1
|
Pastwińska J, Karwaciak I, Karaś K, Sałkowska A, Chałaśkiewicz K, Strapagiel D, Sobalska-Kwapis M, Dastych J, Ratajewski M. α-Hemolysin from Staphylococcus aureus Changes the Epigenetic Landscape of Th17 Cells. Immunohorizons 2024; 8:606-621. [PMID: 39240270 DOI: 10.4049/immunohorizons.2400061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 09/07/2024] Open
Abstract
The human body harbors a substantial population of bacteria, which may outnumber host cells. Thus, there are multiple interactions between both cell types. Given the common presence of Staphylococcus aureus in the human body and the role of Th17 cells in controlling this pathogen on mucous membranes, we sought to investigate the effect of α-hemolysin, which is produced by this bacterium, on differentiating Th17 cells. RNA sequencing analysis revealed that α-hemolysin influences the expression of signature genes for Th17 cells as well as genes involved in epigenetic regulation. We observed alterations in various histone marks and genome methylation levels via whole-genome bisulfite sequencing. Our findings underscore how bacterial proteins can significantly influence the transcriptome, epigenome, and phenotype of human Th17 cells, highlighting the intricate and complex nature of the interaction between immune cells and the microbiota.
Collapse
Affiliation(s)
- Joanna Pastwińska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Iwona Karwaciak
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Kaja Karaś
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Anna Sałkowska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Katarzyna Chałaśkiewicz
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jarosław Dastych
- Laboratory of Cellular Immunology, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Marcin Ratajewski
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| |
Collapse
|
2
|
Oeing CU, Pepin ME, Saul KB, Agircan AS, Assenov Y, Merkel TS, Sedaghat-Hamedani F, Weis T, Meder B, Guan K, Plass C, Weichenhan D, Siede D, Backs J. Indirect epigenetic testing identifies a diagnostic signature of cardiomyocyte DNA methylation in heart failure. Basic Res Cardiol 2023; 118:9. [PMID: 36939901 PMCID: PMC10027651 DOI: 10.1007/s00395-022-00954-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 03/21/2023]
Abstract
Precision-based molecular phenotyping of heart failure must overcome limited access to cardiac tissue. Although epigenetic alterations have been found to underlie pathological cardiac gene dysregulation, the clinical utility of myocardial epigenomics remains narrow owing to limited clinical access to tissue. Therefore, the current study determined whether patient plasma confers indirect phenotypic, transcriptional, and/or epigenetic alterations to ex vivo cardiomyocytes to mirror the failing human myocardium. Neonatal rat ventricular myocytes (NRVMs) and single-origin human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and were treated with blood plasma samples from patients with dilated cardiomyopathy (DCM) and donor subjects lacking history of cardiovascular disease. Following plasma treatments, NRVMs and hiPSC-CMs underwent significant hypertrophy relative to non-failing controls, as determined via automated high-content screening. Array-based DNA methylation analysis of plasma-treated hiPSC-CMs and cardiac biopsies uncovered robust, and conserved, alterations in cardiac DNA methylation, from which 100 sites were validated using an independent cohort. Among the CpG sites identified, hypo-methylation of the ATG promoter was identified as a diagnostic marker of HF, wherein cg03800765 methylation (AUC = 0.986, P < 0.0001) was found to out-perform circulating NT-proBNP levels in differentiating heart failure. Taken together, these findings support a novel approach of indirect epigenetic testing in human HF.
Collapse
Affiliation(s)
- Christian U Oeing
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
- Department of Internal Medicine and Cardiology, Charité University Medicine, DZHK (German Center for Cardiovascular Research), Partner site Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Mark E Pepin
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Kerstin B Saul
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Ayça Seyhan Agircan
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Yassen Assenov
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Tobias S Merkel
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Farbod Sedaghat-Hamedani
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Tanja Weis
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Benjamin Meder
- Department of Cardiology, University of Heidelberg, DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Kaomei Guan
- Institute of Pharmacology and Toxicology, Technische Universität Medical Centre Dresden, Dresden, Germany
| | - Christoph Plass
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Cancer Epigenomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Dominik Siede
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Johannes Backs
- Institute of Experimental Cardiology, University Hospital Heidelberg, University of Heidelberg and DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany.
| |
Collapse
|
3
|
Klutstein M. Cause and effect in epigenetics - where lies the truth, and how can experiments reveal it?: Epigenetic self-reinforcing loops obscure causation in cancer and aging. Bioessays 2020; 43:e2000262. [PMID: 33236359 DOI: 10.1002/bies.202000262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic changes are implicated in aging and cancer. Sometimes, it is clear whether the causing agent of the condition is a genetic factor or epigenetic. In other cases, the causative factor is unclear, and could be either genetic or epigenetic. Is there a general role for epigenetic changes in cancer and aging? Here, I present the paradigm of causative roles executed by epigenetic changes. I discuss cases with clear roles of the epigenome in cancer and aging, and other cases showing involvement of other factors. I also present the possibility that sometimes causality is difficult to assign because of the presence of self-reinforcing loops in epigenetic regulation. Such loops hinder the identification of the causative factor. I provide an experimental framework by which the role of the epigenome can be examined in a better setting and where the presence of such loops could be investigated in more detail.
Collapse
Affiliation(s)
- Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
| |
Collapse
|
4
|
Cresci S, Pereira NL, Ahmad F, Byku M, de las Fuentes L, Lanfear DE, Reilly CM, Owens AT, Wolf MJ. Heart Failure in the Era of Precision Medicine: A Scientific Statement From the American Heart Association. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 12:458-485. [DOI: 10.1161/hcg.0000000000000058] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
One of 5 people will develop heart failure over his or her lifetime. Early diagnosis and better understanding of the pathophysiology of this disease are critical to optimal treatment. The “omics”—genomics, pharmacogenomics, epigenomics, proteomics, metabolomics, and microbiomics— of heart failure represent rapidly expanding fields of science that have, to date, not been integrated into a single body of work. The goals of this statement are to provide a comprehensive overview of the current state of these omics as they relate to the development and progression of heart failure and to consider the current and potential future applications of these data for precision medicine with respect to prevention, diagnosis, and therapy.
Collapse
|
5
|
Zhang P, Li T, Liu YQ, Zhang H, Xue SM, Li G, Cheng HYM, Cao JM. Contribution of DNA methylation in chronic stress-induced cardiac remodeling and arrhythmias in mice. FASEB J 2019; 33:12240-12252. [PMID: 31431066 DOI: 10.1096/fj.201900100r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
It is recognized that stress can induce cardiac dysfunction, but the underlying mechanisms are not well understood. The present study aimed to test the hypothesis that chronic negative stress leads to alterations in DNA methylation of certain cardiac genes, which in turn contribute to pathologic remodeling of the heart. We found that mice that were exposed to chronic restraint stress (CRS) for 4 wk exhibited cardiac remodeling toward heart failure, as characterized by ventricular chamber dilatation, wall thinning, and decreased contractility. CRS also induced cardiac arrhythmias, including intermittent sinus tachycardia and bradycardia, frequent premature ventricular contraction, and sporadic atrioventricular conduction block. Circulating levels of stress hormones were elevated, and the cardiac expression of tyrosine hydroxylase, a marker of sympathetic innervation, was increased in CRS mice. Using reduced representation bisulfite sequencing, we found that although CRS did not lead to global changes in DNA methylation in the murine heart, it nevertheless altered methylation at specific genes that are associated with the dilated cardiomyopathy (DCM) (e.g., desmin) and adrenergic signaling of cardiomyocytes (ASPC) (e.g., adrenergic receptor-α1) pathways. We conclude that CRS induces cardiac remodeling and arrhythmias, potentially through altered methylation of myocardial genes associated with the DCM and ASPC pathways.-Zhang, P., Li, T., Liu, Y.-Q., Zhang, H., Xue, S.-M., Li, G., Cheng, H.-Y.M., Cao, J.-M. Contribution of DNA methylation in chronic stress-induced cardiac remodeling and arrhythmias in mice.
Collapse
Affiliation(s)
- Peng Zhang
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Tao Li
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Ya-Qin Liu
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Hao Zhang
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Si-Meng Xue
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Guang Li
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Ji-Min Cao
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Department of Physiology, Shanxi Medical University, Taiyuan, China
| |
Collapse
|
6
|
Miousse IR, Skinner CM, Sridharan V, Seawright JW, Singh P, Landes RD, Cheema AK, Hauer-Jensen M, Boerma M, Koturbash I. Changes in one-carbon metabolism and DNA methylation in the hearts of mice exposed to space environment-relevant doses of oxygen ions ( 16O). LIFE SCIENCES IN SPACE RESEARCH 2019; 22:8-15. [PMID: 31421852 PMCID: PMC6703167 DOI: 10.1016/j.lssr.2019.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 05/13/2023]
Abstract
Cardiovascular disease constitutes an important threat to humans after space missions beyond the Earth's magnetosphere. Epigenetic alterations have an important role in the etiology and pathogenesis of cardiovascular disease. Previous research in animal models has shown that protons and 56Fe ions cause long-term changes in DNA methylation and expression of repetitive elements in the heart. However, astronauts will be exposed to a variety of ions, including the smaller fragmented products of heavy ions after they interact with the walls of the space craft. Here, we investigated the effects of 16O on the cardiac methylome and one-carbon metabolism in male C57BL/6 J mice. Left ventricles were examined 14 and 90 days after exposure to space-relevant doses of 0.1, 0.25, or 1 Gy of 16O (600 MeV/n). At 14 days, the two higher radiation doses elicited global DNA hypomethylation in the 5'-UTR of Long Interspersed Nuclear Elements 1 (LINE-1) compared to unirradiated, sham-treated mice, whereas specific LINE-1 elements exhibited hypermethylation at day 90. The pericentromeric major satellites were affected both at the DNA methylation and expression levels at the lowest radiation dose. DNA methylation was elevated, particularly after 90 days, while expression showed first a decrease followed by an increase in transcript abundance. Metabolomics analysis revealed that metabolites involved in homocysteine remethylation, central to DNA methylation, were unaffected by radiation, but the transsulfuration pathway was impacted after 90 days, with a large increase in cystathione levels at the lowest dose. In summary, we observed dynamic changes in the cardiac epigenome and metabolome three months after exposure to a single low dose of oxygen ions.
Collapse
Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States; Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
| | - Charles M Skinner
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Vijayalakshmi Sridharan
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - John W Seawright
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Preeti Singh
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Reid D Landes
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Amrita K Cheema
- Georgetown University Medical Center, Departments of Oncology and Biochemistry, Molecular and Cellular Biology, Washington, DC, United States
| | - Martin Hauer-Jensen
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Marjan Boerma
- Division of Radiation Health, Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| |
Collapse
|
7
|
Verheijen M, Lienhard M, Schrooders Y, Clayton O, Nudischer R, Boerno S, Timmermann B, Selevsek N, Schlapbach R, Gmuender H, Gotta S, Geraedts J, Herwig R, Kleinjans J, Caiment F. DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro. Sci Rep 2019; 9:4641. [PMID: 30874586 PMCID: PMC6420634 DOI: 10.1038/s41598-019-40660-0] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/20/2019] [Indexed: 12/16/2022] Open
Abstract
Though clinical trials for medical applications of dimethyl sulfoxide (DMSO) reported toxicity in the 1960s, later, the FDA classified DMSO in the safest solvent category. DMSO became widely used in many biomedical fields and biological effects were overlooked. Meanwhile, biomedical science has evolved towards sensitive high-throughput techniques and new research areas, including epigenomics and microRNAs. Considering its wide use, especially for cryopreservation and in vitro assays, we evaluated biological effect of DMSO using these technological innovations. We exposed 3D cardiac and hepatic microtissues to medium with or without 0.1% DMSO and analyzed the transcriptome, proteome and DNA methylation profiles. In both tissue types, transcriptome analysis detected >2000 differentially expressed genes affecting similar biological processes, thereby indicating consistent cross-organ actions of DMSO. Furthermore, microRNA analysis revealed large-scale deregulations of cardiac microRNAs and smaller, though still massive, effects in hepatic microtissues. Genome-wide methylation patterns also revealed tissue-specificity. While hepatic microtissues demonstrated non-significant changes, findings from cardiac microtissues suggested disruption of DNA methylation mechanisms leading to genome-wide changes. The extreme changes in microRNAs and alterations in the epigenetic landscape indicate that DMSO is not inert. Its use should be reconsidered, especially for cryopreservation of embryos and oocytes, since it may impact embryonic development.
Collapse
Affiliation(s)
- M Verheijen
- Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - M Lienhard
- Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Y Schrooders
- Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - O Clayton
- F. Hoffmann-La Roche AG, Basel, Switzerland
| | | | - S Boerno
- Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - B Timmermann
- Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - N Selevsek
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - R Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | | | - S Gotta
- Genedata AG, Basel, Switzerland
| | - J Geraedts
- Genetics and Cell Biology, Maastricht University, Medical Center, Maastricht, Netherlands
| | - R Herwig
- Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - J Kleinjans
- Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - F Caiment
- Toxicogenomics, Maastricht University, Maastricht, Netherlands.
| |
Collapse
|
8
|
Abstract
BACKGROUND Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and related mechanisms could be investigated through the multi-omic comparative analysis of many inflammatory diseases. Therefore, it is important to use molecular data to study the genesis of the diseases. Here we propose a new methodology to study the relationships between inflammatory diseases and signalling molecules whose dysregulation at molecular levels could lead to systemic pathological events observed in inflammatory diseases. RESULTS We first perform an exploratory analysis of gene expression data of a number of diseases that involve a strong inflammatory component. The comparison of gene expression between disease and healthy samples reveals the importance of members of gene families coding for signalling factors. Next, we focus on interested signalling gene families and a subset of inflammation related diseases with multi-omic features including both gene expression and DNA methylation. We introduce a phylogenetic-based multi-omic method to study the relationships between multi-omic features of inflammation related diseases by integrating gene expression, DNA methylation through sequence based phylogeny of the signalling gene families. The models of adaptations between gene expression and DNA methylation can be inferred from pre-estimated evolutionary relationship of a gene family. Members of the gene family whose expression or methylation levels significantly deviate from the model are considered as the potential disease associated genes. CONCLUSIONS Applying the methodology to four gene families (the chemokine receptor family, the TNF receptor family, the TGF- β gene family, the IL-17 gene family) in nine inflammation related diseases, we identify disease associated genes which exhibit significant dysregulation in gene expression or DNA methylation in the inflammation related diseases, which provides clues for functional associations between the diseases.
Collapse
Affiliation(s)
- Hui Xiao
- Computer Laboratory, University of Cambridge, Cambridge, UK
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Pietro Lio’
- Computer Laboratory, University of Cambridge, Cambridge, UK
| |
Collapse
|
9
|
Jagannathan M, Yamashita YM. Function of Junk: Pericentromeric Satellite DNA in Chromosome Maintenance. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 82:319-327. [PMID: 29610245 DOI: 10.1101/sqb.2017.82.034504] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Satellite DNAs are simple tandem repeats that exist at centromeric and pericentromeric regions on eukaryotic chromosomes. Unlike the centromeric satellite DNA that comprises the vast majority of natural centromeres, function(s) for the much more abundant pericentromeric satellite repeats are poorly understood. In fact, the lack of coding potential allied with rapid divergence of repeat sequences across eukaryotes has led to their dismissal as "junk DNA" or "selfish parasites." Although implicated in various biological processes, a conserved function for pericentromeric satellite DNA remains unidentified. We have addressed the role of satellite DNA through studying chromocenters, a cytological aggregation of pericentromeric satellite DNA from multiple chromosomes into DNA-dense nuclear foci. We have shown that multivalent satellite DNA-binding proteins cross-link pericentromeric satellite DNA on chromosomes into chromocenters. Disruption of chromocenters results in the formation of micronuclei, which arise by budding off the nucleus during interphase. We propose a model that satellite DNAs are critical chromosome elements that are recognized by satellite DNA-binding proteins and incorporated into chromocenters. We suggest that chromocenters function to preserve the entire chromosomal complement in a single nucleus, a fundamental and unquestioned feature of eukaryotic genomes. We speculate that the rapid divergence of satellite DNA sequences between closely related species results in discordant chromocenter function and may underlie speciation and hybrid incompatibility.
Collapse
Affiliation(s)
- Madhav Jagannathan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Yukiko M Yamashita
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
10
|
Perrino C, Barabási AL, Condorelli G, Davidson SM, De Windt L, Dimmeler S, Engel FB, Hausenloy DJ, Hill JA, Van Laake LW, Lecour S, Leor J, Madonna R, Mayr M, Prunier F, Sluijter JPG, Schulz R, Thum T, Ytrehus K, Ferdinandy P. Epigenomic and transcriptomic approaches in the post-genomic era: path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heart. Cardiovasc Res 2018; 113:725-736. [PMID: 28460026 PMCID: PMC5437366 DOI: 10.1093/cvr/cvx070] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/27/2017] [Indexed: 01/19/2023] Open
Abstract
Despite advances in myocardial reperfusion therapies, acute myocardial ischaemia/reperfusion injury and consequent ischaemic heart failure represent the number one cause of morbidity and mortality in industrialized societies. Although different therapeutic interventions have been shown beneficial in preclinical settings, an effective cardioprotective or regenerative therapy has yet to be successfully introduced in the clinical arena. Given the complex pathophysiology of the ischaemic heart, large scale, unbiased, global approaches capable of identifying multiple branches of the signalling networks activated in the ischaemic/reperfused heart might be more successful in the search for novel diagnostic or therapeutic targets. High-throughput techniques allow high-resolution, genome-wide investigation of genetic variants, epigenetic modifications, and associated gene expression profiles. Platforms such as proteomics and metabolomics (not described here in detail) also offer simultaneous readouts of hundreds of proteins and metabolites. Isolated omics analyses usually provide Big Data requiring large data storage, advanced computational resources and complex bioinformatics tools. The possibility of integrating different omics approaches gives new hope to better understand the molecular circuitry activated by myocardial ischaemia, putting it in the context of the human ‘diseasome’. Since modifications of cardiac gene expression have been consistently linked to pathophysiology of the ischaemic heart, the integration of epigenomic and transcriptomic data seems a promising approach to identify crucial disease networks. Thus, the scope of this Position Paper will be to highlight potentials and limitations of these approaches, and to provide recommendations to optimize the search for novel diagnostic or therapeutic targets for acute ischaemia/reperfusion injury and ischaemic heart failure in the post-genomic era.
Collapse
Affiliation(s)
- Cinzia Perrino
- Department of Advanced Biomedical Sciences, Federico II University, Via Pansini 5, 80131 Naples, Italy
| | - Albert-Laszló Barabási
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, USA.,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Center for Network Science, Central European University, Budapest, Hungary.,Department of Medicine, and Division of Network Medicine, Brigham and Womens Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Gianluigi Condorelli
- Department of Cardiovascular Medicine, Humanitas Research Hospital and Humanitas University, Rozzano, Italy.,Institute of Genetic and Biomedical Research, National Research Council of Italy, Rozzano, Milan, Italy
| | - Sean Michael Davidson
- The Hatter Cardiovascular Institute, Institute of Cardiovascular Science, University College London, London, UK
| | - Leon De Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, University Frankfurt, Frankfurt, Germany.,German Center for Cardiovascular Research (DZHK), RheinMain, Germany
| | - Felix Benedikt Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Derek John Hausenloy
- The Hatter Cardiovascular Institute, University College London, London, UK.,The National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, UK.,Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, Singapore.,National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore.,Yong Loo Lin School of Medicine, National University Singapore, Singapore.,Barts Heart Centre, St Bartholomew's Hospital, London, UK
| | - Joseph Addison Hill
- Departments of Medicine (Cardiology) and Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Linda Wilhelmina Van Laake
- Division of Heart and Lungs, Hubrecht Institute, University Medical Center Utrecht, Utrecht, The Netherlands.,UMC Utrecht Regenerative Medicine Center and Hubrecht Institute, Utrecht, The Netherlands
| | - Sandrine Lecour
- Hatter Cardiovascular Research Institute, University of Cape Town, Cape Town, South Africa
| | - Jonathan Leor
- Neufeld Cardiac Research Institute, Tel-Aviv University, Tel-Aviv, Israel.,Tamman Cardiovascular Research Institute, Sheba Medical Center; Sheba Center for Regenerative Medicine, Stem Cell, and Tissue Engineering, Tel Hashomer, Israel
| | - Rosalinda Madonna
- Center of Aging Sciences and Translational Medicine - CESI-MeT, "G. d'Annunzio" University, Chieti, Italy; Institute of Cardiology, Department of Neurosciences, Imaging, and Clinical Sciences, "G. d'Annunzio" University, Chieti, Italy.,The Texas Heart Institute and Center for Cardiovascular Biology and Atherosclerosis Research, Department of Internal Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London, UK
| | - Fabrice Prunier
- Department of Cardiology, Institut MITOVASC, University of Angers, University Hospital of Angers, Angers, France
| | - Joost Petrus Geradus Sluijter
- Cardiology and UMC Utrecht Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rainer Schulz
- Institute of Physiology, Justus Liebig University Giessen, Giessen, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Kirsti Ytrehus
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary.,Cardiovascular Research Group, Department of Biochemistry, University of Szeged, Szeged, Hungary.,Pharmahungary Group, Szeged, Hungary
| |
Collapse
|
11
|
Ratnam S, Bozek G, Martin T, Gallagher SJ, Payne CJ, Storb U. Ssm1b expression and function in germ cells of adult mice and in early embryos. Mol Reprod Dev 2017; 84:596-613. [PMID: 28464323 DOI: 10.1002/mrd.22826] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 04/13/2017] [Indexed: 12/17/2022]
Abstract
Ssm1b (Strain-specific modifier of DNA methylation 1b) is a Krüppel-associated box (KRAB) zinc finger gene that promotes CpG methylation in the mouse transgene HRD (Heavy chain enhancer, rearrangement by deletion). We report here that Ssm1b expression and concomitant HRD methylation are also present in the male and female germ cells of adult mice. Ssm1b is expressed in both diploid (2N) and haploid (1N) oocytes, as well as in 1N spermatids and spermatozoa, but not in 2N spermatogonia. Interestingly, Ssm1b mRNA is not detected in any other adult mouse organ examined, although Ssm1-family mRNAs are highly expressed in the heart. Reflecting strain specificity, Ssm1b expression and HRD methylation are not observed in early-stage C3H/HeJ mouse embryos; however, an Ssm1b-like gene that closely resembles an Ssm1b-like gene previously found in wild-derived mice is expressed in cultured embryonic stem cells derived from C3H/HeJ embryos, suggesting that culture conditions affect its expression. Collectively, this work demonstrates that HRD methylation by Ssm1b is more temporally restricted during spermatogenesis compared to oogenesis, and is altered when embryonic stem cells are cultured from C3H/HeJ inner cell mass cells.
Collapse
Affiliation(s)
- Sarayu Ratnam
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Grazyna Bozek
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Terence Martin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Shannon J Gallagher
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Christopher J Payne
- Human Molecular Genetics Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Departments of Pediatrics and Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ursula Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| |
Collapse
|
12
|
Comparative Analysis of Satellite DNA in the Drosophila melanogaster Species Complex. G3-GENES GENOMES GENETICS 2017; 7:693-704. [PMID: 28007840 PMCID: PMC5295612 DOI: 10.1534/g3.116.035352] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Satellite DNAs are highly repetitive sequences that account for the majority of constitutive heterochromatin in many eukaryotic genomes. It is widely recognized that sequences and locations of satellite DNAs are highly divergent even in closely related species, contributing to the hypothesis that satellite DNA differences may underlie speciation. However, due to its repetitive nature, the mapping of satellite DNAs has been mostly left out of recent genomics analyses, hampering the use of molecular genetics techniques to better understand their role in speciation and evolution. Satellite DNAs are most extensively and comprehensively mapped in Drosophila melanogaster, a species that is also an excellent model system with which to study speciation. Yet the lack of comprehensive knowledge regarding satellite DNA identity and location in its sibling species (D. simulans, D. mauritiana, and D. sechellia) has prevented the full utilization of D. melanogaster in studying speciation. To overcome this problem, we initiated the mapping of satellite DNAs on the genomes of the D. melanogaster species complex (D. melanogaster, D. simulans, D. mauritiana, and D. sechellia) using multi-color fluorescent in situ hybridization (FISH) probes. Our study confirms a striking divergence of satellite DNAs in the D. melanogaster species complex, even among the closely related species of the D. simulans clade (D. simulans, D. mauritiana, and D. sechellia), and suggests the presence of unidentified satellite sequences in these species.
Collapse
|
13
|
Berezin A. Epigenetics in heart failure phenotypes. BBA CLINICAL 2016; 6:31-7. [PMID: 27335803 PMCID: PMC4909708 DOI: 10.1016/j.bbacli.2016.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 12/29/2022]
Abstract
Chronic heart failure (HF) is a leading clinical and public problem posing a higher risk of morbidity and mortality in different populations. HF appears to be in both phenotypic forms: HF with reduced left ventricular ejection fraction (HFrEF) and HF with preserved left ventricular ejection fraction (HFpEF). Although both HF phenotypes can be distinguished through clinical features, co-morbidity status, prediction score, and treatment, the clinical outcomes in patients with HFrEF and HFpEF are similar. In this context, investigation of various molecular and cellular mechanisms leading to the development and progression of both HF phenotypes is very important. There is emerging evidence that epigenetic regulation may have a clue in the pathogenesis of HF. This review represents current available evidence regarding the implication of epigenetic modifications in the development of different HF phenotypes and perspectives of epigenetic-based therapies of HF.
Collapse
|
14
|
Greco CM, Kunderfranco P, Rubino M, Larcher V, Carullo P, Anselmo A, Kurz K, Carell T, Angius A, Latronico MVG, Papait R, Condorelli G. DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy. Nat Commun 2016; 7:12418. [PMID: 27489048 PMCID: PMC4976219 DOI: 10.1038/ncomms12418] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Abstract
Methylation at 5-cytosine (5-mC) is a fundamental epigenetic DNA modification associated recently with cardiac disease. In contrast, the role of 5-hydroxymethylcytosine (5-hmC)-5-mC's oxidation product-in cardiac biology and disease is unknown. Here we assess the hydroxymethylome in embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes, showing that dynamic modulation of hydroxymethylated DNA is associated with specific transcriptional networks during heart development and failure. DNA hydroxymethylation marks the body of highly expressed genes as well as distal regulatory regions with enhanced activity. Moreover, pathological hypertrophy is characterized by a shift towards a neonatal 5-hmC distribution pattern. We also show that the ten-eleven translocation 2 (TET2) enzyme regulates the expression of key cardiac genes, such as Myh7, through 5-hmC deposition on the gene body and at enhancers. Thus, we provide a genome-wide analysis of 5-hmC in the cardiomyocyte and suggest a role for this epigenetic modification in heart development and disease.
Collapse
Affiliation(s)
- Carolina M Greco
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI) 20089, Italy
| | - Paolo Kunderfranco
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI) 20089, Italy
| | - Marcello Rubino
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI) 20089, Italy
| | - Veronica Larcher
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI) 20089, Italy
| | - Pierluigi Carullo
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI) 20089, Italy.,Institute of Genetics and Biomedical Research, National Research Council of Italy, Via Manzoni 56, Rozzano (MI) 20089, Italy
| | - Achille Anselmo
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI) 20089, Italy
| | - Kerstin Kurz
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, 8137 Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München, 8137 Munich, Germany
| | - Andrea Angius
- Institute of Genetics and Biomedical Research, National Research Council of Italy, Via Manzoni 56, Rozzano (MI) 20089, Italy
| | | | - Roberto Papait
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI) 20089, Italy.,Institute of Genetics and Biomedical Research, National Research Council of Italy, Via Manzoni 56, Rozzano (MI) 20089, Italy
| | - Gianluigi Condorelli
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (MI) 20089, Italy.,Institute of Genetics and Biomedical Research, National Research Council of Italy, Via Manzoni 56, Rozzano (MI) 20089, Italy.,Humanitas University, Via Manzoni 56, Rozzano (MI) 20089, Italy.,Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK
| |
Collapse
|
15
|
Shimizu I, Minamino T. Physiological and pathological cardiac hypertrophy. J Mol Cell Cardiol 2016; 97:245-62. [PMID: 27262674 DOI: 10.1016/j.yjmcc.2016.06.001] [Citation(s) in RCA: 616] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 05/10/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022]
Abstract
The heart must continuously pump blood to supply the body with oxygen and nutrients. To maintain the high energy consumption required by this role, the heart is equipped with multiple complex biological systems that allow adaptation to changes of systemic demand. The processes of growth (hypertrophy), angiogenesis, and metabolic plasticity are critically involved in maintenance of cardiac homeostasis. Cardiac hypertrophy is classified as physiological when it is associated with normal cardiac function or as pathological when associated with cardiac dysfunction. Physiological hypertrophy of the heart occurs in response to normal growth of children or during pregnancy, as well as in athletes. In contrast, pathological hypertrophy is induced by factors such as prolonged and abnormal hemodynamic stress, due to hypertension, myocardial infarction etc. Pathological hypertrophy is associated with fibrosis, capillary rarefaction, increased production of pro-inflammatory cytokines, and cellular dysfunction (impairment of signaling, suppression of autophagy, and abnormal cardiomyocyte/non-cardiomyocyte interactions), as well as undesirable epigenetic changes, with these complex responses leading to maladaptive cardiac remodeling and heart failure. This review describes the key molecules and cellular responses involved in physiological/pathological cardiac hypertrophy.
Collapse
Affiliation(s)
- Ippei Shimizu
- Department of Cardiovascular Biology and Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan; Division of Molecular Aging and Cell Biology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.
| | - Tohru Minamino
- Department of Cardiovascular Biology and Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.
| |
Collapse
|
16
|
Abstract
PURPOSE OF REVIEW This article provides an overview, highlighting recent findings, of a major mechanism of gene regulation and its relevance to the pathophysiology of heart failure. RECENT FINDINGS The syndrome of heart failure is a complex and highly prevalent condition, one in which the heart undergoes substantial structural remodeling. Triggered by a wide range of disease-related cues, heart failure pathophysiology is governed by both genetic and epigenetic events. Epigenetic mechanisms, such as chromatin/DNA modifications and noncoding RNAs, have emerged as molecular transducers of environmental stimuli to control gene expression. Here, we emphasize metabolic milieu, aging, and hemodynamic stress as they impact the epigenetic landscape of the myocardium. SUMMARY Recent studies in multiple fields, including cancer, stem cells, development, and cardiovascular biology, have uncovered biochemical ties linking epigenetic machinery and cellular energetics and mitochondrial function. Elucidation of these connections will afford molecular insights into long-established epidemiological observations. With time, exploitation of the epigenetic machinery therapeutically may emerge with clinical relevance.
Collapse
Affiliation(s)
- Soo Young Kim
- Department of Internal Medicine (Cardiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cyndi Morales
- Department of Internal Medicine (Cardiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas G. Gillette
- Department of Internal Medicine (Cardiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph A. Hill
- Department of Internal Medicine (Cardiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
17
|
Radiation-induced changes in DNA methylation of repetitive elements in the mouse heart. Mutat Res 2016; 787:43-53. [PMID: 26963372 DOI: 10.1016/j.mrfmmm.2016.02.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 02/02/2016] [Accepted: 02/28/2016] [Indexed: 01/04/2023]
Abstract
DNA methylation is a key epigenetic mechanism, needed for proper control over the expression of genetic information and silencing of repetitive elements. Exposure to ionizing radiation, aside from its strong genotoxic potential, may also affect the methylation of DNA, within the repetitive elements, in particular. In this study, we exposed C57BL/6J male mice to low absorbed mean doses of two types of space radiation-proton (0.1 Gy, 150 MeV, dose rate 0.53 ± 0.08 Gy/min), and heavy iron ions ((56)Fe) (0.5 Gy, 600 MeV/n, dose rate 0.38 ± 0.06 Gy/min). Radiation-induced changes in cardiac DNA methylation associated with repetitive elements were detected. Specifically, modest hypomethylation of retrotransposon LINE-1 was observed at day 7 after irradiation with either protons or (56)Fe. This was followed by LINE-1, and other retrotransposons, ERV2 and SINE B1, as well as major satellite DNA hypermethylation at day 90 after irradiation with (56)Fe. These changes in DNA methylation were accompanied by alterations in the expression of DNA methylation machinery and affected the one-carbon metabolism pathway. Furthermore, loss of transposable elements expression was detected in the cardiac tissue at the 90-day time-point, paralleled by substantial accumulation of mRNA transcripts, associated with major satellites. Given that the one-carbon metabolism pathway can be modulated by dietary modifications, these findings suggest a potential strategy for the mitigation and, possibly, prevention of the negative effects exerted by ionizing radiation on the cardiovascular system. Additionally, we show that the methylation status and expression of repetitive elements may serve as early biomarkers of exposure to space radiation.
Collapse
|
18
|
Miousse IR, Chalbot MCG, Pathak R, Lu X, Nzabarushimana E, Krager K, Aykin-Burns N, Hauer-Jensen M, Demokritou P, Kavouras IG, Koturbash I. In Vitro Toxicity and Epigenotoxicity of Different Types of Ambient Particulate Matter. Toxicol Sci 2015; 148:473-87. [PMID: 26342214 PMCID: PMC5009441 DOI: 10.1093/toxsci/kfv200] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Exposure to ambient particulate matter (PM) has been associated with adverse health effects, including pulmonary and cardiovascular disease. Studies indicate that ambient PM originated from different sources may cause distinct biological effects. In this study, we sought to investigate the potential of various types of PM to cause epigenetic alterations in the in vitro system. RAW264.7 murine macrophages were exposed for 24 and 72 h to 5- and 50-μg/ml doses of the water soluble extract of 6 types of PM: soil dust, road dust, agricultural dust, traffic exhausts, biomass burning, and pollen, collected in January-April of 2014 in the area of Little Rock, Arkansas. Cytotoxicity, oxidative potential, epigenetic endpoints, and chromosomal aberrations were addressed. Exposure to 6 types of PM resulted in induction of cytotoxicity and oxidative stress in a type-, time-, and dose-dependent manner. Epigenetic alterations were characterized by type-, time-, and dose-dependent decreases of DNA methylation/demethylation machinery, increased DNA methyltransferases enzymatic activity and protein levels, and transcriptional activation and subsequent silencing of transposable elements LINE-1, SINE B1/B2. The most pronounced changes were observed after exposure to soil dust that were also characterized by hypomethylation and reactivation of satellite DNA and structural chromosomal aberrations in the exposed cells. The results of our study indicate that the water-soluble fractions of the various types of PM have differential potential to target the cellular epigenome.
Collapse
Affiliation(s)
- Isabelle R Miousse
- *Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health and
| | - Marie-Cecile G Chalbot
- *Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health and
| | - Rupak Pathak
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Xiaoyan Lu
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts; and
| | - Etienne Nzabarushimana
- *Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health and Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Kimberly Krager
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Nukhet Aykin-Burns
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Martin Hauer-Jensen
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts; and
| | - Ilias G Kavouras
- *Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health and
| | - Igor Koturbash
- *Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health and
| |
Collapse
|
19
|
Nzabarushimana E, Prior S, Miousse IR, Pathak R, Allen AR, Latendresse J, Olsen RHJ, Raber J, Hauer-Jensen M, Nelson GA, Koturbash I. Combined exposure to protons and (56)Fe leads to overexpression of Il13 and reactivation of repetitive elements in the mouse lung. LIFE SCIENCES IN SPACE RESEARCH 2015; 7:1-8. [PMID: 26553631 PMCID: PMC4641818 DOI: 10.1016/j.lssr.2015.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/08/2015] [Accepted: 08/15/2015] [Indexed: 05/15/2023]
Abstract
Interest in deep space exploration underlines the needs to investigate the effects of exposure to combined sources of space radiation. The lung is a target organ for radiation, and exposure to protons and heavy ions as radiation sources may lead to the development of degenerative disease and cancer. In this study, we evaluated the pro-fibrotic and epigenetic effects of exposure to protons (150 MeV/nucleon, 0.1 Gy) and heavy iron ions ((56)Fe, 600 MeV/nucleon, 0.5 Gy) alone or in combination (protons on Day 1 and (56)Fe on Day 2) in C57BL/6 male mice 4 weeks after irradiation. Exposure to (56)Fe, proton or in combination, did not result in histopathological changes in the murine lung. At the same time, combined exposure to protons and (56)Fe resulted in pronounced molecular alterations in comparison with either source of radiation alone. Specifically, we observed a substantial increase in the expression of cytokine Il13, loss of expression of DNA methyltransferase Dnmt1, and reactivation of LINE-1, SINE B1 retrotransposons, and major and minor satellites. Given the deleterious potential of the observed effects that may lead to development of chronic lung injury, pulmonary fibrosis, and cancer, future studies devoted to the investigation of the long-term effects of combined exposures to proton and heavy ions are clearly needed.
Collapse
Affiliation(s)
- Etienne Nzabarushimana
- Department of Environmental Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA; Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Sara Prior
- Department of Environmental Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Isabelle R Miousse
- Department of Environmental Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Rupak Pathak
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Antiño R Allen
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | | | - Reid H J Olsen
- Department of Behavioral Neuroscience, Oregon Health & Science University Portland, OR, 97239, USA
| | - Jacob Raber
- Departments of Neurology and Radiation Medicine, Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University Portland, OR, 97239, USA
| | - Martin Hauer-Jensen
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Gregory A Nelson
- Department of Basic Sciences, Division of Radiation Research, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Igor Koturbash
- Department of Environmental Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| |
Collapse
|
20
|
Chandrashekar DS, Dey P, Acharya KK. GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species. PLoS One 2015. [PMID: 26208093 PMCID: PMC4514817 DOI: 10.1371/journal.pone.0133647] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Genome-wide repeat sequences, such as LINEs, SINEs and LTRs share a considerable part of the mammalian nuclear genomes. These repeat elements seem to be important for multiple functions including the regulation of transcription initiation, alternative splicing and DNA methylation. But it is not possible to study all repeats and, hence, it would help to short-list before exploring their potential functional significance via experimental studies and/or detailed in silico analyses. Result We developed the ‘Genomic Repeat Element Analyzer for Mammals’ (GREAM) for analysis, screening and selection of potentially important mammalian genomic repeats. This web-server offers many novel utilities. For example, this is the only tool that can reveal a categorized list of specific types of transposons, retro-transposons and other genome-wide repetitive elements that are statistically over-/under-represented in regions around a set of genes, such as those expressed differentially in a disease condition. The output displays the position and frequency of identified elements within the specified regions. In addition, GREAM offers two other types of analyses of genomic repeat sequences: a) enrichment within chromosomal region(s) of interest, and b) comparative distribution across the neighborhood of orthologous genes. GREAM successfully short-listed a repeat element (MER20) known to contain functional motifs. In other case studies, we could use GREAM to short-list repetitive elements in the azoospermia factor a (AZFa) region of the human Y chromosome and those around the genes associated with rat liver injury. GREAM could also identify five over-represented repeats around some of the human and mouse transcription factor coding genes that had conserved expression patterns across the two species. Conclusion GREAM has been developed to provide an impetus to research on the role of repetitive sequences in mammalian genomes by offering easy selection of more interesting repeats in various contexts/regions. GREAM is freely available at http://resource.ibab.ac.in/GREAM/.
Collapse
Affiliation(s)
- Darshan Shimoga Chandrashekar
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bengaluru (Bangalore), 560100, Karnataka state, India
- Manipal University, Manipal, 576104, Karnataka state, India
| | - Poulami Dey
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bengaluru (Bangalore), 560100, Karnataka state, India
- Manipal University, Manipal, 576104, Karnataka state, India
| | - Kshitish K. Acharya
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bengaluru (Bangalore), 560100, Karnataka state, India
- Shodhaka Life Sciences Pvt. Ltd., IBAB, Biotech Park, Bengaluru (Bangalore), 560100, Karnataka state, India
- * E-mail:
| |
Collapse
|
21
|
Greco CM, Condorelli G. Epigenetic modifications and noncoding RNAs in cardiac hypertrophy and failure. Nat Rev Cardiol 2015; 12:488-97. [DOI: 10.1038/nrcardio.2015.71] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
22
|
Vujic A, Robinson EL, Ito M, Haider S, Ackers-Johnson M, See K, Methner C, Figg N, Brien P, Roderick HL, Skepper J, A Ferguson-Smith, Foo RS. Experimental heart failure modelled by the cardiomyocyte-specific loss of an epigenome modifier, DNMT3B. J Mol Cell Cardiol 2015; 82:174-83. [PMID: 25784084 DOI: 10.1016/j.yjmcc.2015.03.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 12/18/2022]
Abstract
Differential DNA methylation exists in the epigenome of end-stage failing human hearts but whether it contributes to disease progression is presently unknown. Here, we report that cardiac specific deletion of Dnmt3b, the predominant DNA methyltransferase in adult mouse hearts, leads to an accelerated progression to severe systolic insufficiency and myocardial thinning without a preceding hypertrophic response. This was accompanied by widespread myocardial interstitial fibrosis and myo-sarcomeric disarray. By targeted candidate gene quantitative RT-PCR, we discovered an over-activity of cryptic splice sites in the sarcomeric gene Myh7, resulting in a transcript with 8 exons missing. Moreover, a region of differential methylation overlies the splice site locus in the hearts of the cardiac-specific conditional knockout (CKO) mice. Although abundant and complex forms of alternative splice variants have been reported in diseased hearts and the contribution of each remains to be understood in further detail, our results demonstrate for the first time that a link may exist between alternative splicing and the cardiac epigenome. In particular, this gives the novel evidence whereby the loss of an epigenome modifier promotes the development and progression of heart disease.
Collapse
Affiliation(s)
- A Vujic
- Division of Cardiovascular Medicine, Addenbrooke's Centre for Clinical Investigation Building, University of Cambridge, Cambridge CB2 0QQ, UK; Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, 117599 Singapore
| | - E L Robinson
- Division of Cardiovascular Medicine, Addenbrooke's Centre for Clinical Investigation Building, University of Cambridge, Cambridge CB2 0QQ, UK
| | - M Ito
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - S Haider
- Centre for Molecular Oncology, Barts Cancer Institute, London EC1M 6BQ, UK
| | - M Ackers-Johnson
- Division of Cardiovascular Medicine, Addenbrooke's Centre for Clinical Investigation Building, University of Cambridge, Cambridge CB2 0QQ, UK; Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, 117599 Singapore; Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore
| | - K See
- Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore
| | - C Methner
- Clinical Pharmacology Unit, Addenbrooke's Centre for Clinical Investigation Building, University of Cambridge, Cambridge CB2 0QQ, UK
| | - N Figg
- Division of Cardiovascular Medicine, Addenbrooke's Centre for Clinical Investigation Building, University of Cambridge, Cambridge CB2 0QQ, UK
| | - P Brien
- Epigenetics ISP, Babraham Institute, Cambridge CB22 3AT, UK
| | - H L Roderick
- Epigenetics ISP, Babraham Institute, Cambridge CB22 3AT, UK
| | - J Skepper
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - A Ferguson-Smith
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - R S Foo
- Division of Cardiovascular Medicine, Addenbrooke's Centre for Clinical Investigation Building, University of Cambridge, Cambridge CB2 0QQ, UK; Cardiovascular Research Institute, Centre for Translational Medicine MD6, National University Health System, 117599 Singapore; Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore.
| |
Collapse
|
23
|
Yang J, Xu WW, Hu SJ. Heart failure: advanced development in genetics and epigenetics. BIOMED RESEARCH INTERNATIONAL 2015; 2015:352734. [PMID: 25949994 PMCID: PMC4407520 DOI: 10.1155/2015/352734] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/25/2015] [Accepted: 03/19/2015] [Indexed: 01/16/2023]
Abstract
Heart failure (HF) is a complex pathophysiological syndrome that arises from a primary defect in the ability of the heart to take in and/or eject sufficient blood. Genetic mutations associated with familial dilated cardiomyopathy, hypertrophic cardiomyopathy, and arrhythmogenic right ventricular cardiomyopathy can contribute to the various pathologies of HF. Therefore, genetic screening could be an approach for guiding individualized therapies and surveillance. In addition, epigenetic regulation occurs via key mechanisms, including ATP-dependent chromatin remodeling, DNA methylation, histone modification, and RNA-based mechanisms. MicroRNA is also a hot spot in HF research. This review gives an overview of genetic mutations associated with cardiomyopathy and the roles of some epigenetic mechanisms in HF.
Collapse
Affiliation(s)
- Jian Yang
- Department of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qing-Chun Road, Hangzhou 310003, China
| | - Wei-wei Xu
- Department of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qing-Chun Road, Hangzhou 310003, China
| | - Shen-jiang Hu
- Department of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, No. 79, Qing-Chun Road, Hangzhou 310003, China
| |
Collapse
|
24
|
Siggens L, Ekwall K. Epigenetics, chromatin and genome organization: recent advances from the ENCODE project. J Intern Med 2014; 276:201-14. [PMID: 24605849 DOI: 10.1111/joim.12231] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The organization of the genome into functional units, such as enhancers and active or repressed promoters, is associated with distinct patterns of DNA and histone modifications. The Encyclopedia of DNA Elements (ENCODE) project has advanced our understanding of the principles of genome, epigenome and chromatin organization, identifying hundreds of thousands of potential regulatory regions and transcription factor binding sites. Part of the ENCODE consortium, GENCODE, has annotated the human genome with novel transcripts including new noncoding RNAs and pseudogenes, highlighting transcriptional complexity. Many disease variants identified in genome-wide association studies are located within putative enhancer regions defined by the ENCODE project. Understanding the principles of chromatin and epigenome organization will help to identify new disease mechanisms, biomarkers and drug targets, particularly as ongoing epigenome mapping projects generate data for primary human cell types that play important roles in disease.
Collapse
Affiliation(s)
- L Siggens
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | |
Collapse
|
25
|
Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity. Nat Struct Mol Biol 2014; 21:236-43. [PMID: 24531659 DOI: 10.1038/nsmb.2776] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/22/2014] [Indexed: 01/06/2023]
Abstract
Functional centromeres are essential for proper cell division. Centromeres are established largely by epigenetic processes resulting in incorporation of the histone H3 variant CENP-A. Here, we demonstrate the direct involvement of H2B monoubiquitination, mediated by RNF20 in humans or Brl1 in Schizosaccharomyces pombe, in centromeric chromatin maintenance. Monoubiquinated H2B (H2Bub1) is needed for this maintenance, promoting noncoding transcription, centromere integrity and accurate chromosomal segregation. A transient pulse of centromeric H2Bub1 leads to RNA polymerase II-mediated transcription of the centromere's central domain, coupled to decreased H3 stability. H2Bub1-deficient cells have centromere cores that, despite their intact centromeric heterochromatin barriers, exhibit characteristics of heterochromatin, such as silencing histone modifications, reduced nucleosome turnover and reduced levels of transcription. In the H2Bub1-deficient cells, centromere functionality is hampered, thus resulting in unequal chromosome segregation. Therefore, centromeric H2Bub1 is essential for maintaining active centromeric chromatin.
Collapse
|
26
|
Baris HN, Chan WM, Andrews C, Behar DM, Donovan DJ, Morton CC, Ranells J, Pal T, Ligon AH, Engle EC. Complex cytogenetic rearrangements at the DURS1 locus in syndromic Duane retraction syndrome. Clin Case Rep 2013; 1. [PMID: 24416505 PMCID: PMC3885256 DOI: 10.1002/ccr3.11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Key Clinical Message A patient with syndromic Duane retraction syndrome harbors a chromosome 811.1q13.2 inversion and 8p11.1-q12.3 marker chromosome containing subregions with differing mosaicism and allele frequencies. This case highlights the potential requirement for multiple genetic methods to gain insight into genotype–phenotype correlation, and ultimately into molecular mechanisms that underlie human disease.
Collapse
Affiliation(s)
- Hagit N Baris
- Program in Genomics, Boston Children's Hospital, Boston, MA 02115 USA ; The Recanati Genetic Institute, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel ; Sackler school of Medicine, Tel Aviv University, Israel
| | - Wai-Man Chan
- Program in Genomics, Boston Children's Hospital, Boston, MA 02115 USA ; Department of Medicine (Genetics), Boston Children's Hospital, Boston, MA 02115 USA ; Department of Neurology, Boston Children's Hospital, Boston, MA 02115 USA ; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA ; Harvard Medical School, Boston, MA 02115 USA ; Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
| | - Caroline Andrews
- Program in Genomics, Boston Children's Hospital, Boston, MA 02115 USA ; Department of Medicine (Genetics), Boston Children's Hospital, Boston, MA 02115 USA ; Department of Neurology, Boston Children's Hospital, Boston, MA 02115 USA ; Department of Ophthalmology, Boston Children's Hospital, Boston, MA 02115 USA ; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA ; Harvard Medical School, Boston, MA 02115 USA ; Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
| | - Doron M Behar
- The Recanati Genetic Institute, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Diana J Donovan
- Department of Pathology, Brigham and Women's Hospital, Boston, MA USA
| | - Cynthia C Morton
- Harvard Medical School, Boston, MA 02115 USA ; Department of Pathology, Brigham and Women's Hospital, Boston, MA USA
| | - Judith Ranells
- Department of Pediatrics, University of South Florida, Tampa, FL 33606 USA
| | - Tuya Pal
- H.Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612 USA ; The University of South Florida, College of Medicine, Department of Oncologic Sciences, Tampa, FL 33612 USA
| | - Azra H Ligon
- Harvard Medical School, Boston, MA 02115 USA ; Department of Pathology, Brigham and Women's Hospital, Boston, MA USA
| | - Elizabeth C Engle
- Program in Genomics, Boston Children's Hospital, Boston, MA 02115 USA ; Department of Medicine (Genetics), Boston Children's Hospital, Boston, MA 02115 USA ; Department of Neurology, Boston Children's Hospital, Boston, MA 02115 USA ; Department of Ophthalmology, Boston Children's Hospital, Boston, MA 02115 USA ; FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA ; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA ; Harvard Medical School, Boston, MA 02115 USA ; Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
| |
Collapse
|
27
|
Rosa-Garrido M, Karbassi E, Monte E, Vondriska TM. Regulation of chromatin structure in the cardiovascular system. Circ J 2013; 77:1389-98. [PMID: 23575346 DOI: 10.1253/circj.cj-13-0176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
It has been appreciated for some time that cardiovascular disease involves large-scale transcriptional changes in various cell types. What has become increasingly clear only in the past few years, however, is the role of chromatin remodeling in cardiovascular phenotypes in normal physiology, as well as in development and disease. This review summarizes the state of the chromatin field in terms of distinct mechanisms to regulate chromatin structure in vivo, identifying when these modes of regulation have been demonstrated in cardiovascular tissues. We describe areas in which a better understanding of chromatin structure is leading to new insights into the fundamental biology of cardiovascular disease.
Collapse
Affiliation(s)
- Manuel Rosa-Garrido
- Department of Anesthesiology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | | | | | | |
Collapse
|
28
|
|
29
|
Affiliation(s)
- Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| |
Collapse
|