1
|
Zhang Z, Zou Z, Zhang H, Zhang DM. Regulatory network analysis based on integrated miRNA-TF reveals key genes in heart failure. Sci Rep 2024; 14:13896. [PMID: 38886500 PMCID: PMC11183224 DOI: 10.1038/s41598-024-64732-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
The etiology and pathophysiology of heart failure are still unknown. Increasing evidence suggests that abnormal microRNAs (miRNAs) and transcription factors (TFs) expression may be associated with the development of heart failure. Therefore, this study aims to explore key miRNAs, TFs, and related genes in heart failure to gain a greater understanding of the pathogenesis of heart failure. To search and download the dataset of mRNA chips related to heart failure from the GEO database (GSE59867, GSE9128, and GSE134766), we analyzed differential genes and screened the common differentially expressed genes on two chips using R language software. The binary interactions and circuits among miRNAs, TFs, and corresponding genes were determined by Pearson correlation coefficient. A regulatory network of miRNAs, TFs, and target genes was constructed based on bioinformatics. By comparing the sequences of patients with and without heart failure, five downregulated genes with hypermethylated mRNA and three upregulated genes with hypomethylated mRNA were identified. The miRNA-TF gene regulatory network consisted of 26 miRNAs, 22 TFs and six genes. GO and KEGG analysis results revealed that BP terms like cellular response to organic substance, cellular response to cytokine stimulus, and KEGG pathways like osteoclast differentiation, MAPK signaling pathway, and legionellosis were enriched of the DEGs. TMEM87A, PPP2R2A, DUSP1, and miR-92a have great potential as biomarkers for heart failure. The integrated analysis of the mRNA expression spectrum and microRNA-transcription factor-gene revealed the regulatory network of heart failure, which may provide clues to its alternative treatment.
Collapse
Affiliation(s)
- Ziyue Zhang
- Department of Cardiology, Sir Run Run Hospital, Nanjing Medical University, 109 Longmian Road, Nanjing, 211112, Jiangsu, People's Republic of China
| | - Ziying Zou
- Department of Cardiology, Sir Run Run Hospital, Nanjing Medical University, 109 Longmian Road, Nanjing, 211112, Jiangsu, People's Republic of China
| | - Hui Zhang
- Department of Cardiology, Sir Run Run Hospital, Nanjing Medical University, 109 Longmian Road, Nanjing, 211112, Jiangsu, People's Republic of China
| | - Dai-Min Zhang
- Department of Cardiology, Sir Run Run Hospital, Nanjing Medical University, 109 Longmian Road, Nanjing, 211112, Jiangsu, People's Republic of China.
| |
Collapse
|
2
|
Gao H, Li J, Ma Q, Zhang Q, Li M, Hu X. Causal Associations of DNA Methylation and Cardiovascular Disease: A Two-Sample Mendelian Randomization Study. Glob Heart 2024; 19:48. [PMID: 38765775 PMCID: PMC11100526 DOI: 10.5334/gh.1324] [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: 12/12/2023] [Accepted: 04/16/2024] [Indexed: 05/22/2024] Open
Abstract
Background There is growing evidence that concentrations of DNA methylation are associated with cardiovascular disease; however, it is unclear whether this association reflects a causal relationship. Methods We utilized a two-sample Mendelian randomization (MR) approach to investigate whether DNA methylation can affect the risk of developing cardiovascular disease in human life. We primarily performed the inverse variance weighted (IVW) method to analyze the causal effect of DNA methylation on multiple cardiovascular diseases. Additionally, to ensure the robustness of our findings, we conducted several sensitivity analyses using alternative methodologies. These analysis methods included maximum likelihood, MR-Egger regression, weighted median method, and weighted model methods. Results Inverse variance weighted estimates suggested that an SD increase in DNA methylation Hannum age acceleration exposure increased the risk of cardiac arrhythmias (OR = 1.03, 95% CI 1.00-1.05, p = 0.0290) and atrial fibrillation (OR = 1.03, 95% CI 1.00-1.05, p = 0.0022). We also found that an SD increase in DNA methylation PhenoAge acceleration exposure increased the risk of heart failure (OR = 1.01, 95% CI 1.00-1.03, p = 0.0362). Exposure to DNA methylation-estimated granulocyte proportions was found to increase the risk of hypertension (OR = 1.00, 95% CI 1.00-1.0001, p = 0.0291). Exposure to DNA methylation-estimated plasminogen activator inhibitor-1 levels was found to increase the risk of heart failure (OR = 1.00, 95% CI 1.00-1.00, p = 0.0215). Conclusion This study reveals a causal relationship between DNA methylation and CVD. Exposed to high levels of DNA methylation Hannum age acceleration inhabitants with an increased risk of cardiac arrhythmias and atrial fibrillation. DNA methylation PhenoAge acceleration levels exposure levels were positively associated with the increased risk of developing heart failure. This has important implications for the prevention of cardiovascular diseases.
Collapse
Affiliation(s)
- Hui Gao
- Department of Cardiovascular Medicine, The First People’s Hospital of Shangqiu, Shangqiu 476000, China
- Graduate School, Dalian Medical University, Dalian, 116044, China
| | - Jiahai Li
- Department of Cardiovascular Medicine, The First People’s Hospital of Qinzhou, Qinzhou 535000, China
| | - Qiaoli Ma
- Department of Cardiovascular Medicine, Central Hospital of Zibo, Zibo 255000, China
| | - Qinghui Zhang
- Department of Hypertension, Henan Provincial People’s Hospital, Zhengzhou 450000, China
| | - Man Li
- Department of Cardiovascular Medicine, The First People’s Hospital of Shangqiu, Shangqiu 476000, China
| | - Xiaoliang Hu
- Department of Cardiovascular Medicine, The First People’s Hospital of Shangqiu, Shangqiu 476000, China
| |
Collapse
|
3
|
Dash M, Mahajan B, Dar GM, Sahu P, Saluja SS. An update on the cell-free DNA-derived methylome as a non-invasive biomarker for coronary artery disease. Int J Biochem Cell Biol 2024; 169:106555. [PMID: 38428633 DOI: 10.1016/j.biocel.2024.106555] [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: 05/24/2023] [Revised: 12/22/2023] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
Cardiovascular diseases are the foremost contributor to global mortality, presenting a complex etiology and an expanding array of risk factors. Coronary artery disease characterized by atherosclerotic plaque build-up in the coronary arteries, imposes significant mortality and financial burdens, especially in low- and middle-income nations. The pathogenesis of coronary artery disease involves a multifaceted interplay of genetic, environmental, and epigenetic factors. Epigenetic regulation contributes to the dynamic control of gene expression without altering the underlying DNA sequence. The mounting evidence that highlights the pivotal role of epigenetic regulation in coronary artery disease development and progression, offering potential avenues for the development of novel diagnostic biomarkers and therapeutic targets. Abnormal DNA methylation patterns are linked to the modulation of gene expression involved in crucial processes like lipid metabolism, inflammation, and vascular function in the context of coronary artery disease. Cell-free DNA has become invaluable in tumor biology as a liquid biopsy, while its applications in coronary artery disease are limited, but intriguing. Atherosclerotic plaque rupture causes myocardial infarction, by depriving heart muscles of oxygen, releasing cell-free DNA from dead cardiac cells, and providing a minimally invasive source to explore tissue-specific epigenetic alterations. We discussed the methodologies for studying the global methylome and hydroxy-methylome landscape, their advantages, and limitations. It explores methylome alterations in coronary artery disease, considering risk factors and their relevance in coronary artery disease genesis. The review also details the implications of MI-derived cell-free DNA for developing minimally invasive biomarkers and associated challenges.
Collapse
Affiliation(s)
- Manoswini Dash
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; School of Medicine, Center for Aging, Tulane University, LA, United States
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
| | - Ghulam Mehdi Dar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Parameswar Sahu
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| |
Collapse
|
4
|
Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. J Chem Inf Model 2024; 64:1172-1186. [PMID: 38300851 PMCID: PMC10900289 DOI: 10.1021/acs.jcim.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024]
Abstract
Drug-induced cardiotoxicity (DICT) is a major concern in drug development, accounting for 10-14% of postmarket withdrawals. In this study, we explored the capabilities of chemical and biological data to predict cardiotoxicity, using the recently released DICTrank data set from the United States FDA. We found that such data, including protein targets, especially those related to ion channels (e.g., hERG), physicochemical properties (e.g., electrotopological state), and peak concentration in plasma offer strong predictive ability for DICT. Compounds annotated with mechanisms of action such as cyclooxygenase inhibition could distinguish between most-concern and no-concern DICT. Cell Painting features for ER stress discerned most-concern cardiotoxic from nontoxic compounds. Models based on physicochemical properties provided substantial predictive accuracy (AUCPR = 0.93). With the availability of omics data in the future, using biological data promises enhanced predictability and deeper mechanistic insights, paving the way for safer drug development. All models from this study are available at https://broad.io/DICTrank_Predictor.
Collapse
Affiliation(s)
- Srijit Seal
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Ola Spjuth
- Department
of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box
591, SE-75124 Uppsala, Sweden
| | - Layla Hosseini-Gerami
- Ignota
Labs, The Bradfield Centre, Cambridge Science Park, County Hall, Westminster Bridge Road, Cambridge CB4 0GA, U.K.
| | - Miguel García-Ortegón
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Shantanu Singh
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Andreas Bender
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Anne E. Carpenter
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
5
|
Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.15.562398. [PMID: 37905146 PMCID: PMC10614794 DOI: 10.1101/2023.10.15.562398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Drug-induced cardiotoxicity (DICT) is a major concern in drug development, accounting for 10-14% of postmarket withdrawals. In this study, we explored the capabilities of various chemical and biological data to predict cardiotoxicity, using the recently released Drug-Induced Cardiotoxicity Rank (DICTrank) dataset from the United States FDA. We analyzed a diverse set of data sources, including physicochemical properties, annotated mechanisms of action (MOA), Cell Painting, Gene Expression, and more, to identify indications of cardiotoxicity. We found that such data, including protein targets, especially those related to ion channels (such as hERG), physicochemical properties (such as electrotopological state) as well as peak concentration in plasma offer strong predictive ability as well as valuable insights into DICT. We also found compounds annotated with particular mechanisms of action, such as cyclooxygenase inhibition, could distinguish between most-concern and no-concern DICT compounds. Cell Painting features related to ER stress discern the most-concern cardiotoxic compounds from non-toxic compounds. While models based on physicochemical properties currently provide substantial predictive accuracy (AUCPR = 0.93), this study also underscores the potential benefits of incorporating more comprehensive biological data in future DICT predictive models. With the availability of - omics data in the future, using biological data promises enhanced predictability and delivers deeper mechanistic insights, paving the way for safer therapeutic drug development. All models and data used in this study are publicly released at https://broad.io/DICTrank_Predictor.
Collapse
Affiliation(s)
- Srijit Seal
- Imaging Platform, Broad Institute of MIT and Harvard, US
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Sweden
| | | | | | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, US
| | | | | |
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
|
Cuadrat RRC, Kratzer A, Arnal HG, Rathgeber A, Wreczycka K, Blume A, Gündüz IB, Ebenal V, Mauno T, Osberg B, Moobed M, Hartung J, Jakobs K, Seppelt C, Meteva D, Haghikia A, Leistner D, Landmesser U, Akalin A. Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation. NAR Genom Bioinform 2023; 5:lqad061. [PMID: 37388821 PMCID: PMC10304763 DOI: 10.1093/nargab/lqad061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Acute coronary syndrome (ACS) remains a major cause of worldwide mortality. The syndrome occurs when blood flow to the heart muscle is decreased or blocked, causing muscle tissues to die or malfunction. There are three main types of ACS: Non-ST-elevation myocardial infarction, ST-elevation myocardial infarction, and unstable angina. The treatment depends on the type of ACS, and this is decided by a combination of clinical findings, such as electrocardiogram and plasma biomarkers. Circulating cell-free DNA (ccfDNA) is proposed as an additional marker for ACS since the damaged tissues can release DNA to the bloodstream. We used ccfDNA methylation profiles for differentiating between the ACS types and provided computational tools to repeat similar analysis for other diseases. We leveraged cell type specificity of DNA methylation to deconvolute the ccfDNA cell types of origin and to find methylation-based biomarkers that stratify patients. We identified hundreds of methylation markers associated with ACS types and validated them in an independent cohort. Many such markers were associated with genes involved in cardiovascular conditions and inflammation. ccfDNA methylation showed promise as a non-invasive diagnostic for acute coronary events. These methods are not limited to acute events, and may be used for chronic cardiovascular diseases as well.
Collapse
Affiliation(s)
| | | | | | - Anja C Rathgeber
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Katarzyna Wreczycka
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Alexander Blume
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Irem B Gündüz
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Veronika Ebenal
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Tiina Mauno
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Brendan Osberg
- Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine Berlin, Berlin, Germany
| | - Minoo Moobed
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Johannes Hartung
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Kai Jakobs
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Claudio Seppelt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Universitätsklinikum Frankfurt am Main, Medizinische Klinik 3, Klinik für Kardiologie und Angiologie, Germany
| | - Denitsa Meteva
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Arash Haghikia
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - David M Leistner
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Universitätsklinikum Frankfurt am Main, Medizinische Klinik 3, Klinik für Kardiologie und Angiologie, Germany
| | - Ulf Landmesser
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Cardiology, Campus Benjamin Franklin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Altuna Akalin
- To whom correspondence should be addressed. Tel: +49 30 94 060 42 71; Fax: +49 30 94 060 49 341;
| |
Collapse
|
8
|
Krolevets M, Cate VT, Prochaska JH, Schulz A, Rapp S, Tenzer S, Andrade-Navarro MA, Horvath S, Niehrs C, Wild PS. DNA methylation and cardiovascular disease in humans: a systematic review and database of known CpG methylation sites. Clin Epigenetics 2023; 15:56. [PMID: 36991458 PMCID: PMC10061871 DOI: 10.1186/s13148-023-01468-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/19/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Cardiovascular disease (CVD) is the leading cause of death worldwide and considered one of the most environmentally driven diseases. The role of DNA methylation in response to the individual exposure for the development and progression of CVD is still poorly understood and a synthesis of the evidence is lacking. RESULTS A systematic review of articles examining measurements of DNA cytosine methylation in CVD was conducted in accordance with PRISMA (preferred reporting items for systematic reviews and meta-analyses) guidelines. The search yielded 5,563 articles from PubMed and CENTRAL databases. From 99 studies with a total of 87,827 individuals eligible for analysis, a database was created combining all CpG-, gene- and study-related information. It contains 74,580 unique CpG sites, of which 1452 CpG sites were mentioned in ≥ 2, and 441 CpG sites in ≥ 3 publications. Two sites were referenced in ≥ 6 publications: cg01656216 (near ZNF438) related to vascular disease and epigenetic age, and cg03636183 (near F2RL3) related to coronary heart disease, myocardial infarction, smoking and air pollution. Of 19,127 mapped genes, 5,807 were reported in ≥ 2 studies. Most frequently reported were TEAD1 (TEA Domain Transcription Factor 1) and PTPRN2 (Protein Tyrosine Phosphatase Receptor Type N2) in association with outcomes ranging from vascular to cardiac disease. Gene set enrichment analysis of 4,532 overlapping genes revealed enrichment for Gene Ontology molecular function "DNA-binding transcription activator activity" (q = 1.65 × 10-11) and biological processes "skeletal system development" (q = 1.89 × 10-23). Gene enrichment demonstrated that general CVD-related terms are shared, while "heart" and "vasculature" specific genes have more disease-specific terms as PR interval for "heart" or platelet distribution width for "vasculature." STRING analysis revealed significant protein-protein interactions between the products of the differentially methylated genes (p = 0.003) suggesting that dysregulation of the protein interaction network could contribute to CVD. Overlaps with curated gene sets from the Molecular Signatures Database showed enrichment of genes in hemostasis (p = 2.9 × 10-6) and atherosclerosis (p = 4.9 × 10-4). CONCLUSION This review highlights the current state of knowledge on significant relationship between DNA methylation and CVD in humans. An open-access database has been compiled of reported CpG methylation sites, genes and pathways that may play an important role in this relationship.
Collapse
Affiliation(s)
- Mykhailo Krolevets
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Systems Medicine, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Vincent Ten Cate
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jürgen H Prochaska
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Schulz
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Steffen Rapp
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
| | - Stefan Tenzer
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | - Christof Niehrs
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Philipp S Wild
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
- Systems Medicine, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
| |
Collapse
|
9
|
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
|
10
|
From Iron Metabolism to Ferroptosis: Pathologic Changes in Coronary Heart Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6291889. [PMID: 35993022 PMCID: PMC9385341 DOI: 10.1155/2022/6291889] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022]
Abstract
Coronary heart disease (CHD) is closely related to oxidative stress and inflammatory response and is the most common cardiovascular disease (CVD). Iron is an essential mineral that participates in many physiological and biochemical reactions in the human body. Meanwhile, on the negative side, iron has an active redox capacity, which leads to the accumulation of reactive oxygen species (ROS) and lipid peroxidation. There is growing evidence that disordered iron metabolism is involved in CHD's pathological progression. And the result of disordered iron metabolism is associated with iron overload-induced programmed cell death, often called ferroptosis. That features iron-dependent lipid peroxidation. Ferroptosis may play a crucial role in the development of CHD, and targeting ferroptosis may be a promising option for treating CHD. Here, we review the mechanisms of iron metabolism in cardiomyocytes (CMs) and explain the correlation between iron metabolism and ferroptosis. Meanwhile, we highlight the specific roles of iron metabolism and ferroptosis in the main pathological progression of CHD.
Collapse
|
11
|
Effect of CICARE Communication Mode on Disease Uncertainty, Self-Nursing Ability, and Quality of Life in Patients with Coronary Atherosclerotic Heart Disease after Percutaneous Coronary Intervention. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8654449. [PMID: 36035303 PMCID: PMC9410929 DOI: 10.1155/2022/8654449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 01/09/2023]
Abstract
Objective To study the effect of CICARE (Connect, Introduce, Communicate, Ask, Respond, Exit) communication mode on disease uncertainty, self-nursing ability, and quality of life in patients with coronary atherosclerotic heart disease (CAD) after percutaneous coronary intervention (PCI). Methods From January 2021 to December 2021, 102 patients with CAD after PCI were randomly divided into a research group (n =51) and a control group (n =51). The former received CICARE communication model nursing intervention, and the latter received routine doctor-patient communication nursing. To study the scores of disease uncertainty scale (MUIS), Frankl treatment compliance scale (Frankl), self-care ability scale (exercise of self-care-a), quality of life scale (WHOQOL-BREF), and Newcastle nursing satisfaction scale (NSNS) before and 1 week after nursing. Results After one week of nursing, the MUIS score of the research group was lower than that of the control group, and the score of Frankl treatment compliance scale of the research group was higher than that of the control group. After 1 week of nursing, the ESCA score of the research group was higher compared to the control group (p < 0.05), and the WHOQOL-BREF score of the research group was higher compared to the control group (p < 0.05). After one week of nursing, the NSNS score of the research group was higher compared to the control group (p < 0.05). Conclusion The application value of CICARE communication mode nursing intervention in patients with CAD after PCI is more remarkable, and it is more helpful to reduce patients' disease uncertainty, enhance treatment compliance, promote patients' self-nursing ability, and strengthen quality of life and nursing satisfaction.
Collapse
|
12
|
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
|
13
|
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
|
14
|
Chen D, Kelly C, Haw TJ, Lombard JM, Nordman IIC, Croft AJ, Ngo DTM, Sverdlov AL. Heart Failure in Breast Cancer Survivors: Focus on Early Detection and Novel Biomarkers. Curr Heart Fail Rep 2021; 18:362-377. [PMID: 34731413 DOI: 10.1007/s11897-021-00535-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/29/2021] [Indexed: 01/17/2023]
Abstract
PURPOSE OF REVIEW Breast cancer survival rate has greatly improved in the last two decades due to the emergence of next-generation anti-cancer agents. However, cardiotoxicity remains a significant adverse effect arising from traditional and emerging chemotherapies as well as targeted therapies for breast cancer patients. In this review, we will discuss cardiotoxicities of both traditional and emerging therapies for breast cancer. We will discuss current practices to detect cardiotoxicity of these therapies with the focus on new and emerging biomarkers. We will then focus on 'omics approaches, especially the use of epigenetics to discover novel biomarkers and therapeutics to mitigate cardiotoxicity. RECENT FINDINGS Significant cardiotoxicities of conventional chemotherapies remain and new and unpredictable new forms of cardiac and/or vascular toxicity emerge with the surge in novel and targeted therapies. Yet, there is no clear guidance on detection of cardiotoxicity, except for significant left ventricular systolic dysfunction, and even then, there is no uniform definition of what constitutes cardiotoxicity. The gold standard for detection of cardiotoxicity involves a serial echocardiography in conjunction with blood-based biomarkers to detect early subclinical cardiac dysfunction. However, the ability of these tests to detect early disease remains limited and not all forms of toxicity are detectable with these modalities. There is an unprecedented need to discover novel biomarkers that are sensitive and specific for early detection of subclinical cardiotoxicity. In that space, novel echocardiographic techniques, such as strain, are becoming more common-place and new biomarkers, discovered by epigenetic approaches, seem to become promising alternatives or adjuncts to conventional non-specific cardiac biomarkers.
Collapse
Affiliation(s)
- Dongqing Chen
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia
| | - Conagh Kelly
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia
| | - Tatt Jhong Haw
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia.,Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia
| | - Janine M Lombard
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia
| | - Ina I C Nordman
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia
| | - Amanda J Croft
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia
| | - Doan T M Ngo
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia. .,School of Biomedical Science and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
| | - Aaron L Sverdlov
- Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle, NSW, Callaghan, Australia. .,Cardio-Oncology & Cardiometabolic Research Group, College of Health, Medicine and Wellbeing, Hunter Medical Research Institute & University of Newcastle Calvary Mater Newcastle, NSW, Waratah, Australia. .,Cardiovascular Department, John Hunter Hospital, Hunter New England Local Health District, NSW, New Lambton Heights, Australia. .,School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.
| |
Collapse
|
15
|
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
|
16
|
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
|
17
|
Yang K, Song H, Yin D. PDSS2 Inhibits the Ferroptosis of Vascular Endothelial Cells in Atherosclerosis by Activating Nrf2. J Cardiovasc Pharmacol 2021; 77:767-776. [PMID: 33929387 PMCID: PMC8274586 DOI: 10.1097/fjc.0000000000001030] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/29/2021] [Indexed: 12/21/2022]
Abstract
ABSTRACT Cardiovascular disease ranks the leading cause of mortality worldwide. Prenyldiphosphate synthase subunits collectively participate in the formation and development of atherosclerosis (AS). This study aimed to investigate the role of PDSS2 in AS and its underlying mechanisms. Human coronary artery endothelial cells (HCAECs) were treated with oxidized low-density lipoprotein to establish the AS model. The gene expression levels were determined by qRT-PCR, Western blot, and ELISA. CCK-8, colony formation was applied to determine the proliferation of HCAECs. Chromatin immunoprecipitation assay and luciferase assay were applied to verify the interaction between PDSS2 and Nrf2. The results showed that the serum levels of PDSS2 and Nrf2 were decreased in patients with AS. Overexpression of PDSS2 suppressed the release of reactive oxygen species, iron content and ferroptosis of HCAECs, and promoted the proliferation of HCAECs. Moreover, PDSS2 activated antioxidant Nrf2. PDSS2 interacted with Nrf2 to alleviate the ferroptosis of HCAECs. However, knockdown of Nrf2 alleviated the effects of PDSS2 on the proliferation and ferroptosis of HCAECs. In vivo assays, overexpression of PDSS2 and Nrf2 suppressed the progression of AS. In conclusion, overexpression of PDSS2 suppressed the ferroptosis of HCAECs by promoting the activation of Nrf2 pathways. Thence PDSS2 may play a cardio-protective role in AS.
Collapse
Affiliation(s)
- Kai Yang
- Cardiovascular Medicine Department, the First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China
| | - Hejian Song
- Cardiovascular Medicine Department, the First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China
| | - Delu Yin
- Cardiovascular Medicine Department, the First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China
| |
Collapse
|
18
|
Abstract
PURPOSE OF REVIEW Cardiovascular diseases (CVDs) are typically caused by multifactorial events including mutations in a large number of genes. Epigenetic-derived modifications in the cells are normal but can be amended by aging, lifestyle, and exposure to toxic substances. Major epigenetic modifications are DNA methylation, histone modification, chromatin remodeling as well as the noncoding RNAs. These pivotal players are involved in the epigenetic-induced modifications observed during CVDs. Nevertheless, despite impressive efforts capitalized in epigenetic research in the last 50 years, clinical applications are still not satisfactory. RECENT FINDINGS Briefly, we present some of the recent steps forward in the epigenetic studies of CVDs. There is an increased appreciation for the contribution of epigenetic alterations in the development of CVDs. Now, we have novel epigenetic biomarkers and therapeutic trials with the use of statins, metformin, and some compounds affecting epigenetic pathways including a BET inhibitor apabetalone. The new knowledge of epigenetic regulation is also discussed in the light of precision medicine of CVDs. SUMMARY Epigenetic studies of CVDs have the promise to yield both mechanistic insights as well as adjunct treatments (repurposed drugs and apabetalone). The overall concept of precision medicine is not widely recognized in routine medical practice and the so-called reductionist approach remains the most used way to treat CVD patients.
Collapse
|
19
|
Bain CR, Ziemann M, Kaspi A, Khan AW, Taylor R, Trahair H, Khurana I, Kaipananickal H, Wallace S, El-Osta A, Myles PS, Bozaoglu K. DNA methylation patterns from peripheral blood separate coronary artery disease patients with and without heart failure. ESC Heart Fail 2020; 7:2468-2478. [PMID: 32618141 PMCID: PMC7524212 DOI: 10.1002/ehf2.12810] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/11/2020] [Accepted: 05/14/2020] [Indexed: 01/01/2023] Open
Abstract
Aims Natriuretic peptides are useful for diagnosis and prognostication of heart failure of any cause. Now, research aims to discover novel biomarkers that will more specifically define the heart failure phenotype. DNA methylation plays a critical role in the development of cardiovascular disease with the potential to predict fundamental pathogenic processes. There is a lack of data relating DNA methylation in heart failure that specifically focuses on patients with severe multi‐vessel coronary artery disease. To begin to address this, we conducted a pilot study uniquely exploring the utility of powerful whole‐genome methyl‐binding domain‐capture sequencing in a cohort of cardiac surgery patients, matched for the severity of their coronary artery disease, aiming to identify candidate peripheral blood DNA methylation markers of ischaemic cardiomyopathy and heart failure. Methods and results We recruited a cohort of 20 male patients presenting for coronary artery bypass graft surgery with phenotypic extremes of heart failure but who otherwise share a similar coronary ischaemic burden, age, sex, and ethnicity. Methylation profiling in patient blood samples was performed using methyl‐binding domain‐capture sequencing. Differentially methylated regions were validated using targeted bisulfite sequencing. Gene set enrichment analysis was performed to identify differences in methylation at or near gene promoters in certain known Reactome pathways. We detected 567 188 methylation peaks of which our general linear model identified 68 significantly differentially methylated regions in heart failure with a false discovery rate <0.05. Of these regions, 48 occurred within gene bodies and 25 were located near enhancer elements, some within coding genes and some in non‐coding genes. Gene set enrichment analyses identified 103 significantly enriched gene sets (false discovery rate <0.05) in heart failure. Validation analysis of regions with the strongest differential methylation data was performed for two genes: HDAC9 and the uncharacterized miRNA gene MIR3675. Genes of particular interest as novel candidate markers of the heart failure phenotype with reduced methylation were HDAC9, JARID2, and GREM1 and with increased methylation PDSS2. Conclusions We demonstrate the utility of methyl‐binding domain‐capture sequencing to evaluate peripheral blood DNA methylation markers in a cohort of cardiac surgical patients with severe multi‐vessel coronary artery disease and phenotypic extremes of heart failure. The differential methylation status of specific coding genes identified are candidates for larger longitudinal studies. We have further demonstrated the value and feasibility of examining DNA methylation during the perioperative period to highlight biological pathways and processes contributing to complex phenotypes.
Collapse
Affiliation(s)
- Chris R Bain
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Anaesthesiology and Perioperative Medicine, The Alfred Hospital and Monash University, The Alfred Centre, Level 6, 99 Commercial Road, Melbourne, VIC, 3004, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark Ziemann
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia.,School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Melbourne, VIC, Australia
| | - Antony Kaspi
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | | | - Rachael Taylor
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Hugh Trahair
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Ishant Khurana
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Harikrishnan Kaipananickal
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Sophie Wallace
- Department of Anaesthesiology and Perioperative Medicine, The Alfred Hospital and Monash University, The Alfred Centre, Level 6, 99 Commercial Road, Melbourne, VIC, 3004, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Assam El-Osta
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia.,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Faculty of Health, Department of Technology, Biomedical Laboratory Science, University College Copenhagen, Copenhagen, Denmark
| | - Paul S Myles
- Department of Anaesthesiology and Perioperative Medicine, The Alfred Hospital and Monash University, The Alfred Centre, Level 6, 99 Commercial Road, Melbourne, VIC, 3004, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Kiymet Bozaoglu
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|