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Krumpolec P, Kodada D, Hadžega D, Petrovič O, Babišová K, Dosedla E, Turcsányiová Z, Minárik G. Changes in DNA methylation associated with a specific mode of delivery: a pilot study. Front Med (Lausanne) 2024; 11:1291429. [PMID: 38314203 PMCID: PMC10835804 DOI: 10.3389/fmed.2024.1291429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
Background The mode of delivery represents an epigenetic factor with potential to affect further development of the individual by multiple mechanisms. DNA methylation may be one of them, representing a major epigenetic mechanism involving direct chemical modification of the individual's DNA. This pilot study aims to examine whether a specific mode of delivery induces changes of DNA methylation by comparing the umbilical cord blood and peripheral blood of the newborns. Methods Blood samples from infants born by vaginal delivery and caesarean section were analysed to prepare the Methylseq library according to NEBNext enzymatic Methyl-seq Methylation Library Preparation Kit with further generation of target-enriched DNA libraries using the Twist Human Methylome Panel. DNA methylation status was determined using Illumina next-generation sequencing (NGS). Results We identified 168 differentially methylated regions in umbilical cord blood samples and 157 regions in peripheral blood samples. These were associated with 59 common biological, metabolic and signalling pathways for umbilical cord and peripheral blood samples. Conclusion Caesarean section is likely to represent an important epigenetic factor with the potential to induce changes in the genome that could play an important role in development of a broad spectrum of disorders. Our results could contribute to the elucidation of how epigenetic factors, such as a specific mode of delivery, could have adverse impact on health of an individual later in their life.
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Affiliation(s)
| | - Dominik Kodada
- Medirex Group Academy n.o., Nitra, Slovakia
- Department of Clinical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | | | | | | | - Erik Dosedla
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Zuzana Turcsányiová
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
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2
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Zhang H, Wang SQ, Zhu JB, Wang LN, Lin H, Li LF, Cheng YD, Duan CJ, Zhang CF. LncRNA CALML3-AS1 modulated by m 6A modification induces BTNL9 methylation to drive non-small-cell lung cancer progression. Cancer Gene Ther 2023; 30:1649-1662. [PMID: 37884580 DOI: 10.1038/s41417-023-00670-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 10/28/2023]
Abstract
Non-small cell lung cancer (NSCLC) is a common and lethal malignancy. The carcinogenic roles of lncRNA CALML3 antisense RNA 1 (CALML3-AS1) have been documented. However, the function and potential mechanisms of CALML3-AS1 in the progression of NSCLC need to be further explored. The molecule expression was assessed by qRT-PCR and Western blot. The subcellular localization of CALML3-AS1 was observed by fluorescence in situ hybridization (FISH). The malignant behaviors of NSCLC cells were evaluated by CCK-8, colony formation, EdU, wound healing and transwell assays. In vivo xenograft tumor and liver metastatic models were established. The molecular mechanisms were investigated by RIP, RNA pull-down and ChIP assays. The methylation level was detected by MSP. Herein, we found that CALML3-AS1 was upregulated, while butyrophilin-like 9 (BTNL9) was downregulated in NSCLC. Functionally, CALML3-AS1 depletion repressed NSCLC cell malignant phenotypes, in vivo tumor growth, and liver metastasis. Mechanistically, AlkB homolog 5 (ALKBH5) enhanced CALML3-AS1 stability via N6-methyladenosine (m6A) demethylation, whereas m6A reader YTH domain-containing 2 (YTHDC2) destabilized CALML3-AS1. Moreover, CALML3-AS1 inhibited BTNL9 transcription and expression through the recruitment of Zeste homolog 2 (EZH2). Rescue experiments demonstrated that BTNL9 downregulation counteracted sh-CALML3-AS1-mediated antitumor effects on NSCLC. Taken together, CALML3-AS1 modulated by ALKBH5 and YTHDC2 in an m6A modification dependent manner drives NSCLC progression via epigenetically repressing BTNL9.
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Affiliation(s)
- Heng Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China.
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China.
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, 410008, Hunan Province, P. R. China.
| | - Shao-Qiang Wang
- Department of Thoracic Surgery, Weifang People's Hospital, Weifang Medical University, Weifang, 261041, Shandong Province, P.R. China
- Department of Scientific Research Management, Weifang People's Hospital, Weifang Medical University, Weifang, 261041, Shandong Province, P.R. China
| | - Jie-Bo Zhu
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China
| | - Li-Na Wang
- Department of Thoracic Surgery, Affiliated Hospital of Jining Medical University, Jining, 272029, Shandong Province, P. R. China
| | - Hang Lin
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China
| | - Lin-Feng Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China
| | - Yuan-Da Cheng
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China
| | - Chao-Jun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China
| | - Chun-Fang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China.
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, P. R. China.
- National Clinical Research Center for Geriatric Disorders (Xiangya Hospital), Changsha, 410008, Hunan Province, P. R. China.
- Hunan Engineering Research Center for Pulmonary Nodules Precise Diagosis & Treatment, Changsha, 410008, Hunan Province, P. R. China.
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3
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Tan K, Foo R, Loh M. Cardiomyopathy in Asian Cohorts: Genetic and Epigenetic Insights. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:496-506. [PMID: 37589150 DOI: 10.1161/circgen.123.004079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Previous studies on cardiomyopathies have been particularly valuable for clarifying pathological mechanisms in heart failure, an etiologically heterogeneous disease. In this review, we specifically focus on cardiomyopathies in Asia, where heart failure is particularly pertinent. There has been an increase in prevalence of cardiomyopathies in Asia, in sharp contrast with the decline observed in Western countries. Indeed, important disparities in cardiomyopathy incidence, clinical characteristics, and prognosis have been reported in Asian versus White cohorts. These have been accompanied by emerging descriptions of a distinct rare and common genetic basis for disease among Asian cardiomyopathy patients marked by an increased burden of variants with uncertain significance, reclassification of variants deemed pathogenic based on evidence from predominantly White cohorts, and the discovery of Asian-specific cardiomyopathy-associated loci with underappreciated pathogenicity under conventional classification criteria. Findings from epigenetic studies of heart failure, particularly DNA methylation studies, have complemented genetic findings in accounting for the phenotypic variability in cardiomyopathy. Though extremely limited, findings from Asian ancestry-focused DNA methylation studies of cardiomyopathy have shown potential to contribute to general understanding of cardiomyopathy pathophysiology by proposing disease and cause-relevant pathophysiological mechanisms. We discuss the value of multiomics study designs incorporating genetic, methylation, and transcriptomic information for future DNA methylation studies in Asian cardiomyopathy cohorts to yield Asian ancestry-specific insights that will improve risk stratification in the Asian population.
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Affiliation(s)
- Konstanze Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore (K.T., M.L.)
| | - Roger Foo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore (R.F.)
- Department of Cardiology, National University Heart Centre, National University Health System, Singapore (R.F.)
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore (K.T., M.L.)
- Genome Institute of Singapore, Singapore (GIS), Agency for Science, Technology and Research (A*STAR) (M.L.)
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, United Kingdom (M.L.)
- National Skin Centre, Singapore (M.L.)
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4
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Sopic M, Robinson EL, Emanueli C, Srivastava P, Angione C, Gaetano C, Condorelli G, Martelli F, Pedrazzini T, Devaux Y. Integration of epigenetic regulatory mechanisms in heart failure. Basic Res Cardiol 2023; 118:16. [PMID: 37140699 PMCID: PMC10158703 DOI: 10.1007/s00395-023-00986-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
The number of "omics" approaches is continuously growing. Among others, epigenetics has appeared as an attractive area of investigation by the cardiovascular research community, notably considering its association with disease development. Complex diseases such as cardiovascular diseases have to be tackled using methods integrating different omics levels, so called "multi-omics" approaches. These approaches combine and co-analyze different levels of disease regulation. In this review, we present and discuss the role of epigenetic mechanisms in regulating gene expression and provide an integrated view of how these mechanisms are interlinked and regulate the development of cardiac disease, with a particular attention to heart failure. We focus on DNA, histone, and RNA modifications, and discuss the current methods and tools used for data integration and analysis. Enhancing the knowledge of these regulatory mechanisms may lead to novel therapeutic approaches and biomarkers for precision healthcare and improved clinical outcomes.
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Affiliation(s)
- Miron Sopic
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Emma L Robinson
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Costanza Emanueli
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | - Claudio Angione
- School of Computing, Engineering & Digital Technologies, Teesside University, Tees Valley, Middlesbrough, TS1 3BA, UK
- Centre for Digital Innovation, Teesside University, Campus Heart, Tees Valley, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Darlington, DL1 1HG, UK
| | - Carlo Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 10, 27100, Pavia, Italy
| | - Gianluigi Condorelli
- IRCCS-Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, MI, Italy
- Institute of Genetic and Biomedical Research, National Research Council of Italy, Arnold-Heller-Str.3, 24105, Milan, Italy
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097, Milan, Italy
| | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011, Lausanne, Switzerland
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg.
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5
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Liao X, Kennel PJ, Liu B, Nash TR, Zhuang RZ, Godier-Furnemont AF, Xue C, Lu R, Colombo PC, Uriel N, Reilly MP, Marx SO, Vunjak-Novakovic G, Topkara VK. Effect of mechanical unloading on genome-wide DNA methylation profile of the failing human heart. JCI Insight 2023; 8:161788. [PMID: 36656640 PMCID: PMC9977498 DOI: 10.1172/jci.insight.161788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Heart failure (HF) is characterized by global alterations in myocardial DNA methylation, yet little is known about the epigenetic regulation of the noncoding genome and potential reversibility of DNA methylation with left ventricular assist device (LVAD) therapy. Genome-wide mapping of myocardial DNA methylation in 36 patients with HF at LVAD implantation, 8 patients at LVAD explantation, and 7 nonfailing (NF) donors using a high-density bead array platform identified 2,079 differentially methylated positions (DMPs) in ischemic cardiomyopathy (ICM) and 261 DMPs in nonischemic cardiomyopathy (NICM). LVAD support resulted in normalization of 3.2% of HF-associated DMPs. Methylation-expression correlation analysis yielded several protein-coding genes that are hypomethylated and upregulated (HTRA1, FBXO16, EFCAB13, and AKAP13) or hypermethylated and downregulated (TBX3) in HF. A potentially novel cardiac-specific super-enhancer long noncoding RNA (lncRNA) (LINC00881) is hypermethylated and downregulated in human HF. LINC00881 is an upstream regulator of sarcomere and calcium channel gene expression including MYH6, CACNA1C, and RYR2. LINC00881 knockdown reduces peak calcium amplitude in the beating human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). These data suggest that HF-associated changes in myocardial DNA methylation within coding and noncoding genomes are minimally reversible with mechanical unloading. Epigenetic reprogramming strategies may be necessary to achieve sustained clinical recovery from heart failure.
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Affiliation(s)
- Xianghai Liao
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Peter J Kennel
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Bohao Liu
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | | | - Chenyi Xue
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Rong Lu
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Paolo C Colombo
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Nir Uriel
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Muredach P Reilly
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | - Steven O Marx
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
| | | | - Veli K Topkara
- Division of Cardiology, Columbia University Irving Medical Center - New York Presbyterian, New York, New York, USA
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Carlson JC, Krishnan M, Rosenthal SL, Russell EM, Zhang JZ, Hawley NL, Moors J, Cheng H, Dalbeth N, de Zoysa JR, Watson H, Qasim M, Murphy R, Naseri T, Reupena MS, Viali S, Stamp LK, Tuitele J, Kershaw EE, Deka R, McGarvey ST, Merriman TR, Weeks DE, Minster RL. A stop-gain variant in BTNL9 is associated with atherogenic lipid profiles. HGG ADVANCES 2023; 4:100155. [PMID: 36340932 PMCID: PMC9630829 DOI: 10.1016/j.xhgg.2022.100155] [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: 06/22/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
Current understanding of lipid genetics has come mainly from studies in European-ancestry populations; limited effort has focused on Polynesian populations, whose unique population history and high prevalence of dyslipidemia may provide insight into the biological foundations of variation in lipid levels. Here, we performed an association study to fine map a suggestive association on 5q35 with high-density lipoprotein cholesterol (HDL-C) seen in Micronesian and Polynesian populations. Fine-mapping analyses in a cohort of 2,851 Samoan adults highlighted an association between a stop-gain variant (rs200884524; c.652C>T, p.R218∗; posterior probability = 0.9987) in BTNL9 and both lower HDL-C and greater triglycerides (TGs). Meta-analysis across this and several other cohorts of Polynesian ancestry from Samoa, American Samoa, and Aotearoa New Zealand confirmed the presence of this association (βHDL-C = -1.60 mg/dL, p HDL-C = 7.63 × 10-10; βTG = 12.00 mg/dL, p TG = 3.82 × 10-7). While this variant appears to be Polynesian specific, there is also evidence of association from other multiancestry analyses in this region. This work provides evidence of a previously unexplored contributor to the genetic architecture of lipid levels and underscores the importance of genetic analyses in understudied populations.
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Affiliation(s)
- Jenna C. Carlson
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mohanraj Krishnan
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samantha L. Rosenthal
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emily M. Russell
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jerry Z. Zhang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nicola L. Hawley
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Jaye Moors
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Hong Cheng
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Nicola Dalbeth
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Janak R. de Zoysa
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Huti Watson
- Ngāti Porou Hauora Charitable Trust, Te Puia Springs, Tairāwhiti East Coast, New Zealand
| | - Muhammad Qasim
- Ngāti Porou Hauora Charitable Trust, Te Puia Springs, Tairāwhiti East Coast, New Zealand
| | - Rinki Murphy
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | | | | | - Lisa K. Stamp
- Department of Medicine, University of Otago Christchurch, Christchurch, New Zealand
| | - John Tuitele
- Department of Public Health, Government of American Samoa, Pago Pago, American Samoa
| | - Erin E. Kershaw
- Division of Endocrinology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ranjan Deka
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stephen T. McGarvey
- International Health Institute, Department of Epidemiology, Brown University, Providence, RI, USA
- Department of Anthropology, Brown University, Providence, RI, USA
| | - Tony R. Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Daniel E. Weeks
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan L. Minster
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
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Zhang C, Ma S, Hao X, Wang Z, Sun Z. Methylation status of TK1 correlated with immune infiltrates in prostate cancer. Front Genet 2022; 13:899384. [PMID: 36035114 PMCID: PMC9403003 DOI: 10.3389/fgene.2022.899384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
TK1 is overexpressed in numerous cancers and is associated with to a poor prognosis. However, the relationship between methylation status of TK1 and Immune Infiltrates in Prostate Cancer (PCa) is unknown. The goal of this study was to use comprehensive bioinformatic analyses to elucidate the involvement relationship between methylation status of TK1 and Immune Infiltrates in PCa. TK1 mRNA expression and methylation data in PCa were investigated via GEPIA, TIMER, and UALCAN coupled with MEXPRESS data resources. We employed the LinkedOmics data resource to determine the signaling cascades linked to TK1 expression. Single-cell analysis was performed using the CancerSEA data resource. GeneMANIA and CancerSEA were used to analyze the correlation between TK1 and TK1 coexpressed genes. In addition, TIMER and TISIDB were adopted to assess tumor-invading immune cells and immunomodulators. CTD was utilized to detect the drugs acting on TK1. This study found that TK1 was overexpressed in PCa, and its contents were linked to tumor stage and prognosis. Genes co-expressed with TK1 were enriched in cascades involved in the ribosome, cell cycle, oxidative phosphorylation, DNA replication, oocyte meiosis, and the proteasome. The expression of TK1 along with its methylation status was found to be linked to tumor-invading immune cells, as well as PCa immunomodulators. We also examined the prospect of employing TK1 as a possible target for PCa therapy. This work provides the clinical value of TK1 hypermethylation in PCa and highlights new insights into its novel immunomodulatory functions.
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Affiliation(s)
- Chenming Zhang
- The Second Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
- *Correspondence: Chenming Zhang, ; Zixue Sun,
| | - Sicheng Ma
- The Second Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiaohui Hao
- The Second Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zulong Wang
- Andrology Department, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Zixue Sun
- Reproductive Medicine Department, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China
- *Correspondence: Chenming Zhang, ; Zixue Sun,
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Kalesinskas L, Gupta S, Khatri P. Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology. PLoS Comput Biol 2022; 18:e1010260. [PMID: 35759523 PMCID: PMC9269905 DOI: 10.1371/journal.pcbi.1010260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 07/08/2022] [Accepted: 05/29/2022] [Indexed: 01/07/2023] Open
Abstract
A major limitation of gene expression biomarker studies is that they are not reproducible as they simply do not generalize to larger, real-world, heterogeneous populations. Frequentist multi-cohort gene expression meta-analysis has been frequently used as a solution to this problem to identify biomarkers that are truly differentially expressed. However, the frequentist meta-analysis framework has its limitations-it needs at least 4-5 datasets with hundreds of samples, is prone to confounding from outliers and relies on multiple-hypothesis corrected p-values. To address these shortcomings, we have created a Bayesian meta-analysis framework for the analysis of gene expression data. Using real-world data from three different diseases, we show that the Bayesian method is more robust to outliers, creates more informative estimates of between-study heterogeneity, reduces the number of false positive and false negative biomarkers and selects more generalizable biomarkers with less data. We have compared the Bayesian framework to a previously published frequentist framework and have developed a publicly available R package for use.
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Affiliation(s)
- Laurynas Kalesinskas
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, United States of America
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Sanjana Gupta
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California, United States of America
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, California, United States of America
- * E-mail:
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9
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Development and verification of the nomogram for dilated cardiomyopathy gene diagnosis. Sci Rep 2022; 12:8908. [PMID: 35618744 PMCID: PMC9135684 DOI: 10.1038/s41598-022-13135-y] [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: 11/26/2021] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is a primary myocardial disease of unclear mechanism and poor prevention. The purpose of this study is to explore the potential molecular mechanisms and targets of DCM via bioinformatics methods and try to diagnose and prevent disease progression early. We screened 333 genes differentially expressed between DCM and normal heart samples from GSE141910, and further used Weighted correlation network analysis to identify 197 DCM-related genes. By identifying the key modules in the protein–protein interaction network and Least Absolute Shrinkage and Selection Operator regression analysis, seven hub DCM genes (CX3CR1, AGTR2, ADORA3, CXCL10, CXCL11, CXCL9, SAA1) were identified. Calculating the area under the receiver’s operating curve revealed that these 7 genes have an excellent ability to diagnose and predict DCM. Based on this, we built a logistic regression model and drew a nomogram. The calibration curve showed that the actual incidence is basically the same as the predicted incidence; while the C-index values of the nomogram and the four external validation data sets are 0.95, 0.90, 0.96, and 0.737, respectively, showing excellent diagnostic and predictive ability; while the decision curve indicated the wide applicability of the nomogram is helpful for clinicians to make accurate decisions.
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10
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Fang X, Poulsen R, Zhao L, Wang J, Rivkees SA, Wendler CC. Knockdown of DNA methyltransferase 1 reduces DNA methylation and alters expression patterns of cardiac genes in embryonic cardiomyocytes. FEBS Open Bio 2021. [PMID: 34235895 PMCID: PMC8329956 DOI: 10.1002/2211-5463.13252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/14/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
We previously found that DNA methyltransferase 3a (DNMT3a) plays an important role in regulating embryonic cardiomyocyte gene expression, morphology, and function. In this study, we investigated the role of the most abundant DNMT in mammalian cells, DNMT1, in these processes. It is known that DNMT1 is essential for embryonic development, during which it is involved in regulating cardiomyocyte DNA methylation and gene expression. We used siRNA to knock down DNMT1 expression in primary cultures of mouse embryonic cardiomyocytes. Immunofluorescence staining and multielectrode array were, respectively, utilized to evaluate cardiomyocyte growth and electrophysiology. RNA sequencing (RNA‐Seq) and multiplex bisulfite sequencing were, respectively, performed to examine gene expression and promoter methylation. At 72 h post‐transfection, reduction of DNMT1 expression decreased the number and increased the size of embryonic cardiomyocytes. Beat frequency and the amplitude of field action potentials were decreased by DNMT1 siRNA. RNA‐Seq analysis identified 801 up‐regulated genes and 494 down‐regulated genes in the DNMT1 knockdown cells when compared to controls. Pathway analysis of the differentially expressed genes revealed pathways that were associated with cell death and survival, cell morphology, cardiac function, and cardiac disease. Alternative splicing analysis identified 929 differentially expressed exons, including 583 up‐regulated exons and 308 down‐regulated exons. Moreover, decreased methylation levels were found in the promoters of cardiac genes Myh6, Myh7, Myh7b, Tnnc1, Tnni3, Tnnt2, Nppa, Nppb, mef2c, mef2d, Camta2, Cdkn1A, and Cdkn1C. Of these 13 genes, 6 (Myh6, Tnnc1, Tnni3, Tnnt2, Nppa, Nppb) and 1 (Cdkn1C) had increased or decreased gene expression, respectively. Altogether, these data show that DNMT1 is important in embryonic cardiomyocytes by regulating DNA methylation, gene expression, gene splicing, and cell function.
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Affiliation(s)
- Xiefan Fang
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA.,Charles River Laboratories, Inc., Reno, NV, USA
| | - Ryan Poulsen
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Lu Zhao
- Charles River Laboratories, Inc., Reno, NV, USA
| | | | - Scott A Rivkees
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Christopher C Wendler
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
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11
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Santos JH. Mitochondria signaling to the epigenome: A novel role for an old organelle. Free Radic Biol Med 2021; 170:59-69. [PMID: 33271282 PMCID: PMC8166959 DOI: 10.1016/j.freeradbiomed.2020.11.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022]
Abstract
Epigenetic modifications influence gene expression programs ultimately dictating physiological outcomes. In the past decades, an increasing body of work has demonstrated that the enzymes that deposit and/or remove epigenetic marks on DNA or histones use metabolites as substrates or co-factors, rendering the epigenome sensitive to metabolic changes. In this context, acetyl-CoA and α-ketoglutarate have been recognized as critical for epigenetics, impinging on histone marks and nuclear DNA methylation patterns. Given that these metabolites are primarily generated in the mitochondria through the tricarboxylic acid cycle (TCA), the requirement of proper mitochondrial function for maintenance of the epigenetic landscape seems obvious. Nevertheless, it was not until recently when the epigenomic outcomes of mitochondrial dysfunction were tested, revealing mitochondria's far-reaching impact on epigenetics. This review will focus on data that directly tested the role of mitochondria on the epigenetic landscape, the mechanisms by which mitochondrial dysfunction may dysregulate the epigenome and gene expression, and their potential implications to health and disease.
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Affiliation(s)
- Janine Hertzog Santos
- National Toxicology Program Laboratory (NTPL), National Toxicology Program (NTP), National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park (RTP), NC, USA.
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12
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Russell-Hallinan A, Watson CJ, O'Dwyer D, Grieve DJ, O'Neill KM. Epigenetic Regulation of Endothelial Cell Function by Nucleic Acid Methylation in Cardiac Homeostasis and Disease. Cardiovasc Drugs Ther 2020; 35:1025-1044. [PMID: 32748033 PMCID: PMC8452583 DOI: 10.1007/s10557-020-07019-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pathological remodelling of the myocardium, including inflammation, fibrosis and hypertrophy, in response to acute or chronic injury is central in the development and progression of heart failure (HF). While both resident and infiltrating cardiac cells are implicated in these pathophysiological processes, recent evidence has suggested that endothelial cells (ECs) may be the principal cell type responsible for orchestrating pathological changes in the failing heart. Epigenetic modification of nucleic acids, including DNA, and more recently RNA, by methylation is essential for physiological development due to their critical regulation of cellular gene expression. As accumulating evidence has highlighted altered patterns of DNA and RNA methylation in HF at both the global and individual gene levels, much effort has been directed towards defining the precise role of such cell-specific epigenetic changes in the context of HF. Considering the increasingly apparent crucial role that ECs play in cardiac homeostasis and disease, this article will specifically focus on nucleic acid methylation (both DNA and RNA) in the failing heart, emphasising the key influence of these epigenetic mechanisms in governing EC function. This review summarises current understanding of DNA and RNA methylation alterations in HF, along with their specific role in regulating EC function in response to stress (e.g. hyperglycaemia, hypoxia). Improved appreciation of this important research area will aid in further implicating dysfunctional ECs in HF pathogenesis, whilst informing development of EC-targeted strategies and advancing potential translation of epigenetic-based therapies for specific targeting of pathological cardiac remodelling in HF.
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Affiliation(s)
- Adam Russell-Hallinan
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Chris J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Denis O'Dwyer
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - David J Grieve
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Karla M O'Neill
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK.
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13
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Napoli C, Benincasa G, Donatelli F, Ambrosio G. Precision medicine in distinct heart failure phenotypes: Focus on clinical epigenetics. Am Heart J 2020; 224:113-128. [PMID: 32361531 DOI: 10.1016/j.ahj.2020.03.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/07/2020] [Indexed: 12/31/2022]
Abstract
Heart failure (HF) management is challenging due to high clinical heterogeneity of this disease which makes patients responding differently to evidence-based standard therapy established by the current reductionist approach. Better understanding of the genetic and epigenetic interactions may clarify molecular signatures underlying maladaptive responses in HF, including metabolic shift, myocardial injury, fibrosis, and mitochondrial dysfunction. DNA methylation, histone modifications and micro-RNA (miRNAs) may be major epigenetic players in the pathogenesis of HF. DNA hypermethylation of the kruppel-like factor 15 (KLF15) gene plays a key role in switching the failing heart from oxidative to glycolytic metabolism. Moreover, hypomethylation at H3K9 promoter level of atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) genes also leads to reactivation of fetal genes in man. The role of miRNAs has been investigated in HF patients undergoing heart transplantation, for whom miR-10a, miR-155, miR-31, and miR-92 may be putative useful prognostic biomarkers. Recently, higher RNA methylation levels have been observed in ischemic human hearts, opening the era of "epitranscriptome" in the pathogenesis of HF. Currently, hydralazine, statins, apabetalone, and omega-3 polyunsatured fatty acids (PUFA) are being tested in clinical trials to provide epigenetic-driven therapeutic interventions. Moreover, network-oriented analysis could advance current medical practice by focusing on protein-protein interactions (PPIs) perturbing the "cardiac" interactome. In this review, we provide an epigenetic map of maladaptive responses in HF patients. Furthermore, we propose the "EPi-transgeneratIonal network mOdeling for STratificatiOn of heaRt Morbidity" (EPIKO-STORM), a clinical research strategy offering novel opportunities to stratify the natural history of HF.
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Abstract
PURPOSE OF REVIEW Characterized by enlarged ventricle and loss of systolic function, dilated cardiomyopathy (DCM) has the highest morbidity among all the cardiomyopathies. Although it is well established that DCM is typically caused by mutations in a large number of genes, there is an emerging appreciation for the contribution of epigenetic alteration in the development of DCM. RECENT FINDINGS We present some of the recent progress in the field of epigenetics in DCM by focusing on the four major epigenetic modifications, that is, DNA methylation, histone modification, chromatin remodeling as well as the noncoding RNAs. The major players involved in these DCM-related epigenetic reprogramming will be highlighted. Finally, the diagnostic and the therapeutic implications for DCM based on new knowledge of epigenetic regulation will also be discussed. SUMMARY As a rapidly expanding field, epigenetic studies in DCM have the promise to yield both novel mechanistic insights as well as potential new avenues for more effective treatment of the disease.
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15
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Watanabe T, Okada H, Kanamori H, Miyazaki N, Tsujimoto A, Takada C, Suzuki K, Naruse G, Yoshida A, Nawa T, Tanaka T, Kawasaki M, Ito H, Ogura S, Okura H, Fujiwara T, Fujiwara H, Takemura G. In situ nuclear DNA methylation in dilated cardiomyopathy: an endomyocardial biopsy study. ESC Heart Fail 2020; 7:493-502. [PMID: 31971668 DOI: 10.1002/ehf2.12593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 11/12/2022] Open
Abstract
AIMS Although distinct DNA methylation patterns have been reported, its localization and roles remain to be defined in heart failure. We investigated the cellular and subcellular localization of DNA methylation and its pathophysiological significance in human failing hearts. METHODS AND RESULTS Using left ventricular (LV) endomyocardial biopsy specimens from 75 patients with dilated cardiomyopathy (DCM; age: 58 ± 14 years old, %female: 32%) and 20 patients without heart failure (controls; age: 56 ± 17 years old, %female: 45%), we performed immunohistochemistry and immunoelectron microscopy for methylated DNA, 5-methylcytosine (5-mC). We next investigated possible relations of the incidence of 5-mC-positive (%5-mC+ ) cardiomyocytes with clinicopathological parameters. Immunopositivity for 5-mC was detected in the cardiomyocytes and other cell types. The %5-mC+ cardiomyocytes was significantly greater in DCM hearts than in controls (57 ± 13% in DCM vs. 25 ± 12% in controls, P < 0.0001). The localization of 5-mC immunopositivity in cardiomyocyte nuclei coincided well with that of heterochromatin, as confirmed by immunoelectron microscopy. Substantial DNA methylation was also observed in interstitial non-cardiomyocytes, but the incidences did not differ between control and DCM hearts (39 ± 7.9% in DCM vs. 41 ± 10% in controls, P = 0.4099). In DCM patients, the %5-mC+ cardiomyocytes showed a significant inverse correlation with LV functional parameters such as heart rate (r = 0.2391, P = 0.0388), end-diastolic pressure (r = 0.2397, P = 0.0397), and ejection fraction (r = -0.2917, P = 0.0111) and a positive correlation with LV dilatation (volume index at diastole; r = 0.2442, P = 0.0347; and volume index at systole; r = 0.3136, P = 0.0062) and LV hypertrophy (mass index; r = 0.2287, P = 0.0484)-that is, LV remodelling parameters. No significant correlations between DNA methylation and the histological parameters of the biopsies, including cardiomyocyte hypertrophy, fibrosis, and inflammatory cell infiltration, were noted. CONCLUSIONS The present study revealed increased nuclear DNA methylation in cardiomyocytes, but not other cell types, from DCM hearts, with predominant localization in the heterochromatin. Its significant relations with LV functional and remodelling parameters imply a pathophysiological significance of DNA methylation in heart failure.
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Affiliation(s)
- Takatomo Watanabe
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan.,Department of Informative Clinical Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hideshi Okada
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan.,Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiromitsu Kanamori
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Nagisa Miyazaki
- Department of Internal Medicine, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, 501-0296, Japan
| | - Akiko Tsujimoto
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Chihiro Takada
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kodai Suzuki
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Genki Naruse
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Akihiro Yoshida
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takahide Nawa
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Toshiki Tanaka
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Masanori Kawasaki
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroyasu Ito
- Department of Informative Clinical Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Shinji Ogura
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroyuki Okura
- Department of Cardiology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takako Fujiwara
- Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | | | - Genzou Takemura
- Department of Internal Medicine, Asahi University School of Dentistry, 1851 Hozumi, Mizuho, 501-0296, Japan
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16
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Soler-Botija C, Gálvez-Montón C, Bayés-Genís A. Epigenetic Biomarkers in Cardiovascular Diseases. Front Genet 2019; 10:950. [PMID: 31649728 PMCID: PMC6795132 DOI: 10.3389/fgene.2019.00950] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 09/05/2019] [Indexed: 12/16/2022] Open
Abstract
Cardiovascular diseases are the number one cause of death worldwide and greatly impact quality of life and medical costs. Enormous effort has been made in research to obtain new tools for efficient and quick diagnosis and predicting the prognosis of these diseases. Discoveries of epigenetic mechanisms have related several pathologies, including cardiovascular diseases, to epigenetic dysregulation. This has implications on disease progression and is the basis for new preventive strategies. Advances in methodology and big data analysis have identified novel mechanisms and targets involved in numerous diseases, allowing more individualized epigenetic maps for personalized diagnosis and treatment. This paves the way for what is called pharmacoepigenetics, which predicts the drug response and develops a tailored therapy based on differences in the epigenetic basis of each patient. Similarly, epigenetic biomarkers have emerged as a promising instrument for the consistent diagnosis and prognosis of cardiovascular diseases. Their good accessibility and feasible methods of detection make them suitable for use in clinical practice. However, multicenter studies with a large sample population are required to determine with certainty which epigenetic biomarkers are reliable for clinical routine. Therefore, this review focuses on current discoveries regarding epigenetic biomarkers and its controversy aiming to improve the diagnosis, prognosis, and therapy in cardiovascular patients.
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Affiliation(s)
- Carolina Soler-Botija
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Carolina Gálvez-Montón
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Antoni Bayés-Genís
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Cardiology Service, HUGTiP, Badalona, Spain.,Department of Medicine, Barcelona Autonomous University (UAB), Badalona, Spain
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17
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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.
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18
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Chu M, Novak SM, Cover C, Wang AA, Chinyere IR, Juneman EB, Zarnescu DC, Wong PK, Gregorio CC. Increased Cardiac Arrhythmogenesis Associated With Gap Junction Remodeling With Upregulation of RNA-Binding Protein FXR1. Circulation 2017; 137:605-618. [PMID: 29101288 DOI: 10.1161/circulationaha.117.028976] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/23/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Gap junction remodeling is well established as a consistent feature of human heart disease involving spontaneous ventricular arrhythmia. The mechanisms responsible for gap junction remodeling that include alterations in the distribution of, and protein expression within, gap junctions are still debated. Studies reveal that multiple transcriptional and posttranscriptional regulatory pathways are triggered in response to cardiac disease, such as those involving RNA-binding proteins. The expression levels of FXR1 (fragile X mental retardation autosomal homolog 1), an RNA-binding protein, are critical to maintain proper cardiac muscle function; however, the connection between FXR1 and disease is not clear. METHODS To identify the mechanisms regulating gap junction remodeling in cardiac disease, we sought to identify the functional properties of FXR1 expression, direct targets of FXR1 in human left ventricle dilated cardiomyopathy (DCM) biopsy samples and mouse models of DCM through BioID proximity assay and RNA immunoprecipitation, how FXR1 regulates its targets through RNA stability and luciferase assays, and functional consequences of altering the levels of this important RNA-binding protein through the analysis of cardiac-specific FXR1 knockout mice and mice injected with 3xMyc-FXR1 adeno-associated virus. RESULTS FXR1 expression is significantly increased in tissue samples from human and mouse models of DCM via Western blot analysis. FXR1 associates with intercalated discs, and integral gap junction proteins Cx43 (connexin 43), Cx45 (connexin 45), and ZO-1 (zonula occludens-1) were identified as novel mRNA targets of FXR1 by using a BioID proximity assay and RNA immunoprecipitation. Our findings show that FXR1 is a multifunctional protein involved in translational regulation and stabilization of its mRNA targets in heart muscle. In addition, introduction of 3xMyc-FXR1 via adeno-associated virus into mice leads to the redistribution of gap junctions and promotes ventricular tachycardia, showing the functional significance of FXR1 upregulation observed in DCM. CONCLUSIONS In DCM, increased FXR1 expression appears to play an important role in disease progression by regulating gap junction remodeling. Together this study provides a novel function of FXR1, namely, that it directly regulates major gap junction components, contributing to proper cell-cell communication in the heart.
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Affiliation(s)
- Miensheng Chu
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Stefanie Mares Novak
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Cathleen Cover
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Anne A Wang
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | | | | | | | - Pak Kin Wong
- University of Arizona, Tucson. Department of Biomedical Engineering at Pennsylvania State University, University Park (P.K.W.)
| | - Carol C Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
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19
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Sabia C, Picascia A, Grimaldi V, Amarelli C, Maiello C, Napoli C. The epigenetic promise to improve prognosis of heart failure and heart transplantation. Transplant Rev (Orlando) 2017; 31:249-256. [PMID: 28882368 DOI: 10.1016/j.trre.2017.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 07/03/2017] [Accepted: 08/07/2017] [Indexed: 12/14/2022]
Abstract
Heart transplantation is still the only possible life-saving treatment for end-stage heart failure, the critical epilogue of several cardiac diseases. Epigenetic mechanisms are being intensively investigated because they could contribute to establishing innovative diagnostic and predictive biomarkers, as well as ground-breaking therapies both for heart failure and heart transplantation rejection. DNA methylation and histone modifications can modulate the innate and adaptive immune response by acting on the expression of immune-related genes that, in turn, are crucial determinants of transplantation outcome. Epigenetic drugs acting on methylation and histone-modification pathways may modulate Treg activity by acting as immunosuppressive agents. Moreover, the identification of non-invasive and reliable epigenetic biomarkers for the prediction of allograft rejection and for monitoring immunosuppressive therapies represents an attractive perspective in the management of transplanted patients. MiRNAs seem to fit particularly well to this purpose because they are differently expressed in patients at high and low risk of rejection and are detectable in biological fluids besides biopsies. Although increasing evidence supports the involvement of epigenetic tags in heart failure and transplantation, further short and long-term clinical studies are needed to translate the possible available findings into clinical setting.
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Affiliation(s)
- Chiara Sabia
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, Azienda Ospedaliera Universitaria, Department of Medical, Surgical, Neurological, Aging and Metabolic Sciences, Università degli Studi della Campania "L. Vanvitelli", Italy.
| | - Antonietta Picascia
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, Azienda Ospedaliera Universitaria, Department of Medical, Surgical, Neurological, Aging and Metabolic Sciences, Università degli Studi della Campania "L. Vanvitelli", Italy
| | - Vincenzo Grimaldi
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, Azienda Ospedaliera Universitaria, Department of Medical, Surgical, Neurological, Aging and Metabolic Sciences, Università degli Studi della Campania "L. Vanvitelli", Italy; Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Cristiano Amarelli
- Department of Cardiovascular Surgery and Transplants, Monaldi Hospital, Azienda dei Colli, Naples, Italy
| | - Ciro Maiello
- Department of Cardiovascular Surgery and Transplants, Monaldi Hospital, Azienda dei Colli, Naples, Italy
| | - Claudio Napoli
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Department of Internal Medicine and Specialistics, Azienda Ospedaliera Universitaria, Department of Medical, Surgical, Neurological, Aging and Metabolic Sciences, Università degli Studi della Campania "L. Vanvitelli", Italy; SDN Foundation, Institute of Diagnostic and Nuclear Development, IRCCS, Via Gianturco 113, 80143 Naples, Italy
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20
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van der Harst P, de Windt LJ, Chambers JC. Translational Perspective on Epigenetics in Cardiovascular Disease. J Am Coll Cardiol 2017; 70:590-606. [PMID: 28750703 PMCID: PMC5543329 DOI: 10.1016/j.jacc.2017.05.067] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 12/19/2022]
Abstract
A plethora of environmental and behavioral factors interact, resulting in changes in gene expression and providing a basis for the development and progression of cardiovascular diseases. Heterogeneity in gene expression responses among cells and individuals involves epigenetic mechanisms. Advancing technology allowing genome-scale interrogation of epigenetic marks provides a rapidly expanding view of the complexity and diversity of the epigenome. In this review, the authors discuss the expanding landscape of epigenetic modifications and highlight their importance for future understanding of disease. The epigenome provides a mechanistic link between environmental exposures and gene expression profiles ultimately leading to disease. The authors discuss the current evidence for transgenerational epigenetic inheritance and summarize the data linking epigenetics to cardiovascular disease. Furthermore, the potential targets provided by the epigenome for the development of future diagnostics, preventive strategies, and therapy for cardiovascular disease are reviewed. Finally, the authors provide some suggestions for future directions.
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Affiliation(s)
- Pim van der Harst
- Departments of Cardiology and Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, the Netherlands.
| | - Leon J de Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom; Ealing Hospital NHS Trust, Middlesex, United Kingdom
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21
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Milani-Nejad N, Schultz EJ, Slabaugh JL, Janssen PML, Rafael-Fortney JA. Myocardial Contractile Dysfunction Is Present without Histopathology in a Mouse Model of Limb-Girdle Muscular Dystrophy-2F and Is Prevented after Claudin-5 Virotherapy. Front Physiol 2016; 7:539. [PMID: 27999547 PMCID: PMC5138189 DOI: 10.3389/fphys.2016.00539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/27/2016] [Indexed: 01/18/2023] Open
Abstract
Mutations in several members of the dystrophin glycoprotein complex lead to skeletal and cardiomyopathies. Cardiac care for these muscular dystrophies consists of management of symptoms with standard heart medications after detection of reduced whole heart function. Recent evidence from both Duchenne muscular dystrophy patients and animal models suggests that myocardial dysfunction is present before myocardial damage or deficiencies in whole heart function, and that treatment prior to heart failure symptoms may be beneficial. To determine whether this same early myocardial dysfunction is present in other muscular dystrophy cardiomyopathies, we conducted a physiological assessment of cardiac function at the tissue level in the δ-sarcoglycan null mouse model (Sgcd−/−) of Limb-girdle muscular dystrophy type 2F. Baseline cardiac contractile force measurements using ex vivo intact linear muscle preparations, were severely depressed in these mice without the presence of histopathology. Virotherapy withclaudin-5 prevents the onset of cardiomyopathy in another muscular dystrophy model. After virotherapy with claudin-5, the cardiac contractile force deficits in Sgcd−/− mice are no longer significant. These studies suggest that screening Limb-girdle muscular dystrophy patients using methods that detect earlier functional changes may provide a longer therapeutic window for cardiac care.
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Affiliation(s)
- Nima Milani-Nejad
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical CenterColumbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical CenterColumbus, OH, USA; Medical Scientist Training Program and Biomedical Sciences Graduate Program, The Ohio State University Wexner Medical CenterColumbus, OH, USA
| | - Eric J Schultz
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical CenterColumbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical CenterColumbus, OH, USA; Department of Molecular and Cellular Biochemistry, The Ohio State University Wexner Medical CenterColumbus, OH, USA
| | - Jessica L Slabaugh
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical CenterColumbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical CenterColumbus, OH, USA
| | - Paul M L Janssen
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical CenterColumbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical CenterColumbus, OH, USA
| | - Jill A Rafael-Fortney
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical CenterColumbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical CenterColumbus, OH, USA; Department of Molecular and Cellular Biochemistry, The Ohio State University Wexner Medical CenterColumbus, OH, USA
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22
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Sweeney TE, Haynes WA, Vallania F, Ioannidis JP, Khatri P. Methods to increase reproducibility in differential gene expression via meta-analysis. Nucleic Acids Res 2016; 45:e1. [PMID: 27634930 PMCID: PMC5224496 DOI: 10.1093/nar/gkw797] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/28/2016] [Accepted: 08/31/2016] [Indexed: 12/28/2022] Open
Abstract
Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size.
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Affiliation(s)
- Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Winston A Haynes
- Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Francesco Vallania
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John P Ioannidis
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, CA 94305, USA.,Meta-research Innovation Center at Stanford (METRICS), Stanford, CA 94305, USA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA .,Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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23
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Fang X, Poulsen RR, Wang-Hu J, Shi O, Calvo NS, Simmons CS, Rivkees SA, Wendler CC. Knockdown of DNA methyltransferase 3a alters gene expression and inhibits function of embryonic cardiomyocytes. FASEB J 2016; 30:3238-55. [PMID: 27306334 PMCID: PMC5001511 DOI: 10.1096/fj.201600346r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/31/2016] [Indexed: 12/28/2022]
Abstract
We previously found that in utero caffeine exposure causes down-regulation of DNA methyltransferases (DNMTs) in embryonic heart and results in impaired cardiac function in adulthood. To assess the role of DNMTs in these events, we investigated the effects of reduced DNMT expression on embryonic cardiomyocytes. siRNAs were used to knock down individual DNMT expression in primary cultures of mouse embryonic cardiomyocytes. Immunofluorescence staining was conducted to evaluate cell morphology. A video-based imaging assay and multielectrode array were used to assess cardiomyocyte contractility and electrophysiology, respectively. RNA-Seq and multiplex bisulfite sequencing were performed to examine gene expression and promoter methylation, respectively. At 72 h after transfection, reduced DNMT3a expression, but not DNMT1 or -3b, disrupted sarcomere assembly and decreased beating frequency, contractile movement, amplitude of field action potential, and cytosolic calcium signaling of cardiomyocytes. RNA-Seq analysis revealed that the DNMT3a-deficient cells had deactivated gene networks involved in calcium, endothelin-1, renin-angiotensin, and cardiac β-adrenergic receptor signaling, which were not inhibited by DNMT3b siRNA. Moreover, decreased methylation levels were found in the promoters of Myh7, Myh7b, Tnni3, and Tnnt2, consistent with the up-regulation of these genes by DNMT3a siRNA. These data show that DNMT3a plays an important role in regulating embryonic cardiomyocyte gene expression, morphology and function.-Fang, X., Poulsen, R. R., Wang-Hu, J., Shi, O., Calvo, N. S., Simmons, C. S., Rivkees, S. A., Wendler, C. C. Knockdown of DNA methyltransferase 3a alters gene expression and inhibits function of embryonic cardiomyocytes.
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Affiliation(s)
- Xiefan Fang
- Child Health Research Institute, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA; and
| | - Ryan R Poulsen
- Child Health Research Institute, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA; and
| | - John Wang-Hu
- Child Health Research Institute, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA; and
| | - Olivia Shi
- Child Health Research Institute, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA; and
| | - Nicholas S Calvo
- Department of Mechanical and Aerospace Engineering, College of Engineering, University of Florida, Gainesville, Florida, USA
| | - Chelsey S Simmons
- Department of Mechanical and Aerospace Engineering, College of Engineering, University of Florida, Gainesville, Florida, USA
| | - Scott A Rivkees
- Child Health Research Institute, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA; and
| | - Christopher C Wendler
- Child Health Research Institute, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA; and
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24
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Abstract
Epigenetic regulatory mechanisms play key roles in cardiac development, differentiation, homeostasis, response to stress and injury, and disease. Human heart failure (HF) epigenetic regulatory mechanisms have not been deciphered to date. This 2-part review distills the rapidly evolving research focused on human HF epigenetic regulatory mechanisms. Part I, which was published in the September/October issue, focused on epigenetic regulatory mechanisms involving RNA, specifically the role of short, intermediate, and long noncoding RNAs (lncRNAs) and endogenous competing RNA regulatory networks. Part II, now in the November/December issue, focuses on the epigenetic regulatory mechanisms involving DNA, including DNA methylation, histone modifications, and chromatin conformational changes. Part II concludes with 2 examples of well-studied integrated epigenetic regulatory mechanisms: the structural and functional roles of the Mediator complex in regulating transcription and the epigenetic networked "cross-talk" regulating atrial natriuretic peptide and brain natriuretic peptide promoter activation.
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25
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Jo BS, Koh IU, Bae JB, Yu HY, Jeon ES, Lee HY, Kim JJ, Choi M, Choi SS. Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy. Genomics 2016; 108:84-92. [PMID: 27417303 DOI: 10.1016/j.ygeno.2016.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/23/2016] [Accepted: 07/10/2016] [Indexed: 10/21/2022]
Abstract
Dilated cardiomyopathy (DCM) is one of the main causes of heart failure (called cardiomyopathies) in adults. Alterations in epigenetic regulation (i.e., DNA methylation) have been implicated in the development of DCM. Here, we identified a total of 1828 differentially methylated probes (DMPs) using the Infinium 450K HumanMethylation Bead chip by comparing the methylomes between 18 left ventricles and 9 right ventricles. Alterations in DNA methylation levels were observed mainly in lowly methylated regions corresponding to promoter-proximal regions, which become hypermethylated in severely affected left ventricles. Subsequent mRNA microarray analysis showed that the effect of DNA methylation on gene expression regulation is not unidirectional but is controlled by the functional sub-network context. DMPs were significantly enriched in the transcription factor binding sites (TFBSs) we tested. Alterations in DNA methylation were specifically enriched in the cis-regulatory regions of cardiac development genes, the majority of which are involved in ventricular development (e.g., TBX5 and HAND1).
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Affiliation(s)
- Bong-Seok Jo
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Chuncheon 24341, South Korea
| | - In-Uk Koh
- Division of Structural and Functional Genomics, Center of Genome Science, National Research Institute of Health, Chuncheongbuk-do 28159, South Korea
| | - Jae-Bum Bae
- Division of Structural and Functional Genomics, Center of Genome Science, National Research Institute of Health, Chuncheongbuk-do 28159, South Korea
| | - Ho-Yeong Yu
- Division of Structural and Functional Genomics, Center of Genome Science, National Research Institute of Health, Chuncheongbuk-do 28159, South Korea
| | - Eun-Seok Jeon
- Division of Cardiology, Cardiac and Vascular Center, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon 51353, South Korea
| | - Hae-Young Lee
- Division of Cardiology, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Jae-Joong Kim
- Division of Cardiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 44033, South Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Sun Shim Choi
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Chuncheon 24341, South Korea.
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26
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Kunkel GH, Chaturvedi P, Tyagi SC. Epigenetic revival of a dead cardiomyocyte through mitochondrial interventions. Biomol Concepts 2016. [PMID: 26203602 DOI: 10.1515/bmc-2015-0011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial dysfunction has been reported to underline heart failure, and our earlier report suggests that mitochondrial fusion and fission contributes significantly to volume overload heart failure. Although ample studies highlight mitochondrial dysfunction to be a major cause, studies are lacking to uncover the role of mitochondrial epigenetics, i.e. epigenetic modifications of mtDNA in cardiomyocyte function. Additionally, mitochondrial proteases like calpain and Lon proteases are underexplored. Cardiomyopathies are correlated to mitochondrial damage via increased reactive oxygen species production and free calcium within cardiomyocytes. These abnormalities drive increased proteolytic activity from matrix metalloproteinases and calpains, respectively. These proteases degrade the cytoskeleton of the cardiomyocyte and lead to myocyte death. mtDNA methylation is another factor that can lead to myocyte death by silencing several genes of mitochondria or upregulating the expression of mitochondrial proteases by hypomethylation. Cardiomyocyte resuscitation can occur through mitochondrial interventions by decreasing the proteolytic activity and reverting back the epigenetic changes in the mtDNA which lead to myocyte dysfunction. Epigenetic changes in the mtDNA are triggered by environmental factors like pollution and eating habits with cigarette smoking. An analysis of mitochondrial epigenetics in cigarette-smoking mothers will reveal an underlying novel mechanism leading to mitochondrial dysfunction and eventually heart failure. This review is focused on the mitochondrial dysfunction mechanisms that can be reverted back to resuscitate cardiomyocytes.
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27
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Koczor CA, Ludlow I, Fields E, Jiao Z, Ludaway T, Russ R, Lewis W. Mitochondrial polymerase gamma dysfunction and aging cause cardiac nuclear DNA methylation changes. Physiol Genomics 2016; 48:274-80. [PMID: 26757797 DOI: 10.1152/physiolgenomics.00099.2015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/08/2016] [Indexed: 11/22/2022] Open
Abstract
Cardiomyopathy (CM) is an intrinsic weakening of myocardium with contractile dysfunction and congestive heart failure (CHF). CHF has been postulated to result from decreased mitochondrial energy production and oxidative stress. Effects of decreased mitochondrial oxygen consumption also can accelerate with aging. We previously showed DNA methylation changes in human hearts with CM. This was associated with mitochondrial DNA depletion, being another molecular marker of CM. We examined the relationship between mitochondrial dysfunction and cardiac epigenetic DNA methylation changes in both young and old mice. We used genetically engineered C57Bl/6 mice transgenic for a cardiac-specific mutant of the mitochondrial polymerase-γ (termed Y955C). Y955C mice undergo left ventricular hypertrophy (LVH) at a young age (∼ 94 days old), and LVH decompensated to CHF at old age (∼ 255 days old). Results found 95 genes differentially expressed as a result of Y955C expression, while 4,452 genes were differentially expressed as a result of aging hearts. Moreover, cardiac DNA methylation patterns differed between Y955C (4,506 peaks with 68.5% hypomethylation) and aged hearts (73,286 peaks with 80.2% hypomethylated). Correlatively, of the 95 Y955C-dependent differentially expressed genes, 30 genes (31.6%) also displayed differential DNA methylation; in the 4,452 age-dependent differentially expressed genes, 342 genes (7.7%) displayed associated DNA methylation changes. Both Y955C and aging demonstrated significant enrichment of CACGTG-associated E-box motifs in differentially methylated regions. Cardiac mitochondrial polymerase dysfunction alters nuclear DNA methylation. Furthermore, aging causes a robust change in cardiac DNA methylation that is partially associated with mitochondrial polymerase dysfunction.
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Affiliation(s)
| | - Ivan Ludlow
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Earl Fields
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Zhe Jiao
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Tomika Ludaway
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Rodney Russ
- Department of Pathology, Emory University, Atlanta, Georgia
| | - William Lewis
- Department of Pathology, Emory University, Atlanta, Georgia
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28
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Chen H, Orozco LD, Wang J, Rau CD, Rubbi L, Ren S, Wang Y, Pellegrini M, Lusis AJ, Vondriska TM. DNA Methylation Indicates Susceptibility to Isoproterenol-Induced Cardiac Pathology and Is Associated With Chromatin States. Circ Res 2016; 118:786-97. [PMID: 26838786 DOI: 10.1161/circresaha.115.305298] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/08/2016] [Indexed: 02/04/2023]
Abstract
RATIONALE Only a small portion of the known heritability of cardiovascular diseases, such as heart failure, can be explained based on single-gene mutations. Chromatin structure and regulation provide a substrate through which genetic differences in noncoding regions may affect cellular function and response to disease, but the mechanisms are unknown. OBJECTIVE We conducted genome-wide measurements of DNA methylation in different strains of mice that are susceptible and resistant to isoproterenol-induced dysfunction to test the hypothesis that this epigenetic mark may play a causal role in the development of heart failure. METHODS AND RESULTS BALB/cJ and BUB/BnJ mice, determined to be susceptible and resistant to isoproterenol-induced heart failure, respectively, were administered the drug for 3 weeks via osmotic minipump. Reduced representational bisulfite sequencing was then used to compare the differences between the cardiac DNA methylomes in the basal state between strains and then after isoproterenol treatment. Single-base resolution DNA methylation measurements were obtained and revealed a bimodal distribution of methylation in the heart, enriched in lone intergenic CpGs and depleted from CpG islands around genes. Isoproterenol induced global decreases in methylation in both strains; however, the basal methylation pattern between strains shows striking differences that may be predictive of disease progression before environmental stress. The global correlation between promoter methylation and gene expression (as measured by microarray) was modest and revealed itself only with focused analyses of transcription start site and gene body regions (in contrast to when gene methylation was examined in toto). Modules of comethylated genes displayed correlation with other protein-based epigenetic marks, supporting the hypothesis that chromatin modifications act in a combinatorial manner to specify transcriptional phenotypes in the heart. CONCLUSIONS This study provides the first single-base resolution map of the mammalian cardiac DNA methylome and the first case-control analysis of the changes in DNA methylation with heart failure. The findings demonstrate marked genetic differences in DNA methylation that are associated with disease progression.
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Affiliation(s)
- Haodong Chen
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.).
| | - Luz D Orozco
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Jessica Wang
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Christoph D Rau
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Liudmilla Rubbi
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Shuxun Ren
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Yibin Wang
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Matteo Pellegrini
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Aldons J Lusis
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.)
| | - Thomas M Vondriska
- From the Departments of Anesthesiology and Perioperative Medicine (H.C., C.D.R., S.R., Y.W., T.M.V.), Human Genetics (A.J.L.), Microbiology, Immunology and Molecular Genetics (A.J.L.), Molecular, Cellular and Development Biology (L.D.O., L.R., M.P.), Medicine/Cardiology (J.W., Y.W., A.J.L., T.M.V.), and Physiology, David Geffen School of Medicine, University of California, Los Angeles (Y.W., T.M.V.).
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29
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Koczor CA, Fields E, Jedrzejczak MJ, Jiao Z, Ludaway T, Russ R, Shang J, Torres RA, Lewis W. Methamphetamine and HIV-Tat alter murine cardiac DNA methylation and gene expression. Toxicol Appl Pharmacol 2015; 288:409-19. [PMID: 26307267 DOI: 10.1016/j.taap.2015.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/13/2015] [Accepted: 08/19/2015] [Indexed: 11/18/2022]
Abstract
This study addresses the individual and combined effects of HIV-1 and methamphetamine (N-methyl-1-phenylpropan-2-amine, METH) on cardiac dysfunction in a transgenic mouse model of HIV/AIDS. METH is abused epidemically and is frequently associated with acquisition of HIV-1 infection or AIDS. We employed microarrays to identify mRNA differences in cardiac left ventricle (LV) gene expression following METH administration (10d, 3mg/kg/d, subcutaneously) in C57Bl/6 wild-type littermates (WT) and Tat-expressing transgenic (TG) mice. Arrays identified 880 differentially expressed genes (expression fold change>1.5, p<0.05) following METH exposure, Tat expression, or both. Using pathway enrichment analysis, mRNAs encoding polypeptides for calcium signaling and contractility were altered in the LV samples. Correlative DNA methylation analysis revealed significant LV DNA methylation changes following METH exposure and Tat expression. By combining these data sets, 38 gene promoters (27 related to METH, 11 related to Tat) exhibited differences by both methods of analysis. Among those, only the promoter for CACNA1C that encodes L-type calcium channel Cav1.2 displayed DNA methylation changes concordant with its gene expression change. Quantitative PCR verified that Cav1.2 LV mRNA abundance doubled following METH. Correlative immunoblots specific for Cav1.2 revealed a 3.5-fold increase in protein abundance in METH LVs. Data implicate Cav1.2 in calcium dysregulation and hypercontractility in the murine LV exposed to METH. They suggest a pathogenetic role for METH exposure to promote LV dysfunction that outweighs Tat-induced effects.
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Affiliation(s)
| | - Earl Fields
- Department of Pathology, Emory University, Atlanta, GA 30322, United States
| | - Mark J Jedrzejczak
- Department of Pathology, Emory University, Atlanta, GA 30322, United States
| | - Zhe Jiao
- Department of Pathology, Emory University, Atlanta, GA 30322, United States
| | - Tomika Ludaway
- Department of Pathology, Emory University, Atlanta, GA 30322, United States
| | - Rodney Russ
- Department of Pathology, Emory University, Atlanta, GA 30322, United States
| | - Joan Shang
- Department of Pathology, Emory University, Atlanta, GA 30322, United States
| | - Rebecca A Torres
- Department of Pathology, Emory University, Atlanta, GA 30322, United States
| | - William Lewis
- Department of Pathology, Emory University, Atlanta, GA 30322, United States
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30
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Koczor CA, Ludlow I, Hight RS, Jiao Z, Fields E, Ludaway T, Russ R, Torres RA, Lewis W. Ecstasy (MDMA) Alters Cardiac Gene Expression and DNA Methylation: Implications for Circadian Rhythm Dysfunction in the Heart. Toxicol Sci 2015; 148:183-91. [PMID: 26251327 DOI: 10.1093/toxsci/kfv170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MDMA (ecstasy) is an illicit drug that stimulates monoamine neurotransmitter release and inhibits reuptake. MDMA's acute cardiotoxicity includes tachycardia and arrhythmia which are associated with cardiomyopathy. MDMA acute cardiotoxicity has been explored, but neither long-term MDMA cardiac pathological changes nor epigenetic changes have been evaluated. Microarray analyses were employed to identify cardiac gene expression changes and epigenetic DNA methylation changes. To identify permanent MDMA-induced pathogenetic changes, mice received daily 10- or 35-day MDMA, or daily 10-day MDMA followed by 25-day saline washout (10 + 25 days). MDMA treatment caused differential gene expression (p < .05, fold change >1.5) in 752 genes following 10 days, 558 genes following 35 days, and 113 genes following 10-day MDMA + 25-day saline washout. Changes in MAPK and circadian rhythm gene expression were identified as early as 10 days. After 35 days, circadian rhythm genes (Per3, CLOCK, ARNTL, and NPAS2) persisted to be differentially expressed. MDMA caused DNA hypermethylation and hypomethylation that was independent of gene expression; hypermethylation of genes was found to be 71% at 10 days, 68% at 35 days, and 91% at 10 + 25 days washout. Differential gene expression paralleled DNA methylation in 22% of genes at 10-day treatment, 17% at 35 days, and 48% at 10 + 25 days washout. We show here that MDMA induced cardiac epigenetic changes in DNA methylation where hypermethylation predominated. Moreover, MDMA induced gene expression of key elements of circadian rhythm regulatory genes. This suggests a fundamental organism-level event to explain some of the etiologies of MDMA dysfunction in the heart.
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Affiliation(s)
| | - Ivan Ludlow
- Department of Pathology, Emory University, Atlanta, Georgia 30322
| | - Robert S Hight
- Department of Pathology, Emory University, Atlanta, Georgia 30322
| | - Zhe Jiao
- Department of Pathology, Emory University, Atlanta, Georgia 30322
| | - Earl Fields
- Department of Pathology, Emory University, Atlanta, Georgia 30322
| | - Tomika Ludaway
- Department of Pathology, Emory University, Atlanta, Georgia 30322
| | - Rodney Russ
- Department of Pathology, Emory University, Atlanta, Georgia 30322
| | - Rebecca A Torres
- Department of Pathology, Emory University, Atlanta, Georgia 30322
| | - William Lewis
- Department of Pathology, Emory University, Atlanta, Georgia 30322
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31
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Fang X, Robinson J, Wang-Hu J, Jiang L, Freeman DA, Rivkees SA, Wendler CC. cAMP induces hypertrophy and alters DNA methylation in HL-1 cardiomyocytes. Am J Physiol Cell Physiol 2015. [PMID: 26224577 DOI: 10.1152/ajpcell.00058.2015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
cAMP is a highly regulated secondary messenger involved in many biological processes. Chronic activation of the cAMP pathway by catecholamines results in cardiac hypertrophy and fibrosis; however, the mechanism by which elevated cAMP leads to cardiomyopathy is not fully understood. To address this issue, we increased intracellular cAMP levels in HL-1 cardiomyocytes, a cell line derived from adult mouse atrium, using either the stable cAMP analog N(6),2'-O-dibutyryladenosine 3',5'-cyclic monophosphate (DBcAMP) or phosphodiesterase (PDE) inhibitors caffeine and theophylline. Elevated cAMP levels increased cell size and altered expression levels of cardiac genes and micro-RNAs associated with hypertrophic cardiomyopathy (HCM), including Myh6, Myh7, Myh7b, Tnni3, Anp, Bnp, Gata4, Mef2c, Mef2d, Nfatc1, miR208a, and miR208b. In addition, DBcAMP altered the expression of DNA methyltransferases (Dnmts) and Tet methylcytosine dioxygenases (Tets), enzymes that regulate genomic DNA methylation levels. Changes in expression of DNA methylation genes induced by elevated cAMP led to increased global DNA methylation in HL-1 cells. In contrast, inhibition of DNMT activity with 5-azacytidine treatment decreased global DNA methylation levels and blocked the increased expression of several HCM genes (Myh7, Gata4, Mef2c, Nfatc1, Myh7b, Tnni3, and Bnp) observed with DBcAMP treatment. These results demonstrate that cAMP induces cardiomyocyte hypertrophy and altered HCM gene expression in vitro and that DNA methylation patterns mediate the upregulation of HCM genes induced by cAMP. These data identify a previously unknown mechanism by which elevated levels of cAMP lead to increased expression of genes associated with cardiomyocyte hypertrophy.
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Affiliation(s)
- Xiefan Fang
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Jourdon Robinson
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - John Wang-Hu
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Lingli Jiang
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Daniel A Freeman
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Scott A Rivkees
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
| | - Christopher C Wendler
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, Florida
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Koczor CA, Jiao Z, Fields E, Russ R, Ludaway T, Lewis W. AZT-induced mitochondrial toxicity: an epigenetic paradigm for dysregulation of gene expression through mitochondrial oxidative stress. Physiol Genomics 2015. [PMID: 26199398 DOI: 10.1152/physiolgenomics.00045.2015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial dysfunction causes oxidative stress and cardiomyopathy. Oxidative stress also is a side effect of dideoxynucleoside antiretrovirals (NRTI) and is observed in NRTI-induced cardiomyopathy. We show here that treatment with the NRTI AZT {1-[(2R,4S,5S)-4-azido-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione} modulates cardiac gene expression epigenetically through production of mitochondrially derived reactive oxygen species. Transgenic mice with ubiquitous expression of mitochondrially targeted catalase (MCAT) and C57Bl/6 wild-type mice littermates (WT) were administered AZT (0.22 mg/day po, 35 days), and cardiac DNA and mRNA were isolated. In AZT-treated WT, 95 cardiac genes were differentially expressed compared with vehicle-treated WTs. When MCAT mice were treated with AZT, each of those 95 genes reverted toward the expression of vehicle-treated WTs. In AZT-treated WT hearts, Mthfr [5,10-methylenetetrahydrofolate reductase; a critical enzyme in synthesis of methionine cycle intermediates including S-adenosylmethionine (SAM)], was overexpressed. Steady-state abundance of SAM in cardiac extracts from AZT-treated MCAT mice increased 60% above that of vehicle-treated MCAT. No such change occurred in WT. AZT caused hypermethylation (47%) and hypomethylation (53%) of differentially methylated DNA regions in WT cardiac DNA. AZT-treated MCAT heart DNA exhibited greater hypermethylation (91%) and less hypomethylation (9%) compared with vehicle-treated MCAT controls. The gene encoding protein kinase C-α displayed multifocal epigenetic regulation caused by oxidative stress. Results show that mitochondrially derived oxidative stress in the heart hinders cardiac DNA methylation, alters steady-state abundance of SAM, alters cardiac gene expression, and promotes characteristic pathophysiological changes of cardiomyopathy. This mechanism for NRTI toxicity offers insight into long-term side effects from these commonly used antiviral agents.
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Affiliation(s)
| | - Zhe Jiao
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Earl Fields
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Rodney Russ
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Tomika Ludaway
- Department of Pathology, Emory University, Atlanta, Georgia
| | - William Lewis
- Department of Pathology, Emory University, Atlanta, Georgia
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Butts B, Gary RA, Dunbar SB, Butler J. The Importance of NLRP3 Inflammasome in Heart Failure. J Card Fail 2015; 21:586-93. [PMID: 25982825 DOI: 10.1016/j.cardfail.2015.04.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/08/2015] [Accepted: 04/30/2015] [Indexed: 12/11/2022]
Abstract
Patients with heart failure continue to suffer adverse health consequences despite advances in therapies over the past 2 decades. Identification of novel therapeutic targets that may attenuate disease progression is therefore needed. The inflammasome may play a central role in modulating chronic inflammation and in turn affecting heart failure progression. The inflammasome is a complex of intracellular interaction proteins that trigger maturation of proinflammatory cytokines interleukin-1β and interleukin-18 to initiate the inflammatory response. This response is amplified through production of tumor necrosis factor α and activation of inducible nitric oxide synthase. The purpose of this review is to discuss recent evidence implicating this inflammatory pathway in the pathophysiology of heart failure.
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Affiliation(s)
- Brittany Butts
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA
| | - Rebecca A Gary
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA
| | - Sandra B Dunbar
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA
| | - Javed Butler
- Cardiology Division, Stony Brook University, Stony Brook, NY.
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Swager SA, Delfín DA, Rastogi N, Wang H, Canan BD, Fedorov VV, Mohler PJ, Kilic A, Higgins RSD, Ziolo MT, Janssen PML, Rafael-Fortney JA. Claudin-5 levels are reduced from multiple cell types in human failing hearts and are associated with mislocalization of ephrin-B1. Cardiovasc Pathol 2014; 24:160-167. [PMID: 25440958 DOI: 10.1016/j.carpath.2014.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/02/2014] [Accepted: 10/31/2014] [Indexed: 12/21/2022] Open
Abstract
Claudin-5 is transcriptionally downregulated resulting in dramatically reduced protein levels in human heart failure. Studies in mice have demonstrated that reduced claudin-5 levels occur prior to cardiac damage and far before reduced whole heart function. Therefore, claudin-5 may be a useful early therapeutic target for human heart failure. However, the cell types in which claudin-5 is localized in human heart and from which claudin-5 is reduced in heart failure is not known. The recent identification of claudin-5's interaction with ephrin-B1 in mouse hearts has also not been investigated in non-failing or failing human hearts. In this study we collected human left ventricular mid-myocardium histological samples from 7 non-failing hearts and 16 end-stage failing hearts. Immunoblots demonstrate severe reductions of claudin-5 protein in 14 of 16 failing hearts compared to non-failing controls. Claudin-5 was observed to localize to cardiomyocytes, endothelial cells, and a subset of fibroblasts in non-failing human heart sections. In isolated cardiomyocytes, the transmembrane claudin-5 protein localized in longitudinal striations in lateral membranes. In failing heart, both cardiomyocyte and endothelial claudin-5 localization was severely reduced, but claudin-5 remained in fibroblasts. Absence of claudin-5 staining also correlated with the reduction of the endothelial cell marker CD31. Ephrin-B1 localization, but not protein levels, was altered in failing hearts supporting that claudin-5 is required for ephrin-B1 localization. These data support that loss of claudin-5 in cardiomyocytes and endothelial cells is prevalent in human heart failure. Investigating claudin-5/ephrin-B1 protein complexes and gene regulation may lead to novel therapies.
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Affiliation(s)
- Sarah A Swager
- Dept. of Molecular & Cellular Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Dawn A Delfín
- Dept. of Molecular & Cellular Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Neha Rastogi
- Dept. of Molecular & Cellular Biochemistry, The Ohio State University, Columbus, OH 43210.,Dept. of Physiology & Cell Biology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210.,Davis Heart & Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Honglan Wang
- Dept. of Physiology & Cell Biology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210.,Davis Heart & Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Benjamin D Canan
- Dept. of Physiology & Cell Biology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210.,Davis Heart & Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Vadim V Fedorov
- Dept. of Physiology & Cell Biology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210.,Davis Heart & Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Peter J Mohler
- Dept. of Physiology & Cell Biology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210.,Davis Heart & Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Ahmet Kilic
- Dept. of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Robert S D Higgins
- Dept. of Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Mark T Ziolo
- Dept. of Physiology & Cell Biology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210.,Davis Heart & Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Paul M L Janssen
- Dept. of Physiology & Cell Biology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210.,Davis Heart & Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
| | - Jill A Rafael-Fortney
- Dept. of Molecular & Cellular Biochemistry, The Ohio State University, Columbus, OH 43210.,Dept. of Physiology & Cell Biology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210.,Davis Heart & Lung Research Institute, Wexner Medical Center, The Ohio State University, Columbus, OH 43210
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Affiliation(s)
- Thomas G. Di Salvo
- Division of Cardiovascular Medicine, Vanderbilt Heart and Vascular Institute, Nashville TN
| | - Saptarsi M. Haldar
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland OH
- Harrington Heart & Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH
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Corney DC, Coller HA. On form and function: does chromatin packing regulate the cell cycle? Physiol Genomics 2014; 46:191-4. [PMID: 24474443 PMCID: PMC3949104 DOI: 10.1152/physiolgenomics.00002.2014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/23/2014] [Indexed: 12/26/2022] Open
Abstract
The Systems Biology of Cell State Regulation Section is dedicated to considering how we can define a cellular state and how cells transition between states. One important decision that a cell makes is whether to cycle, that is, replicate DNA and generate daughter cells, or to exit the cell cycle in a reversible manner. The members of the Systems Biology of Cell State Regulation Editorial Board have an interest in the role of epigenetics and the commitment to a dividing or nondividing state. The ability of cells to transition between proliferating and nonproliferating states is essential for the proper formation of tissues. The ability to enter the cell cycle when needed is necessary for complex multicellular processes, such as healing injuries or mounting an immune response. Cells that fail to quiesce properly can contribute to the formation of tumors. In this perspective piece, we focus on research exploring the relationship between epigenetics and the cell cycle.
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Affiliation(s)
- David C Corney
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California; and Department of Biological Chemistry, David Geffen School of Medicine, Los Angeles, California
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Koczor CA, Torres RA, Fields EJ, Boyd A, He S, Patel N, Lee EK, Samarel AM, Lewis W. Thymidine kinase and mtDNA depletion in human cardiomyopathy: epigenetic and translational evidence for energy starvation. Physiol Genomics 2013; 45:590-6. [PMID: 23695887 DOI: 10.1152/physiolgenomics.00014.2013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
This study addresses how depletion of human cardiac left ventricle (LV) mitochondrial DNA (mtDNA) and epigenetic nuclear DNA methylation promote cardiac dysfunction in human dilated cardiomyopathy (DCM) through regulation of pyrimidine nucleotide kinases. Samples of DCM LV and right ventricle (n = 18) were obtained fresh at heart transplant surgery. Parallel samples from nonfailing (NF) controls (n = 12) were from donor hearts found unsuitable for clinical use. We analyzed abundance of mtDNA and nuclear DNA (nDNA) using qPCR. LV mtDNA was depleted in DCM (50%, P < 0.05 each) compared with NF. No detectable change in RV mtDNA abundance occurred. DNA methylation and gene expression were determined using microarray analysis (GEO accession number: GSE43435). Fifty-seven gene promoters exhibited DNA hypermethylation or hypomethylation in DCM LVs. Among those, cytosolic thymidine kinase 1 (TK1) was hypermethylated. Expression arrays revealed decreased abundance of the TK1 mRNA transcript with no change in transcripts for other relevant thymidine metabolism enzymes. Quantitative immunoblots confirmed decreased TK1 polypeptide steady state abundance. TK1 activity remained unchanged in DCM samples while mitochondrial thymidine kinase (TK2) activity was significantly reduced. Compensatory TK activity was found in cardiac myocytes in the DCM LV. Diminished TK2 activity is mechanistically important to reduced mtDNA abundance and identified in DCM LV samples here. Epigenetic and genetic changes result in changes in mtDNA and in nucleotide substrates for mtDNA replication and underpin energy starvation in DCM.
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Affiliation(s)
- Christopher A Koczor
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, USA
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