
| | - Mark Ledwidge
- STOP-HF Unit, St Vincent’s Healthcare Group, D04 T6F4 Dublin, Ireland;
| | - Kenneth McDonald
- School of Medicine, UCD Conway Institute, University College Dublin, D04 V1W8 Dublin, Ireland; (N.G.); (K.M.)
- STOP-HF Unit, St Vincent’s Healthcare Group, D04 T6F4 Dublin, Ireland;
| | - Patrick Collier
- Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - David A. Simpson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (A.R.-H.); (C.T.); (K.E.); (D.A.S.)
| | - Chris J. Watson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (A.R.-H.); (C.T.); (K.E.); (D.A.S.)
| |
Collapse
|
3
|
Bridges J, Ramirez-Guerrero JA, Rosa-Garrido M. Gender-specific genetic and epigenetic signatures in cardiovascular disease. Front Cardiovasc Med 2024; 11:1355980. [PMID: 38529333 PMCID: PMC10962446 DOI: 10.3389/fcvm.2024.1355980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Cardiac sex differences represent a pertinent focus in pursuit of the long-awaited goal of personalized medicine. Despite evident disparities in the onset and progression of cardiac pathology between sexes, historical oversight has led to the neglect of gender-specific considerations in the treatment of patients. This oversight is attributed to a predominant focus on male samples and a lack of sex-based segregation in patient studies. Recognizing these sex differences is not only relevant to the treatment of cisgender individuals; it also holds paramount importance in addressing the healthcare needs of transgender patients, a demographic that is increasingly prominent in contemporary society. In response to these challenges, various agencies, including the National Institutes of Health, have actively directed their efforts toward advancing our comprehension of this phenomenon. Epigenetics has proven to play a crucial role in understanding sex differences in both healthy and disease states within the heart. This review presents a comprehensive overview of the physiological distinctions between males and females during the development of various cardiac pathologies, specifically focusing on unraveling the genetic and epigenetic mechanisms at play. Current findings related to distinct sex-chromosome compositions, the emergence of gender-biased genetic variations, and variations in hormonal profiles between sexes are highlighted. Additionally, the roles of DNA methylation, histone marks, and chromatin structure in mediating pathological sex differences are explored. To inspire further investigation into this crucial subject, we have conducted global analyses of various epigenetic features, leveraging data previously generated by the ENCODE project.
Collapse
Affiliation(s)
| | | | - Manuel Rosa-Garrido
- Department of Biomedical Engineering, School of Medicine, School of Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
4
|
Mitina A, Khan M, Lesurf R, Yin Y, Engchuan W, Hamdan O, Pellecchia G, Trost B, Backstrom I, Guo K, Pallotto LM, Lam Doong PH, Wang Z, Nalpathamkalam T, Thiruvahindrapuram B, Papaz T, Pearson CE, Ragoussis J, Subbarao P, Azad MB, Turvey SE, Mandhane P, Moraes TJ, Simons E, Scherer SW, Lougheed J, Mondal T, Smythe J, Altamirano-Diaz L, Oechslin E, Mital S, Yuen RKC. Genome-wide enhancer-associated tandem repeats are expanded in cardiomyopathy. EBioMedicine 2024; 101:105027. [PMID: 38418263 PMCID: PMC10944212 DOI: 10.1016/j.ebiom.2024.105027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Cardiomyopathy is a clinically and genetically heterogeneous heart condition that can lead to heart failure and sudden cardiac death in childhood. While it has a strong genetic basis, the genetic aetiology for over 50% of cardiomyopathy cases remains unknown. METHODS In this study, we analyse the characteristics of tandem repeats from genome sequence data of unrelated individuals diagnosed with cardiomyopathy from Canada and the United Kingdom (n = 1216) and compare them to those found in the general population. We perform burden analysis to identify genomic and epigenomic features that are impacted by rare tandem repeat expansions (TREs), and enrichment analysis to identify functional pathways that are involved in the TRE-associated genes in cardiomyopathy. We use Oxford Nanopore targeted long-read sequencing to validate repeat size and methylation status of one of the most recurrent TREs. We also compare the TRE-associated genes to those that are dysregulated in the heart tissues of individuals with cardiomyopathy. FINDINGS We demonstrate that tandem repeats that are rarely expanded in the general population are predominantly expanded in cardiomyopathy. We find that rare TREs are disproportionately present in constrained genes near transcriptional start sites, have high GC content, and frequently overlap active enhancer H3K27ac marks, where expansion-related DNA methylation may reduce gene expression. We demonstrate the gene silencing effect of expanded CGG tandem repeats in DIP2B through promoter hypermethylation. We show that the enhancer-associated loci are found in genes that are highly expressed in human cardiomyocytes and are differentially expressed in the left ventricle of the heart in individuals with cardiomyopathy. INTERPRETATION Our findings highlight the underrecognized contribution of rare tandem repeat expansions to the risk of cardiomyopathy and suggest that rare TREs contribute to ∼4% of cardiomyopathy risk. FUNDING Government of Ontario (RKCY), The Canadian Institutes of Health Research PJT 175329 (RKCY), The Azrieli Foundation (RKCY), SickKids Catalyst Scholar in Genetics (RKCY), The University of Toronto McLaughlin Centre (RKCY, SM), Ted Rogers Centre for Heart Research (SM), Data Sciences Institute at the University of Toronto (SM), The Canadian Institutes of Health Research PJT 175034 (SM), The Canadian Institutes of Health Research ENP 161429 under the frame of ERA PerMed (SM, RL), Heart and Stroke Foundation of Ontario & Robert M Freedom Chair in Cardiovascular Science (SM), Bitove Family Professorship of Adult Congenital Heart Disease (EO), Canada Foundation for Innovation (SWS, JR), Canada Research Chair (PS), Genome Canada (PS, JR), The Canadian Institutes of Health Research (PS).
Collapse
Affiliation(s)
- Aleksandra Mitina
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Mahreen Khan
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto; Toronto, Ontario, Canada
| | - Robert Lesurf
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Yue Yin
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Worrawat Engchuan
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Omar Hamdan
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Giovanna Pellecchia
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Brett Trost
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Ian Backstrom
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Keyi Guo
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Linda M Pallotto
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Phoenix Hoi Lam Doong
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Zhuozhi Wang
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Thomas Nalpathamkalam
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Bhooma Thiruvahindrapuram
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada
| | - Tanya Papaz
- Ted Rogers Centre for Heart Research; Toronto, Ontario, Canada; Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto; Toronto, Ontario, Canada
| | - Christopher E Pearson
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto; Toronto, Ontario, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Padmaja Subbarao
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada; Program in Translation Medicine & Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Piushkumar Mandhane
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Theo J Moraes
- Department of Paediatrics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Program in Translation Medicine & Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, Section of Allergy and Clinical Immunology, University of Manitoba, Winnipeg, Manitoba, Canada; Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada; Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jane Lougheed
- Division of Cardiology, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Tapas Mondal
- Division of Cardiology, Department of Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - John Smythe
- Division of Cardiology, Department of Pediatrics, Kingston General Hospital, Kingston, Ontario, Canada
| | - Luis Altamirano-Diaz
- Division of Cardiology, Department of Pediatrics, London Health Sciences Centre, London, Ontario, Canada
| | - Erwin Oechslin
- Division of Cardiology, Toronto Adult Congenital Heart Disease Program at Peter Munk Cardiac Centre, Department of Medicine, University Health Network, and University of Toronto, Toronto, Ontario, Canada
| | - Seema Mital
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; Ted Rogers Centre for Heart Research; Toronto, Ontario, Canada; Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto; Toronto, Ontario, Canada.
| | - Ryan K C Yuen
- Genetics and Genome Biology, The Hospital for Sick Children; Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto; Toronto, Ontario, Canada; The Centre for Applied Genomics, The Hospital for Sick Children; Toronto, Ontario, Canada.
| |
Collapse
|
5
|
Arvunescu AM, Ionescu RF, Cretoiu SM, Dumitrescu SI, Zaharia O, Nanea IT. Inflammation in Heart Failure-Future Perspectives. J Clin Med 2023; 12:7738. [PMID: 38137807 PMCID: PMC10743797 DOI: 10.3390/jcm12247738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Chronic heart failure is a terminal point of a vast majority of cardiac or extracardiac causes affecting around 1-2% of the global population and more than 10% of the people above the age of 65. Inflammation is persistently associated with chronic diseases, contributing in many cases to the progression of disease. Even in a low inflammatory state, past studies raised the question of whether inflammation is a constant condition, or if it is, rather, triggered in different amounts, according to the phenotype of heart failure. By evaluating the results of clinical studies which focused on proinflammatory cytokines, this review aims to identify the ones that are independent risk factors for heart failure decompensation or cardiovascular death. This review assessed the current evidence concerning the inflammatory activation cascade, but also future possible targets for inflammatory response modulation, which can further impact the course of heart failure.
Collapse
Affiliation(s)
- Alexandru Mircea Arvunescu
- Department of Internal Medicine and Cardiology, “Prof. Dr. Th. Burghele” Clinical Hospital, 061344 Bucharest, Romania; (O.Z.); (I.T.N.)
- Department of Cardio-Thoracic Pathology, Cardio-Thoracic Pathology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050471 Bucharest, Romania
| | - Ruxandra Florentina Ionescu
- Department of Cardiology I, Central Military Emergency Hospital “Dr Carol Davila”, 030167 Bucharest, Romania (S.I.D.)
- Department of Morphological Sciences, Cell and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Sanda Maria Cretoiu
- Department of Morphological Sciences, Cell and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Silviu Ionel Dumitrescu
- Department of Cardiology I, Central Military Emergency Hospital “Dr Carol Davila”, 030167 Bucharest, Romania (S.I.D.)
- Department of Cardiology, Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania
| | - Ondin Zaharia
- Department of Internal Medicine and Cardiology, “Prof. Dr. Th. Burghele” Clinical Hospital, 061344 Bucharest, Romania; (O.Z.); (I.T.N.)
- Department of Cardio-Thoracic Pathology, Cardio-Thoracic Pathology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050471 Bucharest, Romania
| | - Ioan Tiberiu Nanea
- Department of Internal Medicine and Cardiology, “Prof. Dr. Th. Burghele” Clinical Hospital, 061344 Bucharest, Romania; (O.Z.); (I.T.N.)
- Department of Cardio-Thoracic Pathology, Cardio-Thoracic Pathology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050471 Bucharest, Romania
| |
Collapse
|
6
|
Wołowiec A, Wołowiec Ł, Grześk G, Jaśniak A, Osiak J, Husejko J, Kozakiewicz M. The Role of Selected Epigenetic Pathways in Cardiovascular Diseases as a Potential Therapeutic Target. Int J Mol Sci 2023; 24:13723. [PMID: 37762023 PMCID: PMC10531432 DOI: 10.3390/ijms241813723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Epigenetics is a rapidly developing science that has gained a lot of interest in recent years due to the correlation between characteristic epigenetic marks and cardiovascular diseases (CVDs). Epigenetic modifications contribute to a change in gene expression while maintaining the DNA sequence. The analysis of these modifications provides a thorough insight into the cardiovascular system from its development to its further functioning. Epigenetics is strongly influenced by environmental factors, including known cardiovascular risk factors such as smoking, obesity, and low physical activity. Similarly, conditions affecting the local microenvironment of cells, such as chronic inflammation, worsen the prognosis in cardiovascular diseases and additionally induce further epigenetic modifications leading to the consolidation of unfavorable cardiovascular changes. A deeper understanding of epigenetics may provide an answer to the continuing strong clinical impact of cardiovascular diseases by improving diagnostic capabilities, personalized medical approaches and the development of targeted therapeutic interventions. The aim of the study was to present selected epigenetic pathways, their significance in cardiovascular diseases, and their potential as a therapeutic target in specific medical conditions.
Collapse
Affiliation(s)
- Anna Wołowiec
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Łukasz Wołowiec
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Grzegorz Grześk
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Albert Jaśniak
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Joanna Osiak
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Jakub Husejko
- Department of Cardiology and Clinical Pharmacology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Mariusz Kozakiewicz
- Department of Geriatrics, Division of Biochemistry and Biogerontology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Torun, Poland
| |
Collapse
|
7
|
Majid A, Hassan FO, Hoque MM, Gbadegoye JO, Lebeche D. Bioactive Compounds and Cardiac Fibrosis: Current Insight and Future Prospect. J Cardiovasc Dev Dis 2023; 10:313. [PMID: 37504569 PMCID: PMC10380727 DOI: 10.3390/jcdd10070313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
Cardiac fibrosis is a pathological condition characterized by excessive deposition of collagen and other extracellular matrix components in the heart. It is recognized as a major contributor to the development and progression of heart failure. Despite significant research efforts in characterizing and identifying key molecular mechanisms associated with myocardial fibrosis, effective treatment for this condition is still out of sight. In this regard, bioactive compounds have emerged as potential therapeutic antifibrotic agents due to their anti-inflammatory and antioxidant properties. These compounds exhibit the ability to modulate fibrogenic processes by inhibiting the production of extracellular matrix proteins involved in fibroblast to myofibroblast differentiation, or by promoting their breakdown. Extensive investigation of these bioactive compounds offers new possibilities for preventing or reducing cardiac fibrosis and its detrimental consequences. This comprehensive review aims to provide a thorough overview of the mechanisms underlying cardiac fibrosis, address the limitations of current treatment strategies, and specifically explore the potential of bioactive compounds as therapeutic interventions for the treatment and/or prevention of cardiac fibrosis.
Collapse
Affiliation(s)
- Abdul Majid
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fasilat Oluwakemi Hassan
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Md Monirul Hoque
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Joy Olaoluwa Gbadegoye
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Djamel Lebeche
- Department of Physiology, College of Medicine, The University of Tennessee Health Science Center, Translational Research Building, Room 318H, 71 S. Manassas, Memphis, TN 38163, USA
- College of Graduate Health Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| |
Collapse
|
8
|
Sopic M, Robinson EL, Emanueli C, Srivastava P, Angione C, Gaetano C, Condorelli G, Martelli F, Pedrazzini T, Devaux Y. Integration of epigenetic regulatory mechanisms in heart failure. Basic Res Cardiol 2023; 118:16. [PMID: 37140699 PMCID: PMC10158703 DOI: 10.1007/s00395-023-00986-3] [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: 02/03/2023] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
The number of "omics" approaches is continuously growing. Among others, epigenetics has appeared as an attractive area of investigation by the cardiovascular research community, notably considering its association with disease development. Complex diseases such as cardiovascular diseases have to be tackled using methods integrating different omics levels, so called "multi-omics" approaches. These approaches combine and co-analyze different levels of disease regulation. In this review, we present and discuss the role of epigenetic mechanisms in regulating gene expression and provide an integrated view of how these mechanisms are interlinked and regulate the development of cardiac disease, with a particular attention to heart failure. We focus on DNA, histone, and RNA modifications, and discuss the current methods and tools used for data integration and analysis. Enhancing the knowledge of these regulatory mechanisms may lead to novel therapeutic approaches and biomarkers for precision healthcare and improved clinical outcomes.
Collapse
Affiliation(s)
- Miron Sopic
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Emma L Robinson
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Costanza Emanueli
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | - Claudio Angione
- School of Computing, Engineering & Digital Technologies, Teesside University, Tees Valley, Middlesbrough, TS1 3BA, UK
- Centre for Digital Innovation, Teesside University, Campus Heart, Tees Valley, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Darlington, DL1 1HG, UK
| | - Carlo Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 10, 27100, Pavia, Italy
| | - Gianluigi Condorelli
- IRCCS-Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, MI, Italy
- Institute of Genetic and Biomedical Research, National Research Council of Italy, Arnold-Heller-Str.3, 24105, Milan, Italy
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097, Milan, Italy
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011, Lausanne, Switzerland
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg.
| |
Collapse
|
9
|
la Torre A, Lo Vecchio F, Greco A. Epigenetic Mechanisms of Aging and Aging-Associated Diseases. Cells 2023; 12:cells12081163. [PMID: 37190071 DOI: 10.3390/cells12081163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
Collapse
Affiliation(s)
- Annamaria la Torre
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Filomena Lo Vecchio
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Antonio Greco
- Complex Unit of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| |
Collapse
|
10
|
Kefayati F, Karimi Babaahmadi A, Mousavi T, Hodjat M, Abdollahi M. Epigenotoxicity: a danger to the future life. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2023; 58:382-411. [PMID: 36942370 DOI: 10.1080/10934529.2023.2190713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Environmental toxicants can regulate gene expression in the absence of DNA mutations via epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNAs' (ncRNAs). Here, all three epigenetic modifications for seven important categories of diseases and the impact of eleven main environmental factors on epigenetic modifications were discussed. Epigenetic-related mechanisms are among the factors that could explain the root cause of a wide range of common diseases. Its overall impression on the development of diseases can help us diagnose and treat diseases, and besides, predict transgenerational and intergenerational effects. This comprehensive article attempted to address the relationship between environmental factors and epigenetic modifications that cause diseases in different categories. The studies main gap is that the precise role of environmentally-induced epigenetic alterations in the etiology of the disorders is unknown; thus, still more well-designed researches need to be accomplished to fill this gap. The present review aimed to first summarize the adverse effect of certain chemicals on the epigenome that may involve in the onset of particular disease based on in vitro and in vivo models. Subsequently, the possible adverse epigenetic changes that can lead to many human diseases were discussed.
Collapse
Affiliation(s)
- Farzaneh Kefayati
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Karimi Babaahmadi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Taraneh Mousavi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshid Hodjat
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Abdollahi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
11
|
Xu X, Elkenani M, Tan X, Hain JK, Cui B, Schnelle M, Hasenfuss G, Toischer K, Mohamed BA. DNA Methylation Analysis Identifies Novel Epigenetic Loci in Dilated Murine Heart upon Exposure to Volume Overload. Int J Mol Sci 2023; 24:ijms24065885. [PMID: 36982963 PMCID: PMC10059258 DOI: 10.3390/ijms24065885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Left ventricular (LV) dilatation, a prominent risk factor for heart failure (HF), precedes functional deterioration and is used to stratify patients at risk for arrhythmias and cardiac mortality. Aberrant DNA methylation contributes to maladaptive cardiac remodeling and HF progression following pressure overload and ischemic cardiac insults. However, no study has examined cardiac DNA methylation upon exposure to volume overload (VO) despite being relatively common among HF patients. We carried out global methylome analysis of LV harvested at a decompensated HF stage following exposure to VO induced by aortocaval shunt. VO resulted in pathological cardiac remodeling, characterized by massive LV dilatation and contractile dysfunction at 16 weeks after shunt. Although methylated DNA was not markedly altered globally, 25 differentially methylated promoter regions (DMRs) were identified in shunt vs. sham hearts (20 hypermethylated and 5 hypomethylated regions). The validated hypermethylated loci in Junctophilin-2 (Jph2), Signal peptidase complex subunit 3 (Spcs3), Vesicle-associated membrane protein-associated protein B (Vapb), and Inositol polyphosphate multikinase (Ipmk) were associated with the respective downregulated expression and were consistently observed in dilated LV early after shunt at 1 week after shunt, before functional deterioration starts to manifest. These hypermethylated loci were also detected peripherally in the blood of the shunt mice. Altogether, we have identified conserved DMRs that could be novel epigenetic biomarkers in dilated LV upon VO exposure.
Collapse
Affiliation(s)
- Xingbo Xu
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| | - Manar Elkenani
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Xiaoying Tan
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
- Department of Nephrology and Rheumatology, University Medical Center of Göttingen, 37075 Göttingen, Germany
| | - Jara Katharina Hain
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Baolong Cui
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| | - Moritz Schnelle
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Gerd Hasenfuss
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| | - Karl Toischer
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| | - Belal A Mohamed
- Department of Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), 37075 Göttingen, Germany
| |
Collapse
|
12
|
Soboleva AG, Sobolev VV, Karapetyan MM, Mezentsev A, Rud’ko OI, Davydova ED, Mogulevtseva JA, Zhukova OV, Korsunskaya IM. Laser Therapy Changes the Expression of Matrix Metalloproteinases in Bleomycin-Induced Skin Fibrosis. Life (Basel) 2023; 13:life13030810. [PMID: 36983965 PMCID: PMC10056988 DOI: 10.3390/life13030810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/05/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Matrix metalloproteinases (MMPs) are often considered biomarkers of skin fibrosis. At the early stages of the pathological process, an elevation of their enzymatic activity causes significant changes in the composition of the extracellular matrix. MMPs secreted by immune cells facilitate their migration to the site of damage. Then, the immune cells eliminate the affected cells and biomolecules. Moreover, bidirectional changes in the activity of proteolytic enzymes, including MMPs, accompany wound healing. This study aimed to assess changes in the expression of Mmp2, Mmp3, and Mmp9 after treating mice with laser therapy using the experimental model of bleomycin-induced skin fibrosis. Using immunohistochemistry, we characterized the histological features of scarred skin. We also analyzed changes in the expression of MMPs using real-time polymerase chain reaction before and after laser irradiation. We showed that treatment of the mice with a CO2 laser partially normalized the histological features of scarred skin. We also noticed a decrease in the expression of Mmp2, Mmp3 (both p < 0.05), and Mmp9 (p = 0.065) during scar healing. The obtained results suggest that normalization of skin homeostasis requires control of MMP activity via induction of genes.
Collapse
Affiliation(s)
- Anna G. Soboleva
- Center for Theoretical Problems in Physico-Chemical Pharmacology, Russian Academy of Sciences, 30 Srednaya Kalitnikovskaya Street, 109029 Moscow, Russia
- Avtsyn Research Institute of Human Morphology of Petrovsky National Research Centre of Surgery, 3 Tsyurupy Street, 117418 Moscow, Russia
| | - Vladimir V. Sobolev
- Center for Theoretical Problems in Physico-Chemical Pharmacology, Russian Academy of Sciences, 30 Srednaya Kalitnikovskaya Street, 109029 Moscow, Russia
- Correspondence:
| | | | - Alexandre Mezentsev
- Center for Theoretical Problems in Physico-Chemical Pharmacology, Russian Academy of Sciences, 30 Srednaya Kalitnikovskaya Street, 109029 Moscow, Russia
| | - Olga I. Rud’ko
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | | | - Julia A. Mogulevtseva
- Department of Agronomy and Biotechnology, Russian Agrarian University (Moscow Timiryazev Agricultural Academy), 49 Timiryazeva Street, 127550 Moscow, Russia
| | - Olga V. Zhukova
- Moscow Center of Dermatology and Cosmetology, 17 Leninsky Avenue, 119071 Moscow, Russia
| | - Irina M. Korsunskaya
- Center for Theoretical Problems in Physico-Chemical Pharmacology, Russian Academy of Sciences, 30 Srednaya Kalitnikovskaya Street, 109029 Moscow, Russia
| |
Collapse
|
13
|
Liang L, Wo C, Yuan Y, Cao H, Tan W, Zhou X, Wang D, Chen R, Shi M, Zhang F, Xiao Y, Liu L, Zhou Y, Zhang T, Wang Y, Guo B. miR-124-3p improves mitochondrial function of renal tubular epithelial cells in db/db mice. FASEB J 2023; 37:e22794. [PMID: 36753399 DOI: 10.1096/fj.202201202rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 02/09/2023]
Abstract
Diabetic kidney disease (DKD) is one of the most serious complications of diabetes mellitus (DM) and the main cause of end-stage renal failure. However, the pathogenesis of DKD is complicated. In this study, we found that miR-124-3p plays a key role in regulating renal mitochondrial function and explored its possible mechanism in DKD progression by performing a series of in vitro and in vivo experiments. Decreased expression of miR-124-3p was found in db/db mice compared to db/m mice. Moreover, miR-124-3p down-regulated FOXQ1 by targeting FOXQ1 mRNA 3'-UTR in NRK-52E cells. Also, an increase in FOXQ1 and down-regulation of Sirt4 were found in db/db mouse kidney and renal tubular epithelial cells cultured with high glucose and high lipid. Overexpression of FOXQ1 could further down-regulate the expression of Sirt4 and aggravate the damage of mitochondria. Conversely, the knockdown of the FOXQ1 gene induced Sirt4 expression and partially restored mitochondrial function. To verify the effects of miR-124-3p on Sirt4 and mitochondria, we found that miR-124-3p mimics could up-regulate Sirt4 and inhibit ROS production and MitoSOX, thus restoring the number and morphology of mitochondria. These results showed that under high-glucose and high-lipid conditions, the down-regulation of miR-124-3p induces FOXQ1 in renal tubular epithelial cells, which in turn suppresses Sirt4 and leads to mitochondrial dysfunction, promoting the development of DKD.
Collapse
Affiliation(s)
- Luqun Liang
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Chunxin Wo
- Department of Pain, Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, China
| | - Yao Yuan
- Clinical Medical Imaging, Guizhou Medical University, Guiyang, China
| | - Hongjuan Cao
- Clinical Medical Imaging, Guizhou Medical University, Guiyang, China
| | - Wanlin Tan
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Xingcheng Zhou
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Dan Wang
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Rongyu Chen
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Mingjun Shi
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Fan Zhang
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Ying Xiao
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Lingling Liu
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Yuxia Zhou
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Tian Zhang
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Yuanyuan Wang
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,Guizhou Province Innovation Base of Common Major Chronic Disease Pathogenesis and Drug Development and Application, Guizhou Medical University, Guiyang, China
| | - Bing Guo
- Department of Pathophysiology, Basic Medical College, Guizhou Medical University, Guiyang, China.,International Scientific and Technological Cooperation Base of Pathogenesis and Drug Research on Common Major Diseases, Guizhou Medical University, Guiyang, China
| |
Collapse
|
14
|
Yuan X, Huang J, Wen L, Novakovic B, Kilby MD, Tong C, Qi H, Saffery R, Baker PN. Genome-wide DNA methylation analysis of discordant monozygotic twins reveals consistent sites of differential methylation associated with congenital heart disease. Genomics 2023; 115:110565. [PMID: 36690264 DOI: 10.1016/j.ygeno.2023.110565] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/04/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
BACKGROUND Despite being essentially genetically identical, monozygotic (MZ) twins can be discordant for congenital heart disease (CHD), thus highlighting the importance of in utero environmental factors for CHD pathogenesis. This study aimed to identify the epigenetic variations between discordant MZ twin pairs that are associated with CHD at birth. METHODS Cord blood of CHD-discordant MZ twins from the Chongqing Longitudinal Twin Study Cohort was subjected to whole-genome bisulfite sequencing, then validated by MeDIP-qPCR and qRT-PCR. RESULTS 379 DMRs mapped to 175 differentially methylated genes (DMGs) were associated with CHD. Functional enrichment analysis identified these DMGs are involved in histone methylation, actin cytoskeleton organization, the regulation of cell differentiation, and adrenergic signaling in cardiomyocytes. Of note, SPESP1 and NOX5 were hypermethylated in CHD, and associated with lower gene expression levels. CONCLUSIONS Specific DNA methy (DNAm) variations in cord blood were associated with CHD, thus illustrating new biomarkers and potential interventional targets for CHD. TRIAL REGISTRATION ChiCTR-OOC-16008203, registered on 1 April 2016 at the Chinese Clinical Trial Registry.
Collapse
Affiliation(s)
- Xi Yuan
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jiayu Huang
- Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Wen
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Boris Novakovic
- Molecular Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Mark D Kilby
- Fetal Medicine Centre, Birmingham Women's & Children's Foundation Trust, Birmingham B15 2TG, UK; Institute of Metabolism & Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chao Tong
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Hongbo Qi
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China.
| | - Richard Saffery
- Molecular Immunity, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia; Department of Pediatrics, University of Melbourne, Parkville, VIC, Australia.
| | - Philip N Baker
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; College of Life Sciences, University of Leicester, Leicester LE1 7RH, UK.
| |
Collapse
|
15
|
Liao X, Kennel PJ, Liu B, Nash TR, Zhuang RZ, Godier-Furnemont AF, Xue C, Lu R, Colombo PC, Uriel N, Reilly MP, Marx SO, Vunjak-Novakovic G, Topkara VK. Effect of mechanical unloading on genome-wide DNA methylation profile of the failing human heart. JCI Insight 2023; 8:161788. [PMID: 36656640 PMCID: PMC9977498 DOI: 10.1172/jci.insight.161788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Heart failure (HF) is characterized by global alterations in myocardial DNA methylation, yet little is known about the epigenetic regulation of the noncoding genome and potential reversibility of DNA methylation with left ventricular assist device (LVAD) therapy. Genome-wide mapping of myocardial DNA methylation in 36 patients with HF at LVAD implantation, 8 patients at LVAD explantation, and 7 nonfailing (NF) donors using a high-density bead array platform identified 2,079 differentially methylated positions (DMPs) in ischemic cardiomyopathy (ICM) and 261 DMPs in nonischemic cardiomyopathy (NICM). LVAD support resulted in normalization of 3.2% of HF-associated DMPs. Methylation-expression correlation analysis yielded several protein-coding genes that are hypomethylated and upregulated (HTRA1, FBXO16, EFCAB13, and AKAP13) or hypermethylated and downregulated (TBX3) in HF. A potentially novel cardiac-specific super-enhancer long noncoding RNA (lncRNA) (LINC00881) is hypermethylated and downregulated in human HF. LINC00881 is an upstream regulator of sarcomere and calcium channel gene expression including MYH6, CACNA1C, and RYR2. LINC00881 knockdown reduces peak calcium amplitude in the beating human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). These data suggest that HF-associated changes in myocardial DNA methylation within coding and noncoding genomes are minimally reversible with mechanical unloading. Epigenetic reprogramming strategies may be necessary to achieve sustained clinical recovery from heart failure.
Collapse
Affiliation(s)
- Xianghai Liao
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Peter J Kennel
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Bohao Liu
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | | | - Chenyi Xue
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Rong Lu
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Paolo C Colombo
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Nir Uriel
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Muredach P Reilly
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Steven O Marx
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | | | - Veli K Topkara
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| |
Collapse
|
16
|
Chew NWS, Loong SSE, Foo R. Progress in molecular biology and translational science: Epigenetics in cardiovascular health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:105-134. [PMID: 37019589 DOI: 10.1016/bs.pmbts.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Conrad Waddington's epigenetics landscape has provided a metaphorical framework for how cells progress from undifferentiated states to one of several discrete, distinct, differentiated cell fates. The understanding of epigenetics has evolved over time, with DNA methylation being the most studied epigenetic modification, followed by histone modifications and non-coding RNA. Cardiovascular diseases (CVD) are leading contributors to death worldwide, with the prevalence of CVDs increasing across the last couple of decades. Significant amount of resources being poured into researching key mechanisms and underpinnings of the various CVDs. These molecular studies looked at the genetics, epigenetics as well as the transcriptomics of various cardiovascular conditions, aiming to provide mechanistic insights. It has paved the way for therapeutics to be developed and in recent years, epi-drugs for the treatment of CVDs. This chapter aims to cover the various roles of epigenetics in the context of cardiovascular health and disease. The following will be examined in detail: the developments in basic experimental techniques used to study epigenetics, the role of epigenetics in various CVDs (hypertension, atrial fibrillation, atherosclerosis, and heart failure), and current advances in epi-therapeutics, providing a holistic view of the current concerted efforts in advancing the field of epigenetics in CVDs.
Collapse
Affiliation(s)
- Nicholas W S Chew
- Department of Cardiology, National University Heart Centre, National University Health System, Singapore, Singapore.
| | - Shaun S E Loong
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Roger Foo
- Department of Cardiology, National University Heart Centre, National University Health System, Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
17
|
Novel Genes Involved in Hypertrophic Cardiomyopathy: Data of Transcriptome and Methylome Profiling. Int J Mol Sci 2022; 23:ijms232315280. [PMID: 36499607 PMCID: PMC9739701 DOI: 10.3390/ijms232315280] [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: 10/10/2022] [Revised: 11/19/2022] [Accepted: 12/02/2022] [Indexed: 12/08/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease; its pathogenesis is still being intensively studied to explain the reasons for the significant genetic and phenotypic heterogeneity of the disease. To search for new genes involved in HCM development, we analyzed gene expression profiles coupled with DNA methylation profiles in the hypertrophied myocardia of HCM patients. The transcriptome analysis identified significant differences in the levels of 193 genes, most of which were underexpressed in HCM. The methylome analysis revealed 1755 nominally significant differentially methylated positions (DMPs), mostly hypomethylated in HCM. Based on gene ontology enrichment analysis, the majority of biological processes, overrepresented by both differentially expressed genes (DEGs) and DMP-containing genes, are involved in the regulation of locomotion and muscle structure development. The intersection of 193 DEGs and 978 DMP-containing genes pinpointed eight common genes, the expressions of which correlated with the methylation levels of the neighboring DMPs. Half of these genes (AUTS2, BRSK2, PRRT1, and SLC17A7), regulated by the mechanism of DNA methylation, were underexpressed in HCM and were involved in neurogenesis and synapse functioning. Our data, suggesting the involvement of innervation-associated genes in HCM, provide additional insights into disease pathogenesis and expand the field of further research.
Collapse
|
18
|
Lizcano F, Bustamante L. Molecular perspectives in hypertrophic heart disease: An epigenetic approach from chromatin modification. Front Cell Dev Biol 2022; 10:1070338. [DOI: 10.3389/fcell.2022.1070338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/18/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenetic changes induced by environmental factors are increasingly relevant in cardiovascular diseases. The most frequent molecular component in cardiac hypertrophy is the reactivation of fetal genes caused by various pathologies, including obesity, arterial hypertension, aortic valve stenosis, and congenital causes. Despite the multiple investigations performed to achieve information about the molecular components of this pathology, its influence on therapeutic strategies is relatively scarce. Recently, new information has been taken about the proteins that modify the expression of fetal genes reactivated in cardiac hypertrophy. These proteins modify the DNA covalently and induce changes in the structure of chromatin. The relationship between histones and DNA has a recognized control in the expression of genes conditioned by the environment and induces epigenetic variations. The epigenetic modifications that regulate pathological cardiac hypertrophy are performed through changes in genomic stability, chromatin architecture, and gene expression. Histone 3 trimethylation at lysine 4, 9, or 27 (H3-K4; -K9; -K27me3) and histone demethylation at lysine 9 and 79 (H3-K9; -K79) are mediators of reprogramming in pathologic hypertrophy. Within the chromatin architecture modifiers, histone demethylases are a group of proteins that have been shown to play an essential role in cardiac cell differentiation and may also be components in the development of cardiac hypertrophy. In the present work, we review the current knowledge about the influence of epigenetic modifications in the expression of genes involved in cardiac hypertrophy and its possible therapeutic approach.
Collapse
|
19
|
Lewandowski P, Goławski M, Baron M, Reichman-Warmusz E, Wojnicz R. A Systematic Review of miRNA and cfDNA as Potential Biomarkers for Liquid Biopsy in Myocarditis and Inflammatory Dilated Cardiomyopathy. Biomolecules 2022; 12:biom12101476. [PMID: 36291684 PMCID: PMC9599237 DOI: 10.3390/biom12101476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Myocarditis and inflammatory dilated cardiomyopathy are cardiac diseases leading to heart failure. Liquid biopsy is a concept of replacing traditional biopsy with specialized blood tests. The study aim was to summarize and assess the usefulness of microRNAs and circulating free DNA as biomarkers of myocardial inflammation. For this systematic review, we searched Scopus, Embase, Web of Science, and PubMed. All studies measuring microRNAs in serum/plasma/cardiac tissue or circulating free DNA during myocarditis and non-ischemic dilated cardiomyopathy in humans in which healthy subjects or another cardiac disease served as a comparator were included. Data were extracted and miRNAs were screened and assessed using a scale created in-house. Then, highly graded miRNAs were assessed for usability as liquid biopsy biomarkers. Of 1185 records identified, 56 were eligible and 187 miRNAs were found. We did not identify any studies measuring circulating free DNA. In total, 24 of the screened miRNAs were included in the final assessment, 3 of which were selected as the best and 3 as potential candidates. We were not able to assess the risk of bias and the final inclusion decision was made by consensus. Serum levels of three miRNAs—miR-Chr8:96, miR-155, and miR-206—are the best candidates for myocardial inflammation liquid biopsy panel. Further studies are necessary to prove their role, specificity, and sensitivity.
Collapse
Affiliation(s)
- Piotr Lewandowski
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
- Correspondence: ; Tel.: +48-32-275-50-09
| | - Marcin Goławski
- Department of Pharmacology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Maciej Baron
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Edyta Reichman-Warmusz
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Romuald Wojnicz
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
- Silesian Nanomicroscopy Center, Silesia LabMed—Research and Implementation Center, Medical University of Silesia, 40-055 Katowice, Poland
| |
Collapse
|
20
|
Desale H, Buekens P, Alger J, Cafferata ML, Harville EW, Herrera C, Truyens C, Dumonteil E. Epigenetic signature of exposure to maternal Trypanosoma cruzi infection in cord blood cells from uninfected newborns. Epigenomics 2022; 14:913-927. [PMID: 36039408 PMCID: PMC9475499 DOI: 10.2217/epi-2022-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To assess the epigenetic effects of in utero exposure to maternal Trypanosoma cruzi infection. Methods: We performed an epigenome-wide association study to compare the DNA methylation patterns of umbilical cord blood cells from uninfected babies from chagasic and uninfected mothers. DNA methylation was measured using Infinium EPIC arrays. Results: We identified a differential DNA methylation signature of fetal exposure to maternal T. cruzi infection, in the absence of parasite transmission, with 12 differentially methylated sites in B cells and CD4+ T cells, including eight protein-coding genes. Conclusion: These genes participate in hematopoietic cell differentiation and the immune response and may be involved in immune disorders. They also have been associated with several developmental disorders and syndromes.
Collapse
Affiliation(s)
- Hans Desale
- Department of Tropical Medicine, Tulane University School of Public Health & Tropical Medicine & Tulane University Vector-Borne & Infectious Disease Research Center, New Orleans, LA 70112, USA
| | - Pierre Buekens
- Department of Epidemiology, Tulane University School of Public Health & Tropical Medicine, New Orleans, LA 70112, USA
| | - Jackeline Alger
- Instituto de Enfermedades Infecciosas y Parasitologia Antonio Vidal, Tegucigalpa, Honduras.,Ministry of Health, Hospital Escuela, Tegucigalpa, Honduras
| | - Maria Luisa Cafferata
- Unidad de Investigación Clínica y Epidemiológica Montevideo (UNICEM), Hospital de Clínicas, Montevideo, 11600, Uruguay
| | - Emily Wheeler Harville
- Department of Epidemiology, Tulane University School of Public Health & Tropical Medicine, New Orleans, LA 70112, USA
| | - Claudia Herrera
- Department of Tropical Medicine, Tulane University School of Public Health & Tropical Medicine & Tulane University Vector-Borne & Infectious Disease Research Center, New Orleans, LA 70112, USA
| | - Carine Truyens
- Laboratory of Parasitology, Faculty of Medicine, & ULB Center for Research in Immunology (UCRI), Université Libre de Bruxelles, Brussels, Belgium
| | - Eric Dumonteil
- Department of Tropical Medicine, Tulane University School of Public Health & Tropical Medicine & Tulane University Vector-Borne & Infectious Disease Research Center, New Orleans, LA 70112, USA
| |
Collapse
|
21
|
Zhang Y, Jia Z, Zhou Q, Zhang Y, Li D, Qi Y, Xu F. A bibliometric analysis of DNA methylation in cardiovascular diseases from 2001 to 2021. Medicine (Baltimore) 2022; 101:e30029. [PMID: 35984203 PMCID: PMC9388003 DOI: 10.1097/md.0000000000030029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DNA methylation is a dynamically reversible form of epigenetics. Dynamic regulation plays an important role in cardiovascular diseases (CVDs). However, there have been few bibliometric studies in this field. We aimed to visualize the research results and hotspots of DNA methylation in CVDs using a bibliometric analysis to provide a scientific direction for future research. METHODS Publications related to DNA methylation in CVDs from January 1, 2001, to September 15, 2021, were searched and confirmed from the Web of Science Core Collection. CiteSpace 5.7 and VOSviewer 1.6.15 were used for bibliometric and knowledge-map analyses. RESULTS A total of 2617 publications were included in 912 academic journals by 15,584 authors from 963 institutions from 85 countries/regions. Among them, the United States of America, China, and England were the top 3 countries contributing to the field of DNA methylation. Harvard University, Columbia University, and University of Cambridge were the top 3 contributing institutions in terms of publications and were closely linked. PLoS One was the most published and co-cited journal. Baccarelli Andrea A published the most content, while Barker DJP had the highest frequency of co-citations. The keyword cluster focused on the mechanism, methyl-containing substance, exposure/risk factor, and biomarker. In terms of research hotspots, references with strong bursts, which are still ongoing, recently included "epigenetic clock" (2017-2021), "obesity, smoking, aging, and DNA methylation" (2017-2021), and "biomarker and epigenome-wide association study" (2019-2021). CONCLUSIONS We used bibliometric and visual methods to identify research hotspots and trends in DNA methylation in CVDs. Epigenetic clocks, biomarkers, environmental exposure, and lifestyle may become the focus and frontier of future research.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Cardiovascular, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zijun Jia
- Department of Cardiovascular, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Qingbing Zhou
- Department of Cardiovascular, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Zhang
- Department of Cardiovascular, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dandan Li
- Department of Cardiovascular, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yifei Qi
- Department of Cardiovascular, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengqin Xu
- Department of Cardiovascular, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Fengqin Xu, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China (e-mail: )
| |
Collapse
|
22
|
Multi-omics assessment of dilated cardiomyopathy using non-negative matrix factorization. PLoS One 2022; 17:e0272093. [PMID: 35980883 PMCID: PMC9387871 DOI: 10.1371/journal.pone.0272093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
Dilated cardiomyopathy (DCM), a myocardial disease, is heterogeneous and often results in heart failure and sudden cardiac death. Unavailability of cardiac tissue has hindered the comprehensive exploration of gene regulatory networks and nodal players in DCM. In this study, we carried out integrated analysis of transcriptome and methylome data using non-negative matrix factorization from a cohort of DCM patients to uncover underlying latent factors and covarying features between whole-transcriptome and epigenome omics datasets from tissue biopsies of living patients. DNA methylation data from Infinium HM450 and mRNA Illumina sequencing of n = 33 DCM and n = 24 control probands were filtered, analyzed and used as input for matrix factorization using R NMF package. Mann-Whitney U test showed 4 out of 5 latent factors are significantly different between DCM and control probands (P<0.05). Characterization of top 10% features driving each latent factor showed a significant enrichment of biological processes known to be involved in DCM pathogenesis, including immune response (P = 3.97E-21), nucleic acid binding (P = 1.42E-18), extracellular matrix (P = 9.23E-14) and myofibrillar structure (P = 8.46E-12). Correlation network analysis revealed interaction of important sarcomeric genes like Nebulin, Tropomyosin alpha-3 and ERC-protein 2 with CpG methylation of ATPase Phospholipid Transporting 11A0, Solute Carrier Family 12 Member 7 and Leucine Rich Repeat Containing 14B, all with significant P values associated with correlation coefficients >0.7. Using matrix factorization, multi-omics data derived from human tissue samples can be integrated and novel interactions can be identified. Hypothesis generating nature of such analysis could help to better understand the pathophysiology of complex traits such as DCM.
Collapse
|
23
|
Epigenetic regulation in cardiovascular disease: mechanisms and advances in clinical trials. Signal Transduct Target Ther 2022; 7:200. [PMID: 35752619 PMCID: PMC9233709 DOI: 10.1038/s41392-022-01055-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/18/2022] [Accepted: 06/08/2022] [Indexed: 12/17/2022] Open
Abstract
Epigenetics is closely related to cardiovascular diseases. Genome-wide linkage and association analyses and candidate gene approaches illustrate the multigenic complexity of cardiovascular disease. Several epigenetic mechanisms, such as DNA methylation, histone modification, and noncoding RNA, which are of importance for cardiovascular disease development and regression. Targeting epigenetic key enzymes, especially the DNA methyltransferases, histone methyltransferases, histone acetylases, histone deacetylases and their regulated target genes, could represent an attractive new route for the diagnosis and treatment of cardiovascular diseases. Herein, we summarize the knowledge on epigenetic history and essential regulatory mechanisms in cardiovascular diseases. Furthermore, we discuss the preclinical studies and drugs that are targeted these epigenetic key enzymes for cardiovascular diseases therapy. Finally, we conclude the clinical trials that are going to target some of these processes.
Collapse
|
24
|
Monayo SM, Liu X. The Prospective Application of Melatonin in Treating Epigenetic Dysfunctional Diseases. Front Pharmacol 2022; 13:867500. [PMID: 35668933 PMCID: PMC9163742 DOI: 10.3389/fphar.2022.867500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/14/2022] [Indexed: 01/09/2023] Open
Abstract
In the past, different human disorders were described by scientists from the perspective of either environmental factors or just by genetically related mechanisms. The rise in epigenetic studies and its modifications, i.e., heritable alterations in gene expression without changes in DNA sequences, have now been confirmed in diseases. Modifications namely, DNA methylation, posttranslational histone modifications, and non-coding RNAs have led to a better understanding of the coaction between epigenetic alterations and human pathologies. Melatonin is a widely-produced indoleamine regulator molecule that influences numerous biological functions within many cell types. Concerning its broad spectrum of actions, melatonin should be investigated much more for its contribution to the upstream and downstream mechanistic regulation of epigenetic modifications in diseases. It is, therefore, necessary to fill the existing gaps concerning corresponding processes associated with melatonin with the physiological abnormalities brought by epigenetic modifications. This review outlines the findings on melatonin’s action on epigenetic regulation in human diseases including neurodegenerative diseases, diabetes, cancer, and cardiovascular diseases. It summarizes the ability of melatonin to act on molecules such as proteins and RNAs which affect the development and progression of diseases.
Collapse
|
25
|
Kucher AN, Sleptcov AA, Nazarenko MS. Genetic Landscape of Dilated Cardiomyopathy. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422030085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
26
|
Ambrosini S, Gorica E, Mohammed SA, Costantino S, Ruschitzka F, Paneni F. Epigenetic remodeling in heart failure with preserved ejection fraction. Curr Opin Cardiol 2022; 37:219-226. [PMID: 35275888 PMCID: PMC9415220 DOI: 10.1097/hco.0000000000000961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW In this review, we critically address the role of epigenetic processing and its therapeutic modulation in heart failure with preserved ejection fraction (HFpEF). RECENT FINDINGS HFpEF associates with a poor prognosis and the identification of novel molecular targets and therapeutic approaches are in high demand. Emerging evidence indicates a key involvement of epigenetic signals in the regulation of transcriptional programs underpinning features of HFpEF. The growing understanding of chromatin dynamics has led to the development of selective epigenetic drugs able to reset transcriptional changes thus delaying or preventing the progression toward HFpEF. Epigenetic information in the setting of HFpEF can be employed to: (i) dissect novel epigenetic networks and chromatin marks contributing to HFpEF; (ii) unveil circulating and cell-specific epigenetic biomarkers; (iii) build predictive models by using computational epigenetics and deep machine learning; (iv) develop new chromatin modifying drugs for personalized management of HFpEF. SUMMARY Acquired epigenetic signatures during the lifetime can contribute to derail molecular pathways involved in HFpEF. A scrutiny investigation of the individual epigenetic landscape will offer opportunities to develop personalized epigenetic biomarkers and therapies to fight HFpEF in the decades to come.
Collapse
Affiliation(s)
- Samuele Ambrosini
- Center for Molecular Cardiology, University of Zurich, Zurich, Switzerland
| | - Era Gorica
- Center for Molecular Cardiology, University of Zurich, Zurich, Switzerland
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | | | - Sarah Costantino
- Center for Molecular Cardiology, University of Zurich, Zurich, Switzerland
| | | | - Francesco Paneni
- Center for Molecular Cardiology, University of Zurich, Zurich, Switzerland
- University Heart Center, Cardiology
- Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
| |
Collapse
|
27
|
DNMT3B System Dysregulation Contributes to the Hypomethylated State in Ischaemic Human Hearts. Biomedicines 2022; 10:biomedicines10040866. [PMID: 35453616 PMCID: PMC9029641 DOI: 10.3390/biomedicines10040866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 12/10/2022] Open
Abstract
A controversial understanding of the state of the DNA methylation machinery exists in ischaemic cardiomyopathy (ICM). Moreover, its relationship to other epigenetic alterations is incomplete. Therefore, we carried out an in-depth study of the DNA methylation process in human cardiac tissue. We showed a dysregulation of the DNA methylation machinery accordingly with the genome-wide hypomethylation that we observed: specifically, an overexpression of main genes involved in the elimination of methyl groups (TET1, SMUG1), and underexpression of molecules implicated in the maintenance of methylation (MBD2, UHRF1). By contrast, we found DNMT3B upregulation, a key molecule in the addition of methyl residues in DNA, and an underexpression of miR-133a-3p, an inhibitor of DNMT3B transcription. However, we found many relevant alterations that would counteract the upregulation observed, such as the overexpression of TRAF6, responsible for Dnmt3b degradation. Furthermore, we showed that molecules regulating Dnmts activity were altered; specifically, SAM/SAH ratio reduction. All these results are in concordance with the Dnmts normal function that we show. Our analysis revealed genome-wide hypomethylation along with dysregulation in the mechanisms of addition, elimination and maintenance of methyl groups in the DNA of ICM. We describe relevant alterations in the DNMT3B system, which promote a normal Dnmt3b function despite its upregulation.
Collapse
|
28
|
Qiu BQ, Lin XH, Lai SQ, Lu F, Lin K, Long X, Zhu SQ, Zou HX, Xu JJ, Liu JC, Wu YB. ITGB1-DT/ARNTL2 axis may be a novel biomarker in lung adenocarcinoma: a bioinformatics analysis and experimental validation. Cancer Cell Int 2021; 21:665. [PMID: 34906142 PMCID: PMC8670189 DOI: 10.1186/s12935-021-02380-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Lung cancer is one of the most lethal malignant tumors that endangers human health. Lung adenocarcinoma (LUAD) has increased dramatically in recent decades, accounting for nearly 40% of all lung cancer cases. Increasing evidence points to the importance of the competitive endogenous RNA (ceRNA) intrinsic mechanism in various human cancers. However, behavioral characteristics of the ceRNA network in lung adenocarcinoma need further study. METHODS Groups based on SLC2A1 expression were used in this study to identify associated ceRNA networks and potential prognostic markers in lung adenocarcinoma. The Cancer Genome Atlas (TCGA) database was used to obtain the patients' lncRNA, miRNA, and mRNA expression profiles, as well as clinical data. Informatics techniques were used to investigate the effect of hub genes on prognosis. The Cox regression analyses were performed to evaluate the prognostic effect of hub genes. The methylation, GSEA, and immune infiltration analyses were utilized to explore the potential mechanisms of the hub gene. The CCK-8, transwell, and colony formation assays were performed to detect the proliferation and invasion of lung cancer cells. RESULTS We eventually identified the ITGB1-DT/ARNTL2 axis as an independent fact may promote lung adenocarcinoma progression. Furthermore, methylation analysis revealed that hypo-methylation may cause the dysregulated ITGB1-DT/ARNTL2 axis, and immune infiltration analysis revealed that the ITGB1-DT/ARNTL2 axis may affect the immune microenvironment and the progression of lung adenocarcinoma. The CCK-8, transwell, and colonu formation assays suggested that ITGB1-DT/ARNTL2 promotes the progression of lung adenocarcinoma. And hsa-miR-30b-3p reversed the ITGB1/ARNTL2-mediated oncogenic processes. CONCLUSION Our study identified the ITGB1-DT/ARNTL2 axis as a novel prognostic biomarker affects the prognosis of lung adenocarcinoma.
Collapse
Affiliation(s)
- Bai-Quan Qiu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xia-Hui Lin
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Song-Qing Lai
- Institute of Cardiovascular Disease, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Feng Lu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kun Lin
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiang Long
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shu-Qiang Zhu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Hua-Xi Zou
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jian-Jun Xu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ji-Chun Liu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
| | - Yong-Bing Wu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
| |
Collapse
|
29
|
Yang M, Wang X, Wang T. Regulation of Mitochondrial Function by Noncoding RNAs in Heart Failure and Its Application in Diagnosis and Treatment. J Cardiovasc Pharmacol 2021; 78:377-387. [PMID: 34132686 DOI: 10.1097/fjc.0000000000001081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
ABSTRACT Heart failure (HF) is the terminal stage of multiple cardiovascular diseases. However, the pathogenesis of HF remains unclear and prompt; appropriate diagnosis and treatment of HF are crucial. Cardiomyocytes isolated from HF subjects frequently present mitochondrial impairment and dysfunction. Many studies have suggested that the regulation by noncoding RNAs (ncRNAs) of mitochondria can affect the occurrence and progression of HF. The regulation by ncRNAs of myocardial mitochondria during HF and the recent applications of ncRNAs in the diagnosis and treatment of HF are summarized in this review that is intended to gain keen insights into the mechanisms of HF and more effective treatments.
Collapse
Affiliation(s)
- Miaomiao Yang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | | | | |
Collapse
|
30
|
Pagiatakis C, Di Mauro V. The Emerging Role of Epigenetics in Therapeutic Targeting of Cardiomyopathies. Int J Mol Sci 2021; 22:ijms22168721. [PMID: 34445422 PMCID: PMC8395924 DOI: 10.3390/ijms22168721] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiomyopathies (CMPs) are a heterogeneous group of myocardial diseases accountable for the majority of cases of heart failure (HF) and/or sudden cardiac death (SCD) worldwide. With the recent advances in genomics, the original classification of CMPs on the basis of morphological and functional criteria (dilated (DCM), hypertrophic (HCM), restrictive (RCM), and arrhythmogenic ventricular cardiomyopathy (AVC)) was further refined into genetic (inherited or familial) and acquired (non-inherited or secondary) forms. Despite substantial progress in the identification of novel CMP-associated genetic variations, as well as improved clinical recognition diagnoses, the functional consequences of these mutations and the exact details of the signaling pathways leading to hypertrophy, dilation, and/or contractile impairment remain elusive. To date, global research has mainly focused on the genetic factors underlying CMP pathogenesis. However, growing evidence shows that alterations in molecular mediators associated with the diagnosis of CMPs are not always correlated with genetic mutations, suggesting that additional mechanisms, such as epigenetics, may play a role in the onset or progression of CMPs. This review summarizes published findings of inherited CMPs with a specific focus on the potential role of epigenetic mechanisms in regulating these cardiac disorders.
Collapse
Affiliation(s)
- Christina Pagiatakis
- IRCCS-Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
- Correspondence: (C.P.); (V.D.M.)
| | - Vittoria Di Mauro
- IRCCS-Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
- Institute of Genetic and Biomedical Research (IRGB), Milan Unit, National Research Council, Via Fantoli 16/15, 20138 Milan, Italy
- Correspondence: (C.P.); (V.D.M.)
| |
Collapse
|
31
|
Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development. Sci Rep 2021; 11:15240. [PMID: 34315913 PMCID: PMC8316452 DOI: 10.1038/s41598-021-94014-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/05/2021] [Indexed: 11/08/2022] Open
Abstract
Skeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that long intergenic non-coding RNAs (lincRNAs) are implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of Duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, and 228 putative lincRNAs were identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Expression profile analysis showed that a total of 120 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for differentially expressed lincRNAs (DE lincRNAs), 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for further exploring the molecular mechanisms of lincRNAs during skeletal muscle development.
Collapse
|
32
|
Hamdani N, Costantino S, Mügge A, Lebeche D, Tschöpe C, Thum T, Paneni F. Leveraging clinical epigenetics in heart failure with preserved ejection fraction: a call for individualized therapies. Eur Heart J 2021; 42:1940-1958. [PMID: 36282124 DOI: 10.1093/eurheartj/ehab197] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Described as the 'single largest unmet need in cardiovascular medicine', heart failure with preserved ejection fraction (HFpEF) remains an untreatable disease currently representing 65% of new heart failure diagnoses. HFpEF is more frequent among women and associates with a poor prognosis and unsustainable healthcare costs. Moreover, the variability in HFpEF phenotypes amplifies complexity and difficulties in the approach. In this perspective, unveiling novel molecular targets is imperative. Epigenetic modifications-defined as changes of DNA, histones, and non-coding RNAs (ncRNAs)-represent a molecular framework through which the environment modulates gene expression. Epigenetic signals acquired over the lifetime lead to chromatin remodelling and affect transcriptional programmes underlying oxidative stress, inflammation, dysmetabolism, and maladaptive left ventricular remodelling, all conditions predisposing to HFpEF. The strong involvement of epigenetic signalling in this setting makes the epigenetic information relevant for diagnostic and therapeutic purposes in patients with HFpEF. The recent advances in high-throughput sequencing, computational epigenetics, and machine learning have enabled the identification of reliable epigenetic biomarkers in cardiovascular patients. Contrary to genetic tools, epigenetic biomarkers mirror the contribution of environmental cues and lifestyle changes and their reversible nature offers a promising opportunity to monitor disease states. The growing understanding of chromatin and ncRNAs biology has led to the development of several Food and Drug Administration approved 'epidrugs' (chromatin modifiers, mimics, anti-miRs) able to prevent transcriptional alterations underpinning left ventricular remodelling and HFpEF. In the present review, we discuss the importance of clinical epigenetics as a new tool to be employed for a personalized management of HFpEF.
Collapse
Affiliation(s)
- Nazha Hamdani
- Institute of Physiology, Ruhr University, Bochum, Germany.,Molecular and Experimental Cardiology, Ruhr University, Bochum, Germany.,Department of Cardiology, St-Josef Hospital, Ruhr University, Bochum, Germany.,Clinical Pharmacology, Ruhr University, Bochum, Germany
| | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, Schlieren CH-8952, Switzerland
| | - Andreas Mügge
- Molecular and Experimental Cardiology, Ruhr University, Bochum, Germany.,Department of Cardiology, St-Josef Hospital, Ruhr University, Bochum, Germany
| | - Djamel Lebeche
- Department of Medicine, Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY 10029, USA.,Department of Medicine, Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Medicine, Graduate School of Biological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carsten Tschöpe
- Berlin Institute of Health Center for Regenerative Therapies and Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin, Germany.,Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum (CVK), Berlin, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany.,REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany.,Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover 30625, Germany
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, Schlieren CH-8952, Switzerland.,University Heart Center, Cardiology, University Hospital Zurich, Zürich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zürich, Switzerland
| |
Collapse
|
33
|
Chair SY, Chan JYW, Waye MMY, Liu T, Law BMH, Chien WT. Exploration of Potential Genetic Biomarkers for Heart Failure: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18115904. [PMID: 34072866 PMCID: PMC8198957 DOI: 10.3390/ijerph18115904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022]
Abstract
Patients with heart failure (HF) often present with signs and symptoms that are often nonspecific and with a wide differential diagnosis, making diagnosis and prognosis of HF by clinical presentation alone challenging. Our knowledge on genetic diversity is rapidly evolving with high-throughput DNA sequencing technology, which makes a great potential for genetic biomarker development. The present review attempts to provide a comprehensive review on the modification of major genetic components in HF patients and to explore the potential application of these components as clinical biomarkers in the diagnosis and in monitoring the progress of HF. The literature search was conducted using six databases, resulting in the inclusion of eighteen studies in the review. The findings of these studies were summarized narratively. An appraisal of the reporting quality of the included studies was conducted using a twelve-item checklist adapted from the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist. The findings showed that changes in genetic components in patients with HF compared to healthy controls could be noninvasive diagnostic or prognostic tools for HF with higher specificity and sensitivity in comparison with the traditional biomarkers. This review provided evidence for the potential of developing genetic biomarkers of HF.
Collapse
Affiliation(s)
- Sek-Ying Chair
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Judy-Yuet-Wa Chan
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Correspondence:
| | - Mary-Miu-Yee Waye
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- The Croucher Laboratory for Human Genomics, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Liu
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
| | - Bernard-Man-Hin Law
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
| | - Wai-Tong Chien
- The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; (S.-Y.C.); (M.-M.-Y.W.); (T.L.); (B.-M.-H.L.); (W.-T.C.)
- Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
34
|
Fischer MA, Vondriska TM. Clinical epigenomics for cardiovascular disease: Diagnostics and therapies. J Mol Cell Cardiol 2021; 154:97-105. [PMID: 33561434 PMCID: PMC8330446 DOI: 10.1016/j.yjmcc.2021.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/05/2021] [Accepted: 01/10/2021] [Indexed: 12/28/2022]
Abstract
The study of epigenomics has advanced in recent years to span the regulation of a single genetic locus to the structure and orientation of entire chromosomes within the nucleus. In this review, we focus on the challenges and opportunities of clinical epigenomics in cardiovascular disease. As an integrator of genetic and environmental inputs, and because of advances in measurement techniques that are highly reproducible and provide sequence information, the epigenome is a rich source of potential biosignatures of cardiovascular health and disease. Most of the studies to date have focused on the latter, and herein we discuss observations on epigenomic changes in human cardiovascular disease, examining the role of protein modifiers of chromatin, noncoding RNAs and DNA modification. We provide an overview of cardiovascular epigenomics, discussing the challenges of data sovereignty, data analysis, doctor-patient ethics and innovations necessary to implement precision health.
Collapse
Affiliation(s)
- Matthew A Fischer
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, USA.
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine at UCLA, USA
| |
Collapse
|
35
|
Chandra S, Ehrlich KC, Lacey M, Baribault C, Ehrlich M. Epigenetics and expression of key genes associated with cardiac fibrosis: NLRP3, MMP2, MMP9, CCN2/CTGF and AGT. Epigenomics 2021; 13:219-234. [PMID: 33538177 PMCID: PMC7907962 DOI: 10.2217/epi-2020-0446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aims: Excessive inflammatory signaling and pathological remodeling of the extracellular matrix drive cardiac fibrosis and require changes in gene expression. Materials and methods: Using bioinformatics, both tissue-specific expression profiles and epigenomic profiles of some genes critical for cardiac fibrosis were examined, namely, NLRP3, MMP2, MMP9, CCN2/CTGF, AGT (encodes angiotensin II precursors) and hsa-mir-223 (post-transcriptionally regulates NLRP3). Results: In monocytes, neutrophils, fibroblasts, venous cells, liver and brain, enhancers or super-enhancers were found that correlate with high expression of these genes. One enhancer extended into a silent gene neighbor. These enhancers harbored tissue-specific foci of DNA hypomethylation, open chromatin and transcription factor binding. Conclusions: This study identified previously undescribed enhancers containing hypomethylated transcription factor binding subregions that are predicted to regulate expression of these cardiac fibrosis-inducing genes.
Collapse
Affiliation(s)
- Sruti Chandra
- Tulane Research Innovation for Arrhythmia Discoveries, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Kenneth C Ehrlich
- Tulane Center for Biomedical Informatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA, 70112, USA.,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Carl Baribault
- Center for Research & Scientific Computing, Tulane University Information Technology, New Orleans, LA, 70112, USA
| | - Melanie Ehrlich
- Tulane Center for Biomedical Informatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.,Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA
| |
Collapse
|
36
|
Lee S, Zhou J, Li KHC, Leung KSK, Lakhani I, Liu T, Wong ICK, Mok NS, Mak C, Jeevaratnam K, Zhang Q, Tse G. Territory-wide cohort study of Brugada syndrome in Hong Kong: predictors of long-term outcomes using random survival forests and non-negative matrix factorisation. Open Heart 2021; 8:e001505. [PMID: 33547222 PMCID: PMC7871343 DOI: 10.1136/openhrt-2020-001505] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Brugada syndrome (BrS) is an ion channelopathy that predisposes affected patients to spontaneous ventricular tachycardia/fibrillation (VT/VF) and sudden cardiac death. The aim of this study is to examine the predictive factors of spontaneous VT/VF. METHODS This was a territory-wide retrospective cohort study of patients diagnosed with BrS between 1997 and 2019. The primary outcome was spontaneous VT/VF. Cox regression was used to identify significant risk predictors. Non-linear interactions between variables (latent patterns) were extracted using non-negative matrix factorisation (NMF) and used as inputs into the random survival forest (RSF) model. RESULTS This study included 516 consecutive BrS patients (mean age of initial presentation=50±16 years, male=92%) with a median follow-up of 86 (IQR: 45-118) months. The cohort was divided into subgroups based on initial disease manifestation: asymptomatic (n=314), syncope (n=159) or VT/VF (n=41). Annualised event rates per person-year were 1.70%, 0.05% and 0.01% for the VT/VF, syncope and asymptomatic subgroups, respectively. Multivariate Cox regression analysis revealed initial presentation of VT/VF (HR=24.0, 95% CI=1.21 to 479, p=0.037) and SD of P-wave duration (HR=1.07, 95% CI=1.00 to 1.13, p=0.044) were significant predictors. The NMF-RSF showed the best predictive performance compared with RSF and Cox regression models (precision: 0.87 vs 0.83 vs. 0.76, recall: 0.89 vs. 0.85 vs 0.73, F1-score: 0.88 vs 0.84 vs 0.74). CONCLUSIONS Clinical history, electrocardiographic markers and investigation results provide important information for risk stratification. Machine learning techniques using NMF and RSF significantly improves overall risk stratification performance.
Collapse
Affiliation(s)
- Sharen Lee
- Cardiovascular Analytics Group, Laboratory of Cardiovascular Physiology, Hong Kong, China
| | - Jiandong Zhou
- School of Data Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Ka Hou Christien Li
- Faculty of Medicine, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | | | - Ishan Lakhani
- Cardiovascular Analytics Group, Laboratory of Cardiovascular Physiology, Hong Kong, China
| | - Tong Liu
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Ian Chi Kei Wong
- Research department of Practice and Policy, University College London School of Pharmacy, London, UK
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Ngai Shing Mok
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Chloe Mak
- Department of Pathology, Hong Kong Children's Hospital, Hong Kong, Hong Kong
| | - Kamalan Jeevaratnam
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Qingpeng Zhang
- School of Data Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Gary Tse
- Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease, Department of Cardiology, Tianjin Institute of Cardiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| |
Collapse
|
37
|
Luo H, Wei W, Ye Z, Zheng J, Xu RH. Liquid Biopsy of Methylation Biomarkers in Cell-Free DNA. Trends Mol Med 2021; 27:482-500. [PMID: 33500194 DOI: 10.1016/j.molmed.2020.12.011] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 02/09/2023]
Abstract
Liquid biopsies, in particular, analysis of cell-free DNA (cfDNA), have emerged as a promising noninvasive diagnostic approach in oncology. Abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. Systemic analysis of cfDNA methylation profiles is being developed for cancer early detection, monitoring for minimal residual disease (MRD), predicting treatment response and prognosis, and tracing the tissue origin. This review highlights the advantages and disadvantages of ctDNA profiling for noninvasive diagnosis of early-stage cancers and explores recent advances in the clinical application of ctDNA methylation assays. We also summarize the technologies for ctDNA methylation analysis and provide a brief overview of the bioinformatic approaches for analyzing DNA methylation sequencing data.
Collapse
Affiliation(s)
- Huiyan Luo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Wei Wei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Ziyi Ye
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jiabo Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Rui-Hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
| |
Collapse
|
38
|
Colpaert RMW, Calore M. Epigenetics and microRNAs in cardiovascular diseases. Genomics 2021; 113:540-551. [PMID: 33482325 DOI: 10.1016/j.ygeno.2020.12.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/12/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023]
Abstract
Cardiovascular diseases are among the leading causes of mortality worldwide. Besides environmental and genetic changes, these disorders can be influenced by processes which do not affect DNA sequence yet still play an important role in gene expression and which can be inherited. These so-called 'epigenetic' changes include DNA methylation, histone modifications, and ATP-dependent chromatin remodeling enzymes, which influence chromatin remodeling and gene expression. Next to these, microRNAs are non-coding RNA molecules that silence genes post-transcriptionally. Both epigenetic factors and microRNAs are known to influence cardiac development and homeostasis, in an individual fashion but also in a complex regulatory network. In this review, we will discuss how epigenetic factors and microRNAs interact with each other and how together they can influence cardiovascular diseases.
Collapse
Affiliation(s)
- Robin M W Colpaert
- Department of Molecular Genetics, Faculty of Health, Medicine and Life Sciences, Faculty of Science and Engineering, Maastricht University, the Netherlands
| | - Martina Calore
- Department of Molecular Genetics, Faculty of Health, Medicine and Life Sciences, Faculty of Science and Engineering, Maastricht University, the Netherlands.
| |
Collapse
|
39
|
Russell-Hallinan A, Neary R, Watson CJ, Baugh JA. Repurposing From Oncology to Cardiology: Low-Dose 5-Azacytidine Attenuates Pathological Cardiac Remodeling in Response to Pressure Overload Injury. J Cardiovasc Pharmacol Ther 2020; 26:375-385. [PMID: 33264040 DOI: 10.1177/1074248420979235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Recent evidence suggests that transcriptional reprogramming is involved in the pathogenesis of cardiac remodeling (cardiomyocyte hypertrophy and fibrosis) and the development of heart failure. 5-Azacytidine (5aza), an inhibitor of DNA methylation approved for hematological malignancies, has previously demonstrated beneficial effects on cardiac remodeling in hypertension. The aim of our work was to investigate whether pressure overload is associated with alterations in DNA methylation and if intervention with low-dose 5aza can attenuate the associated pathological changes. METHODS AND RESULTS C57Bl6/J mice underwent surgical constriction of the aortic arch for 8 weeks. Mice began treatment 4 weeks post-surgery with either vehicle or 5aza (5 mg/kg). Cardiac structure and function was examined in vivo using echocardiography followed by post mortem histological assessment of hypertrophy and fibrosis. Global DNA methylation was examined by immunostaining for 5-methylcytosine (5MeC) and assessment of DNA methyltransferase expression. The results highlighted that pressure overload-induced pathological cardiac remodeling is associated with increased DNA methylation (elevated cardiac 5MeC positivity and Dnmt1 expression). Administration of 5aza attenuated pathological remodeling and diastolic dysfunction. These beneficial changes were mirrored by a treatment-related reduction in global 5MeC levels and expression of Dnmt1 and Dnmt3B in the heart. CONCLUSION DNA methylation plays an important role in the pathogenesis of pressure overload-induced cardiac remodeling. Therapeutic intervention with 5aza, at a dose 5 times lower than clinically given for oncology treatment, attenuated myocardial hypertrophy and fibrosis. Our work supports the rationale for its potential use in cardiac pathologies associated with aberrant cardiac wound healing.
Collapse
Affiliation(s)
- Adam Russell-Hallinan
- Wellcome-Wolfson Institute for Experimental Medicine, 1596Queen's University Belfast, Northern Ireland, United Kingdom.,UCD School of Medicine, Conway Institute, 231327University College Dublin, Belfield, Dublin, Ireland
| | - Roisin Neary
- UCD School of Medicine, Conway Institute, 231327University College Dublin, Belfield, Dublin, Ireland
| | - Chris J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, 1596Queen's University Belfast, Northern Ireland, United Kingdom
| | - John A Baugh
- UCD School of Medicine, Conway Institute, 231327University College Dublin, Belfield, Dublin, Ireland
| |
Collapse
|
40
|
Epigenetics and Heart Failure. Int J Mol Sci 2020; 21:ijms21239010. [PMID: 33260869 PMCID: PMC7729735 DOI: 10.3390/ijms21239010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetics refers to changes in phenotypes without changes in genotypes. These changes take place in a number of ways, including via genomic DNA methylation, DNA interacting proteins, and microRNAs. The epigenome is the second dimension of the genome and it contains key information that is specific to every type of cell. Epigenetics is essential for many fundamental processes in biology, but its importance in the development and progression of heart failure, which is one of the major causes of morbidity and mortality worldwide, remains unclear. Our understanding of the underlying molecular mechanisms is incomplete. While epigenetics is one of the most innovative research areas in modern biology and medicine, compounds that directly target the epigenome, such as epidrugs, have not been well translated into therapies. This paper focuses on epigenetics in terms of genomic DNA methylation, such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications. These appear to be more dynamic than previously anticipated and may underlie a wide variety of conditions, including heart failure. We also outline possible new strategies for the development of novel therapies.
Collapse
|
41
|
Song R, Zhang L. Cardiac ECM: Its Epigenetic Regulation and Role in Heart Development and Repair. Int J Mol Sci 2020; 21:ijms21228610. [PMID: 33203135 PMCID: PMC7698074 DOI: 10.3390/ijms21228610] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022] Open
Abstract
The extracellular matrix (ECM) is the non-cellular component in the cardiac microenvironment, and serves essential structural and regulatory roles in establishing and maintaining tissue architecture and cellular function. The patterns of molecular and biochemical ECM alterations in developing and adult hearts depend on the underlying injury type. In addition to exploring how the ECM regulates heart structure and function in heart development and repair, this review conducts an inclusive discussion of recent developments in the role, function, and epigenetic guidelines of the ECM. Moreover, it contributes to the development of new therapeutics for cardiovascular disease.
Collapse
Affiliation(s)
- Rui Song
- Correspondence: (R.S.); (L.Z.); Tel.: +1-909-558-4325 (R.S. & L.Z.)
| | - Lubo Zhang
- Correspondence: (R.S.); (L.Z.); Tel.: +1-909-558-4325 (R.S. & L.Z.)
| |
Collapse
|
42
|
Russell-Hallinan A, Watson CJ, O'Dwyer D, Grieve DJ, O'Neill KM. Epigenetic Regulation of Endothelial Cell Function by Nucleic Acid Methylation in Cardiac Homeostasis and Disease. Cardiovasc Drugs Ther 2020; 35:1025-1044. [PMID: 32748033 PMCID: PMC8452583 DOI: 10.1007/s10557-020-07019-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pathological remodelling of the myocardium, including inflammation, fibrosis and hypertrophy, in response to acute or chronic injury is central in the development and progression of heart failure (HF). While both resident and infiltrating cardiac cells are implicated in these pathophysiological processes, recent evidence has suggested that endothelial cells (ECs) may be the principal cell type responsible for orchestrating pathological changes in the failing heart. Epigenetic modification of nucleic acids, including DNA, and more recently RNA, by methylation is essential for physiological development due to their critical regulation of cellular gene expression. As accumulating evidence has highlighted altered patterns of DNA and RNA methylation in HF at both the global and individual gene levels, much effort has been directed towards defining the precise role of such cell-specific epigenetic changes in the context of HF. Considering the increasingly apparent crucial role that ECs play in cardiac homeostasis and disease, this article will specifically focus on nucleic acid methylation (both DNA and RNA) in the failing heart, emphasising the key influence of these epigenetic mechanisms in governing EC function. This review summarises current understanding of DNA and RNA methylation alterations in HF, along with their specific role in regulating EC function in response to stress (e.g. hyperglycaemia, hypoxia). Improved appreciation of this important research area will aid in further implicating dysfunctional ECs in HF pathogenesis, whilst informing development of EC-targeted strategies and advancing potential translation of epigenetic-based therapies for specific targeting of pathological cardiac remodelling in HF.
Collapse
Affiliation(s)
- Adam Russell-Hallinan
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Chris J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Denis O'Dwyer
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - David J Grieve
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Karla M O'Neill
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK.
| |
Collapse
|
43
|
Wang Q, Liu B, Wang Y, Bai B, Yu T, Chu XM. The biomarkers of key miRNAs and target genes associated with acute myocardial infarction. PeerJ 2020; 8:e9129. [PMID: 32440375 PMCID: PMC7229769 DOI: 10.7717/peerj.9129] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Background Acute myocardial infarction (AMI) is considered one of the most prominent causes of death from cardiovascular disease worldwide. Knowledge of the molecular mechanisms underlying AMI remains limited. Accurate biomarkers are needed to predict the risk of AMI and would be beneficial for managing the incidence rate. The gold standard for the diagnosis of AMI, the cardiac troponin T (cTnT) assay, requires serial testing, and the timing of measurement with respect to symptoms affects the results. As attractive candidate diagnostic biomarkers in AMI, circulating microRNAs (miRNAs) are easily detectable, generally stable and tissue specific. Methods The Gene Expression Omnibus (GEO) database was used to compare miRNA expression between AMI and control samples, and the interactions between miRNAs and mRNAs were analysed for expression and function. Furthermore, a protein-protein interaction (PPI) network was constructed. The miRNAs identified in the bioinformatic analysis were verified by RT-qPCR in an H9C2 cell line. The miRNAs in plasma samples from patients with AMI (n = 11) and healthy controls (n = 11) were used to construct receiver operating characteristic (ROC) curves to evaluate the clinical prognostic value of the identified miRNAs. Results We identified eight novel miRNAs as potential candidate diagnostic biomarkers for patients with AMI. In addition, the predicted target genes provide insight into the molecular mechanisms underlying AMI.
Collapse
Affiliation(s)
- Qi Wang
- Department of Cardiology, The Affiliated hospital of Qingdao University, Qingdao, China
| | - Bingyan Liu
- School of Basic Medicine, Qingdao University, Qingdao, China.,Institute for Translational Medicine, Qingdao University, Qingdao, China
| | - Yuanyong Wang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Baochen Bai
- Department of Cardiology, The Affiliated hospital of Qingdao University, Qingdao, China
| | - Tao Yu
- Institute for Translational Medicine, Qingdao University, Qingdao, China
| | - Xian-Ming Chu
- Department of Cardiology, The Affiliated hospital of Qingdao University, Qingdao, China.,Department of Cardiology, The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
44
|
Watanabe T, Okada H, Kanamori H, Miyazaki N, Tsujimoto A, Takada C, Suzuki K, Naruse G, Yoshida A, Nawa T, Tanaka T, Kawasaki M, Ito H, Ogura S, Okura H, Fujiwara T, Fujiwara H, Takemura G. In situ nuclear DNA methylation in dilated cardiomyopathy: an endomyocardial biopsy study. ESC Heart Fail 2020; 7:493-502. [PMID: 31971668 DOI: 10.1002/ehf2.12593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 11/12/2022] Open
Abstract
AIMS Although distinct DNA methylation patterns have been reported, its localization and roles remain to be defined in heart failure. We investigated the cellular and subcellular localization of DNA methylation and its pathophysiological significance in human failing hearts. METHODS AND RESULTS Using left ventricular (LV) endomyocardial biopsy specimens from 75 patients with dilated cardiomyopathy (DCM; age: 58 ± 14 years old, %female: 32%) and 20 patients without heart failure (controls; age: 56 ± 17 years old, %female: 45%), we performed immunohistochemistry and immunoelectron microscopy for methylated DNA, 5-methylcytosine (5-mC). We next investigated possible relations of the incidence of 5-mC-positive (%5-mC+ ) cardiomyocytes with clinicopathological parameters. Immunopositivity for 5-mC was detected in the cardiomyocytes and other cell types. The %5-mC+ cardiomyocytes was significantly greater in DCM hearts than in controls (57 ± 13% in DCM vs. 25 ± 12% in controls, P < 0.0001). The localization of 5-mC immunopositivity in cardiomyocyte nuclei coincided well with that of heterochromatin, as confirmed by immunoelectron microscopy. Substantial DNA methylation was also observed in interstitial non-cardiomyocytes, but the incidences did not differ between control and DCM hearts (39 ± 7.9% in DCM vs. 41 ± 10% in controls, P = 0.4099). In DCM patients, the %5-mC+ cardiomyocytes showed a significant inverse correlation with LV functional parameters such as heart rate (r = 0.2391, P = 0.0388), end-diastolic pressure (r = 0.2397, P = 0.0397), and ejection fraction (r = -0.2917, P = 0.0111) and a positive correlation with LV dilatation (volume index at diastole; r = 0.2442, P = 0.0347; and volume index at systole; r = 0.3136, P = 0.0062) and LV hypertrophy (mass index; r = 0.2287, P = 0.0484)-that is, LV remodelling parameters. No significant correlations between DNA methylation and the histological parameters of the biopsies, including cardiomyocyte hypertrophy, fibrosis, and inflammatory cell infiltration, were noted. CONCLUSIONS The present study revealed increased nuclear DNA methylation in cardiomyocytes, but not other cell types, from DCM hearts, with predominant localization in the heterochromatin. Its significant relations with LV functional and remodelling parameters imply a pathophysiological significance of DNA methylation in heart failure.
Collapse
Affiliation(s)
- Takatomo Watanabe
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan.,Department of Informative Clinical Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hideshi Okada
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan.,Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiromitsu Kanamori
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Nagisa Miyazaki
- Department of Internal Medicine, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, 501-0296, Japan
| | - Akiko Tsujimoto
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Chihiro Takada
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kodai Suzuki
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Genki Naruse
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akihiro Yoshida
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takahide Nawa
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Toshiki Tanaka
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Masanori Kawasaki
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroyasu Ito
- Department of Informative Clinical Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Shinji Ogura
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroyuki Okura
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takako Fujiwara
- Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | | | - Genzou Takemura
- Department of Internal Medicine, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, 501-0296, Japan
| |
Collapse
|
45
|
Liu CF, Tang WW. Epigenetics in Cardiac Hypertrophy and Heart Failure. JACC Basic Transl Sci 2019; 4:976-993. [PMID: 31909304 PMCID: PMC6938823 DOI: 10.1016/j.jacbts.2019.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
Abstract
Heart failure (HF) is a complex syndrome affecting millions of people around the world. Over the past decade, the therapeutic potential of targeting epigenetic regulators in HF has been discussed extensively. Recent advances in next-generation sequencing techniques have contributed substantial progress in our understanding of the role of DNA methylation, post-translational modifications of histones, adenosine triphosphate (ATP)-dependent chromatin conformation and remodeling, and non-coding RNAs in HF pathophysiology. In this review, we summarize epigenomic studies on human and animal models in HF.
Collapse
Key Words
- BET, bromodomain
- EZH2, Enhancer of zeste homolog 2
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- HDM, histone demethylase
- HF, heart failure
- HMT, histone methyltransferase
- PRC2, polycomb repressor complex 2
- PTMs, post-translational modifications
- TAD, topologically associating domains
- TMAO, trimethylamine N-oxide
- cardiac hypertrophy
- epigenetics
- heart failure
- lnc-RNAs, long ncRNAs
Collapse
Affiliation(s)
- Chia-Feng Liu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - W.H. Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Cardiovascular Medicine, Heart and Vascular Institute, Cleveland Clinic, Cleveland, Ohio
| |
Collapse
|
46
|
Soler-Botija C, Gálvez-Montón C, Bayés-Genís A. Epigenetic Biomarkers in Cardiovascular Diseases. Front Genet 2019; 10:950. [PMID: 31649728 PMCID: PMC6795132 DOI: 10.3389/fgene.2019.00950] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/05/2019] [Indexed: 12/16/2022] Open
Abstract
Cardiovascular diseases are the number one cause of death worldwide and greatly impact quality of life and medical costs. Enormous effort has been made in research to obtain new tools for efficient and quick diagnosis and predicting the prognosis of these diseases. Discoveries of epigenetic mechanisms have related several pathologies, including cardiovascular diseases, to epigenetic dysregulation. This has implications on disease progression and is the basis for new preventive strategies. Advances in methodology and big data analysis have identified novel mechanisms and targets involved in numerous diseases, allowing more individualized epigenetic maps for personalized diagnosis and treatment. This paves the way for what is called pharmacoepigenetics, which predicts the drug response and develops a tailored therapy based on differences in the epigenetic basis of each patient. Similarly, epigenetic biomarkers have emerged as a promising instrument for the consistent diagnosis and prognosis of cardiovascular diseases. Their good accessibility and feasible methods of detection make them suitable for use in clinical practice. However, multicenter studies with a large sample population are required to determine with certainty which epigenetic biomarkers are reliable for clinical routine. Therefore, this review focuses on current discoveries regarding epigenetic biomarkers and its controversy aiming to improve the diagnosis, prognosis, and therapy in cardiovascular patients.
Collapse
Affiliation(s)
- Carolina Soler-Botija
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Carolina Gálvez-Montón
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Antoni Bayés-Genís
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Cardiology Service, HUGTiP, Badalona, Spain.,Department of Medicine, Barcelona Autonomous University (UAB), Badalona, Spain
| |
Collapse
|
47
|
Forini F, Nicolini G, Pitto L, Iervasi G. Novel Insight Into the Epigenetic and Post-transcriptional Control of Cardiac Gene Expression by Thyroid Hormone. Front Endocrinol (Lausanne) 2019; 10:601. [PMID: 31555215 PMCID: PMC6727178 DOI: 10.3389/fendo.2019.00601] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/16/2019] [Indexed: 12/17/2022] Open
Abstract
Thyroid hormone (TH) signaling is critically involved in the regulation of cardiovascular physiology. Even mild reductions of myocardial TH levels, as occur in hypothyroidism or low T3 state conditions, are thought to play a role in the progression of cardiac disorders. Due to recent advances in molecular mechanisms underlying TH action, it is now accepted that TH-dependent modulation of gene expression is achieved at multiple transcriptional and post-transcriptional levels and involves the cooperation of many processes. Among them, the epigenetic remodeling of chromatin structure and the interplay with non-coding RNA have emerged as novel TH-dependent pathways that add further degrees of complexity and broaden the network of genes controlled by TH signaling. Increasing experimental and clinical findings indicate that aberrant function of these regulatory mechanisms promotes the evolution of cardiac disorders such as post-ischemic injury, pathological hypertrophy, and heart failure, which may be reversed by the correction of the underlying TH dyshomeostasis. To encourage the clinical implementation of a TH replacement strategy in cardiac disease, here we discuss the crucial effect of epigenetic modifications and control of non-coding RNA in TH-dependent regulation of biological processes relevant for cardiac disease evolution.
Collapse
|