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Meza-León A, Montoya-Estrada A, Reyes-Muñoz E, Romo-Yáñez J. Diabetes Mellitus and Pregnancy: An Insight into the Effects on the Epigenome. Biomedicines 2024; 12:351. [PMID: 38397953 PMCID: PMC10886464 DOI: 10.3390/biomedicines12020351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/17/2023] [Accepted: 01/08/2024] [Indexed: 02/25/2024] Open
Abstract
Worldwide, diabetes mellitus represents a growing health problem. If it occurs during pregnancy, it can increase the risk of various abnormalities in early and advanced life stages of exposed individuals due to fetal programming occurring in utero. Studies have determined that maternal conditions interfere with the genotypes and phenotypes of offspring. Researchers are now uncovering the mechanisms by which epigenetic alterations caused by diabetes affect the expression of genes and, therefore, the development of various diseases. Among the numerous possible epigenetic changes in this regard, the most studied to date are DNA methylation and hydroxymethylation, as well as histone acetylation and methylation. This review article addresses critical findings in epigenetic studies involving diabetes mellitus, including variations reported in the expression of specific genes and their transgenerational effects.
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Affiliation(s)
| | | | | | - José Romo-Yáñez
- Coordinación de Endocrinología Ginecológica y Perinatal, Instituto Nacional de Perinatología, Montes Urales 800, Lomas Virreyes, Mexico City 11000, Mexico
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Hong J, Tong H, Wang X, Lv X, He L, Yang X, Wang Y, Xu K, Liang Q, Feng Q, Niu T, Niu X, Lu Y. Embryonic diapause due to high glucose is related to changes in glycolysis and oxidative phosphorylation, as well as abnormalities in the TCA cycle and amino acid metabolism. Front Endocrinol (Lausanne) 2023; 14:1135837. [PMID: 38170036 PMCID: PMC10759208 DOI: 10.3389/fendo.2023.1135837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction The adverse effects of high glucose on embryos can be traced to the preimplantation stage. This study aimed to observe the effect of high glucose on early-stage embryos. Methods and results Seven-week-old ICR female mice were superovulated and mated, and the zygotes were collected. The zygotes were randomly cultured in 5 different glucose concentrations (control, 20mM, 40mM, 60mM and 80mM glucose). The cleavage rate, blastocyst rate and total cell number of blastocyst were used to assess the embryo quality. 40 mM glucose was selected to model high glucose levels in this study. 40mM glucose arrested early embryonic development, and the blastocyst rate and total cell number of the blastocyst decreased significantly as glucose concentration was increased. The reduction in the total cell number of blastocysts in the high glucose group was attributed to decreased proliferation and increased cell apoptosis, which is associated with the diminished expression of GLUTs (GLUT1, GLUT2, GLUT3). Furthermore, the metabolic characterization of blastocyst culture was observed in the high-glucose environment. Discussion The balance of glycolysis and oxidative phosphorylation at the blastocyst stage was disrupted. And embryo development arrest due to high glucose is associated with changes in glycolysis and oxidative phosphorylation, as well as abnormalities in the TCA cycle and amino acid metabolism.
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Affiliation(s)
- Jiewei Hong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Hongxuan Tong
- Institute of Basic Theory of Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuan Wang
- Party Committee Office, Shanxi Health Vocational College, Shanxi, China
| | - Xiaoyan Lv
- Library Collection and Editing Department, Beijing University of Chinese Medicine, Beijing, China
| | - Lijuan He
- Rehabilitation Department, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Xuezhi Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yingli Wang
- Experimental Management Center, Shanxi University of Traditional Chinese Medicine, Shanxi, China
| | - Kaixia Xu
- School of Basic Medicine, Shanxi University of Traditional Chinese Medicine, Shanxi, China
| | - Qi Liang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Qianjin Feng
- Experimental Management Center, Shanxi University of Traditional Chinese Medicine, Shanxi, China
| | - Tingli Niu
- Medical Insurance Office, Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Xin Niu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yu Lu
- Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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Ballesteros M, Gil-Lluís P, Ejarque M, Diaz-Perdigones C, Martinez-Guasch L, Fernández-Veledo S, Vendrell J, Megía A. DNA Methylation in Gestational Diabetes and its Predictive Value for Postpartum Glucose Disturbances. J Clin Endocrinol Metab 2022; 107:2748-2757. [PMID: 35914803 PMCID: PMC9516049 DOI: 10.1210/clinem/dgac462] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 11/21/2022]
Abstract
CONTEXT DNA methylation in the diagnosis of gestational diabetes. OBJECTIVE To assess the value of DNA methylation in the diagnosis of gestational diabetes (GDM) and in the prediction of maternal postpartum glucose disturbances. METHODS Two-stage observational study performed between July 2006 and December 2010, at University Hospital. Forty-eight randomly selected pregnant women formed the discovery cohort (24 with GDM and 24 controls) and 252 pregnant women (94 with GDM and 158 controls) formed the replication cohort. GDM women were re-evaluated 4 years postpartum. The main outcome measures were GDM, type 2 diabetes or prediabetes at 4 years postpartum. RESULTS We identified 3 CpG sites related to LINC00917, TRAPPC9, and LEF1 that were differentially methylated in women with GDM and abnormal glucose tolerance; and sites associated with LINC00917 and TRAPPC9 were independently associated with an abnormal glucose tolerance status 4 years postpartum after controlling for clinical variables. Moreover, the site associated with LINC00917 and the combination of the 3 sites had the highest predictive values. CONCLUSION Our results suggest that some of these sites may be implicated in the development of GDM and postpartum abnormal glucose tolerance.
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Affiliation(s)
- Mónica Ballesteros
- Mónica Ballesteros, Rovira i Virgili University, 43005, Tarragona, Spain.
| | - Pilar Gil-Lluís
- Department of Endocrinology and Nutrition, University Hospital of Tortosa Verge de la Cinta, Tarragona, Spain
| | - Miriam Ejarque
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition. Research Unit. University Hospital of Tarragona Joan XXIII-Institut d´Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
| | - Cristina Diaz-Perdigones
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition. Research Unit. University Hospital of Tarragona Joan XXIII-Institut d´Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
| | - Laia Martinez-Guasch
- Department of Medicine and Surgery, Rovira i Virgili University, Tarragona, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition. Research Unit. University Hospital of Tarragona Joan XXIII-Institut d´Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
| | - Sonia Fernández-Veledo
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM)-Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology and Nutrition. Research Unit. University Hospital of Tarragona Joan XXIII-Institut d´Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
| | - Joan Vendrell
- Correspondence: Joan Vendrell, PhD, MD, Hospital Universitari de Tarragona Joan XXIII, Dr. Mallafre Guasch, 4, 43005 Tarragona, Spain.
| | - Ana Megía
- Ana Megia, PhD, MD, Hospital Universitari de Tarragona Joan XXIII, Dr. Mallafre Guasch, 4, 43005 Tarragona, Spain.
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Li K, Song Y, Qin L, Li A, Jiang S, Ren L, Zang C, Sun J, Zhao Y, Zhang Y. A CpG Methylation Signature as a Potential Marker for Early Diagnosis of Hepatocellular Carcinoma From HBV-Related Liver Disease Using Multiplex Bisulfite Sequencing. Front Oncol 2021; 11:756326. [PMID: 34745991 PMCID: PMC8564137 DOI: 10.3389/fonc.2021.756326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/27/2021] [Indexed: 12/04/2022] Open
Abstract
Background Aberrant methylation of CpG sites served as an epigenetic marker for building diagnostic, prognostic, and recurrence models for hepatocellular carcinoma (HCC). Methods Using Illumina 450K and EPIC Beadchip, we identified 34 CpG sites in peripheral blood mononuclear cell (PBMC) DNA that were differentially methylated in early HCC versus HBV-related liver diseases (HBVLD). We employed multiplex bisulfite sequencing (MBS) based on next-generation sequencing (NGS) to measure methylation of 34 CpG sites in PBMC DNA from 654 patients that were divided into a training set (n = 442) and a test set (n = 212). Using the training set, we selected and built a six-CpG-scorer (namely, cg14171514, cg07721852, cg05166871, cg18087306, cg05213896, and cg18772205), applying least absolute shrinkage and selection operator (LASSO) regression. We performed multivariable analyses of four candidate risk predictors (namely, six-CpG-scorer, age, sex, and AFP level), using 20 times imputation of missing data, non-linearly transformed, and backwards feature selection with logistic regression. The final model’s regression coefficients were calculated according to “Rubin’s Rules”. The diagnostic accuracy of the model was internally validated with a 10,000 bootstrap validation dataset and then applied to the test set for validation. Results The area under the receiver operating characteristic curve (AUROC) of the model was 0.81 (95% CI, 0.77–0.85) and it showed good calibration and decision curve analysis. Using enhanced bootstrap validation, adjusted C-statistics and adjusted Brier score were 0.809 and 0.199, respectively. The model also showed an AUROC value of 0.84 (95% CI 0.79–0.88) of diagnosis for early HCC in the test set. Conclusions Our model based on the six-CpG-scorer was a reliable diagnosis tool for early HCC from HBVLD. The usage of the MBS method can realize large-scale detection of CpG sites in clinical diagnosis of early HCC and benefit the majority of patients.
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Affiliation(s)
- Kang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yi Song
- Experimental Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Ling Qin
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Ang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | | | - Lei Ren
- Pharmacology Department, Air Force Medical Center, People's Liberation Army of China (PLA), Beijing, China
| | - Chaoran Zang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Jianping Sun
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yan Zhao
- Clinical Laboratory Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yonghong Zhang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
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Aref-Eshghi E, Kerkhof J, Pedro VP, Barat-Houari M, Ruiz-Pallares N, Andrau JC, Lacombe D, Van-Gils J, Fergelot P, Dubourg C, Cormier-Daire V, Rondeau S, Lecoquierre F, Saugier-Veber P, Nicolas G, Lesca G, Chatron N, Sanlaville D, Vitobello A, Faivre L, Thauvin-Robinet C, Laumonnier F, Raynaud M, Alders M, Mannens M, Henneman P, Hennekam RC, Velasco G, Francastel C, Ulveling D, Ciolfi A, Pizzi S, Tartaglia M, Heide S, Héron D, Mignot C, Keren B, Whalen S, Afenjar A, Bienvenu T, Campeau PM, Rousseau J, Levy MA, Brick L, Kozenko M, Balci TB, Siu VM, Stuart A, Kadour M, Masters J, Takano K, Kleefstra T, de Leeuw N, Field M, Shaw M, Gecz J, Ainsworth PJ, Lin H, Rodenhiser DI, Friez MJ, Tedder M, Lee JA, DuPont BR, Stevenson RE, Skinner SA, Schwartz CE, Genevieve D, Sadikovic B, Sadikovic B. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders. Am J Hum Genet 2020; 106:356-370. [PMID: 32109418 DOI: 10.1016/j.ajhg.2020.01.019] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/27/2020] [Indexed: 01/24/2023] Open
Abstract
Genetic syndromes frequently present with overlapping clinical features and inconclusive or ambiguous genetic findings which can confound accurate diagnosis and clinical management. An expanding number of genetic syndromes have been shown to have unique genomic DNA methylation patterns (called "episignatures"). Peripheral blood episignatures can be used for diagnostic testing as well as for the interpretation of ambiguous genetic test results. We present here an approach to episignature mapping in 42 genetic syndromes, which has allowed the identification of 34 robust disease-specific episignatures. We examine emerging patterns of overlap, as well as similarities and hierarchical relationships across these episignatures, to highlight their key features as they are related to genetic heterogeneity, dosage effect, unaffected carrier status, and incomplete penetrance. We demonstrate the necessity of multiclass modeling for accurate genetic variant classification and show how disease classification using a single episignature at a time can sometimes lead to classification errors in closely related episignatures. We demonstrate the utility of this tool in resolving ambiguous clinical cases and identification of previously undiagnosed cases through mass screening of a large cohort of subjects with developmental delays and congenital anomalies. This study more than doubles the number of published syndromes with DNA methylation episignatures and, most significantly, opens new avenues for accurate diagnosis and clinical assessment in individuals affected by these disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada.
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Schulze KV, Swaminathan S, Howell S, Jajoo A, Lie NC, Brown O, Sadat R, Hall N, Zhao L, Marshall K, May T, Reid ME, Taylor-Bryan C, Wang X, Belmont JW, Guan Y, Manary MJ, Trehan I, McKenzie CA, Hanchard NA. Edematous severe acute malnutrition is characterized by hypomethylation of DNA. Nat Commun 2019; 10:5791. [PMID: 31857576 PMCID: PMC6923441 DOI: 10.1038/s41467-019-13433-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 11/06/2019] [Indexed: 02/06/2023] Open
Abstract
Edematous severe acute childhood malnutrition (edematous SAM or ESAM), which includes kwashiorkor, presents with more overt multi-organ dysfunction than non-edematous SAM (NESAM). Reduced concentrations and methyl-flux of methionine in 1-carbon metabolism have been reported in acute, but not recovered, ESAM, suggesting downstream DNA methylation changes could be relevant to differences in SAM pathogenesis. Here, we assess genome-wide DNA methylation in buccal cells of 309 SAM children using the 450 K microarray. Relative to NESAM, ESAM is characterized by multiple significantly hypomethylated loci, which is not observed among SAM-recovered adults. Gene expression and methylation show both positive and negative correlation, suggesting a complex transcriptional response to SAM. Hypomethylated loci link to disorders of nutrition and metabolism, including fatty liver and diabetes, and appear to be influenced by genetic variation. Our epigenetic findings provide a potential molecular link to reported aberrant 1-carbon metabolism in ESAM and support consideration of methyl-group supplementation in ESAM.
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Affiliation(s)
- Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Shanker Swaminathan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Sharon Howell
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Aarti Jajoo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Natasha C Lie
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Orgen Brown
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Roa Sadat
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Nancy Hall
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Liang Zhao
- Precision Medicine Research Center, Taihe Hospital, Shiyan City, China
| | - Kwesi Marshall
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Thaddaeus May
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Marvin E Reid
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Carolyn Taylor-Bryan
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Xueqing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Yongtao Guan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Mark J Manary
- Departments of Paediatrics and Child Health and Community Health, University of Malawi, Blantyre, Malawi
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| | - Indi Trehan
- Departments of Paediatrics and Child Health and Community Health, University of Malawi, Blantyre, Malawi
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
- Departments of Pediatrics and Global Health, University of Washington, Seattle, WA, USA
| | - Colin A McKenzie
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA.
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Epigenetics and Mechanobiology in Heart Development and Congenital Heart Disease. Diseases 2019; 7:diseases7030052. [PMID: 31480510 PMCID: PMC6787645 DOI: 10.3390/diseases7030052] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 12/14/2022] Open
Abstract
: Congenital heart disease (CHD) is the most common birth defect worldwide and the number one killer of live-born infants in the United States. Heart development occurs early in embryogenesis and involves complex interactions between multiple cell populations, limiting the understanding and consequent treatment of CHD. Furthermore, genome sequencing has largely failed to predict or yield therapeutics for CHD. In addition to the underlying genome, epigenetics and mechanobiology both drive heart development. A growing body of evidence implicates the aberrant regulation of these two extra-genomic systems in the pathogenesis of CHD. In this review, we describe the stages of human heart development and the heart defects known to manifest at each stage. Next, we discuss the distinct and overlapping roles of epigenetics and mechanobiology in normal development and in the pathogenesis of CHD. Finally, we highlight recent advances in the identification of novel epigenetic biomarkers and environmental risk factors that may be useful for improved diagnosis and further elucidation of CHD etiology.
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