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Zhu M, Chen Y, Cheng L, Li X, Shen Y, Guo G, Xu X, Li H, Yang H, Liu C, He K. Calsyntenin-1 Promotes Doxorubicin-induced Dilated Cardiomyopathy in Rats. Cardiovasc Drugs Ther 2024; 38:237-252. [PMID: 36350487 PMCID: PMC10959838 DOI: 10.1007/s10557-022-07389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
Abstract
PURPOSE Doxorubicin is an important cancer chemotherapeutic agent with severe cardiotoxic effects that eventually lead to dilated cardiomyopathy (DCM). Calsyntenin-1(CLSTN1) plays a critical role in the nervous system, but its relevance in cardiovascular diseases is unknown. We investigated the significance of CLSTN1 in doxorubicin-induced DCM. METHODS CLSTN1 expression in doxorubicin-induced DCM rats and H9c2 cells was determined using western blotting. To further explore the functions of CLSTN1, a cardiac-specific CLSTN1 overexpression rat model was constructed. The rats were subjected to analysis using echocardiographic, hemodynamic, and electrocardiographic parameters. Potential downstream molecules in CLSTN1 overexpression heart tissue were investigated using proteomics and western blotting. Finally, a knockdown of CLSTN1 was constructed to investigate the rescue function on doxorubicin-induced cell toxicity. RESULTS CLSTN1 protein expression increased drastically in doxorubicin-induced DCM rats and H9c2 cells. Under doxorubicin treatment, CLSTN1 protein-specific overexpression in the heart muscle promoted cardiac chamber enlargement and heart failure, while the knockdown of CLSTN1 reduced doxorubicin-induced cardiomyocyte toxicity in vitro. At the mechanistic level, overexpression of CLSTN1 downregulated SERCA2 expression and increased the phosphorylation levels of PI3K-Akt and CaMK2. CONCLUSION Our findings demonstrated that CLSTN1 promotes the pathogenesis of doxorubicin-induced DCM. CLSTN1 could be a therapeutic target to prevent the development of doxorubicin-induced DCM.
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Affiliation(s)
- Mingxiang Zhu
- Medical School of Chinese PLA, Beijing, 100853, China
- Medical Big Data Research Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yibing Chen
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Liting Cheng
- Medical School of Chinese PLA, Beijing, 100853, China
- Medical Big Data Research Center, Chinese PLA General Hospital, Beijing, 100853, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Xin Li
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Yanying Shen
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Ge Guo
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiang Xu
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Hanlu Li
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Hao Yang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital and Affiliated People's Hospital of Inner Mongolia Medical University, Huhhot, China
| | - Chunlei Liu
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China.
| | - Kunlun He
- Medical Big Data Research Center, Chinese PLA General Hospital, Beijing, 100853, China.
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Raghubeer S. The influence of epigenetics and inflammation on cardiometabolic risks. Semin Cell Dev Biol 2024; 154:175-184. [PMID: 36804178 DOI: 10.1016/j.semcdb.2023.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Cardiometabolic diseases include metabolic syndrome, obesity, type 2 diabetes mellitus, and hypertension. Epigenetic modifications participate in cardiometabolic diseases through several pathways, including inflammation, vascular dysfunction, and insulin resistance. Epigenetic modifications, which encompass alterations to gene expression without mutating the DNA sequence, have gained much attention in recent years, since they have been correlated with cardiometabolic diseases and may be targeted for therapeutic interventions. Epigenetic modifications are greatly influenced by environmental factors, such as diet, physical activity, cigarette smoking, and pollution. Some modifications are heritable, indicating that the biological expression of epigenetic alterations may be observed across generations. Moreover, many patients with cardiometabolic diseases present with chronic inflammation, which can be influenced by environmental and genetic factors. The inflammatory environment worsens the prognosis of cardiometabolic diseases and further induces epigenetic modifications, predisposing patients to the development of other metabolism-associated diseases and complications. A deeper understanding of inflammatory processes and epigenetic modifications in cardiometabolic diseases is necessary to improve our diagnostic capabilities, personalized medicine approaches, and the development of targeted therapeutic interventions. Further understanding may also assist in predicting disease outcomes, especially in children and young adults. This review describes epigenetic modifications and inflammatory processes underlying cardiometabolic diseases, and further discusses advances in the research field with a focus on specific points for interventional therapy.
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Affiliation(s)
- Shanel Raghubeer
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health & Wellness Sciences, Cape Peninsula University of Technology, South Africa.
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3
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Liu T, Li T, Ke S. Role of the CASZ1 transcription factor in tissue development and disease. Eur J Med Res 2023; 28:562. [PMID: 38053207 DOI: 10.1186/s40001-023-01548-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Abstract
The zinc finger transcription factor gene, CASZ1/Castor (Castor zinc finger 1), initially identified in Drosophila, plays a critical role in neural, cardiac, and cardiovascular development, exerting a complex, multifaceted influence on cell fate and tissue morphogenesis. During neurogenesis, CASZ1 exhibits dynamic expression from early embryonic development to the perinatal period, constituting a key regulator in this process. Additionally, CASZ1 controls the transition between neurogenesis and gliomagenesis. During human cardiovascular system development, CASZ1 is essential for cardiomyocyte differentiation, cardiac morphogenesis, and vascular morphology homeostasis and formation. The deletion or inactivation of CASZ1 mutations can lead to human developmental diseases or tumors, including congenital heart disease, cardiovascular disease, and neuroblastoma. CASZ1 can be used as a biomarker for disease prevention and diagnosis as well as a prognostic indicator for cancer. This review explores the unique functions of CASZ1 in tissue morphogenesis and associated diseases, offering new insights for elucidating the molecular mechanisms underlying diseases and identifying potential therapeutic targets for disease prevention and treatment.
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Affiliation(s)
- Tiantian Liu
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou, 450046, Henan, China.
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China.
| | - Tao Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shaorui Ke
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou, 450046, Henan, China
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
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Jian H, Poetsch A. CASZ1: Current Implications in Cardiovascular Diseases and Cancers. Biomedicines 2023; 11:2079. [PMID: 37509718 PMCID: PMC10377389 DOI: 10.3390/biomedicines11072079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/09/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Castor zinc finger 1 (CASZ1) is a C2H2 zinc finger family protein that has two splicing variants, CASZ1a and CASZ1b. It is involved in multiple physiological processes, such as tissue differentiation and aldosterone antagonism. Genetic and epigenetic alternations of CASZ1 have been characterized in multiple cardiovascular disorders, such as congenital heart diseases, chronic venous diseases, and hypertension. However, little is known about how CASZ1 mechanically participates in the pathogenesis of these diseases. Over the past decades, at first glance, paradoxical influences on cell behaviors and progressions of different cancer types have been discovered for CASZ1, which may be explained by a "double-agent" role for CASZ1. In this review, we discuss the physiological function of CASZ1, and focus on the association of CASZ1 aberrations with the pathogenesis of cardiovascular diseases and cancers.
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Affiliation(s)
- Heng Jian
- Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Ansgar Poetsch
- Queen Mary School, Nanchang University, Nanchang 330006, China
- School of Basic Medical Sciences, Nanchang University, Nanchang 330006, China
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5
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Krolevets M, Cate VT, Prochaska JH, Schulz A, Rapp S, Tenzer S, Andrade-Navarro MA, Horvath S, Niehrs C, Wild PS. DNA methylation and cardiovascular disease in humans: a systematic review and database of known CpG methylation sites. Clin Epigenetics 2023; 15:56. [PMID: 36991458 PMCID: PMC10061871 DOI: 10.1186/s13148-023-01468-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/19/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Cardiovascular disease (CVD) is the leading cause of death worldwide and considered one of the most environmentally driven diseases. The role of DNA methylation in response to the individual exposure for the development and progression of CVD is still poorly understood and a synthesis of the evidence is lacking. RESULTS A systematic review of articles examining measurements of DNA cytosine methylation in CVD was conducted in accordance with PRISMA (preferred reporting items for systematic reviews and meta-analyses) guidelines. The search yielded 5,563 articles from PubMed and CENTRAL databases. From 99 studies with a total of 87,827 individuals eligible for analysis, a database was created combining all CpG-, gene- and study-related information. It contains 74,580 unique CpG sites, of which 1452 CpG sites were mentioned in ≥ 2, and 441 CpG sites in ≥ 3 publications. Two sites were referenced in ≥ 6 publications: cg01656216 (near ZNF438) related to vascular disease and epigenetic age, and cg03636183 (near F2RL3) related to coronary heart disease, myocardial infarction, smoking and air pollution. Of 19,127 mapped genes, 5,807 were reported in ≥ 2 studies. Most frequently reported were TEAD1 (TEA Domain Transcription Factor 1) and PTPRN2 (Protein Tyrosine Phosphatase Receptor Type N2) in association with outcomes ranging from vascular to cardiac disease. Gene set enrichment analysis of 4,532 overlapping genes revealed enrichment for Gene Ontology molecular function "DNA-binding transcription activator activity" (q = 1.65 × 10-11) and biological processes "skeletal system development" (q = 1.89 × 10-23). Gene enrichment demonstrated that general CVD-related terms are shared, while "heart" and "vasculature" specific genes have more disease-specific terms as PR interval for "heart" or platelet distribution width for "vasculature." STRING analysis revealed significant protein-protein interactions between the products of the differentially methylated genes (p = 0.003) suggesting that dysregulation of the protein interaction network could contribute to CVD. Overlaps with curated gene sets from the Molecular Signatures Database showed enrichment of genes in hemostasis (p = 2.9 × 10-6) and atherosclerosis (p = 4.9 × 10-4). CONCLUSION This review highlights the current state of knowledge on significant relationship between DNA methylation and CVD in humans. An open-access database has been compiled of reported CpG methylation sites, genes and pathways that may play an important role in this relationship.
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Affiliation(s)
- Mykhailo Krolevets
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Systems Medicine, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Vincent Ten Cate
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jürgen H Prochaska
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andreas Schulz
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Steffen Rapp
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
| | - Stefan Tenzer
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | - Christof Niehrs
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
| | - Philipp S Wild
- Preventive Cardiology and Preventive Medicine, Department of Cardiology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
- Systems Medicine, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
- Clinical Epidemiology and Systems Medicine, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine Main, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
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Siecinski SK, Giamberardino SN, Spanos M, Hauser AC, Gibson JR, Chandrasekhar T, Trelles MDP, Rockhill CM, Palumbo ML, Cundiff AW, Montgomery A, Siper P, Minjarez M, Nowinski LA, Marler S, Kwee LC, Shuffrey LC, Alderman C, Weissman J, Zappone B, Mullett JE, Crosson H, Hong N, Luo S, She L, Bhapkar M, Dean R, Scheer A, Johnson JL, King BH, McDougle CJ, Sanders KB, Kim SJ, Kolevzon A, Veenstra-VanderWeele J, Hauser ER, Sikich L, Gregory SG. Genetic and epigenetic signatures associated with plasma oxytocin levels in children and adolescents with autism spectrum disorder. Autism Res 2023; 16:502-523. [PMID: 36609850 PMCID: PMC10023458 DOI: 10.1002/aur.2884] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023]
Abstract
Oxytocin (OT), the brain's most abundant neuropeptide, plays an important role in social salience and motivation. Clinical trials of the efficacy of OT in autism spectrum disorder (ASD) have reported mixed results due in part to ASD's complex etiology. We investigated whether genetic and epigenetic variation contribute to variable endogenous OT levels that modulate sensitivity to OT therapy. To carry out this analysis, we integrated genome-wide profiles of DNA-methylation, transcriptional activity, and genetic variation with plasma OT levels in 290 participants with ASD enrolled in a randomized controlled trial of OT. Our analysis identified genetic variants with novel association with plasma OT, several of which reside in known ASD risk genes. We also show subtle but statistically significant association of plasma OT levels with peripheral transcriptional activity and DNA-methylation profiles across several annotated gene sets. These findings broaden our understanding of the effects of the peripheral oxytocin system and provide novel genetic candidates for future studies to decode the complex etiology of ASD and its interaction with OT signaling and OT-based interventions. LAY SUMMARY: Oxytocin (OT) is an abundant chemical produced by neurons that plays an important role in social interaction and motivation. We investigated whether genetic and epigenetic factors contribute to variable OT levels in the blood. To this, we integrated genetic, gene expression, and non-DNA regulated (epigenetic) signatures with blood OT levels in 290 participants with autism enrolled in an OT clinical trial. We identified genetic association with plasma OT, several of which reside in known autism risk genes. We also show statistically significant association of plasma OT levels with gene expression and epigenetic across several gene pathways. These findings broaden our understanding of the factors that influence OT levels in the blood for future studies to decode the complex presentation of autism and its interaction with OT and OT-based treatment.
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Affiliation(s)
- Stephen K Siecinski
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Marina Spanos
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Annalise C Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jason R Gibson
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tara Chandrasekhar
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - M D Pilar Trelles
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carol M Rockhill
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Michelle L Palumbo
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Paige Siper
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mendy Minjarez
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Lisa A Nowinski
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sarah Marler
- Department of Psychiatry, Vanderbilt University, Nashville, TN, USA
| | - Lydia C Kwee
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Cheryl Alderman
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jordana Weissman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brooke Zappone
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Jennifer E Mullett
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hope Crosson
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Natalie Hong
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Sheng Luo
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Lilin She
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Manjushri Bhapkar
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Russell Dean
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abby Scheer
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Jacqueline L Johnson
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bryan H King
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Christopher J McDougle
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin B Sanders
- Department of Psychiatry, Vanderbilt University, Nashville, TN, USA
| | - Soo-Jeong Kim
- Department of Psychiatry, Seattle Children’s Hospital and the University of Washington, Seattle, WA, USA
| | - Alexander Kolevzon
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Elizabeth R Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Linmarie Sikich
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC, USA
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7
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Jiang R, Hauser ER, Kwee LC, Shah SH, Regan JA, Huebner JL, Kraus VB, Kraus WE, Ward-Caviness CK. The association of accelerated epigenetic age with all-cause mortality in cardiac catheterization patients as mediated by vascular and cardiometabolic outcomes. Clin Epigenetics 2022; 14:165. [PMID: 36461124 PMCID: PMC9719253 DOI: 10.1186/s13148-022-01380-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/16/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Epigenetic age is a DNA methylation-based biomarker of aging that is accurate across the lifespan and a range of cell types. The difference between epigenetic age and chronological age, termed age acceleration (AA), is a strong predictor of lifespan and healthspan. The predictive capabilities of AA for all-cause mortality have been evaluated in the general population; however, its utility is less well evaluated in those with chronic conditions. Additionally, the pathophysiologic pathways whereby AA predicts mortality are unclear. We hypothesized that AA predicts mortality in individuals with underlying cardiovascular disease; and the association between AA and mortality is mediated, in part, by vascular and cardiometabolic measures. METHODS We evaluated 562 participants in an urban, three-county area of central North Carolina from the CATHGEN cohort, all of whom received a cardiac catheterization procedure. We analyzed three AA biomarkers, Horvath epigenetic age acceleration (HAA), phenotypic age acceleration (PhenoAA), and Grim age acceleration (GrimAA), by Cox regression models, to assess whether AAs were associated with all-cause mortality. We also evaluated if these associations were mediated by vascular and cardiometabolic outcomes, including left ventricular ejection fraction (LVEF), blood cholesterol concentrations, angiopoietin-2 (ANG2) protein concentration, peripheral artery disease, coronary artery disease, diabetes, and hypertension. The total effect, direct effect, indirect effect, and percentage mediated were estimated using pathway mediation tests with a regression adjustment approach. RESULTS PhenoAA (HR = 1.05, P < 0.0001), GrimAA (HR = 1.10, P < 0.0001) and HAA (HR = 1.03, P = 0.01) were all associated with all-cause mortality. The association of mortality and PhenoAA was partially mediated by ANG2, a marker of vascular function (19.8%, P = 0.016), and by diabetes (8.2%, P = 0.043). The GrimAA-mortality association was mediated by ANG2 (12.3%, P = 0.014), and showed weaker evidence for mediation by LVEF (5.3%, P = 0.065). CONCLUSIONS Epigenetic age acceleration remains strongly predictive of mortality even in individuals already burdened with cardiovascular disease. Mortality associations were mediated by ANG2, which regulates endothelial permeability and angiogenic functions, suggesting that specific vascular pathophysiology may link accelerated epigenetic aging with increased mortality risks.
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Affiliation(s)
- Rong Jiang
- grid.26009.3d0000 0004 1936 7961Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC USA
| | - Elizabeth R. Hauser
- grid.26009.3d0000 0004 1936 7961Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC USA
| | - Lydia Coulter Kwee
- grid.26009.3d0000 0004 1936 7961Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC USA
| | - Svati H. Shah
- grid.26009.3d0000 0004 1936 7961Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Division of Cardiology, Department of Medicine, Duke University School of Medicine, Duke University, Durham, NC USA
| | - Jessica A. Regan
- grid.26009.3d0000 0004 1936 7961Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Division of Cardiology, Department of Medicine, Duke University School of Medicine, Duke University, Durham, NC USA
| | - Janet L. Huebner
- grid.26009.3d0000 0004 1936 7961Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC USA
| | - Virginia B. Kraus
- grid.26009.3d0000 0004 1936 7961Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Division of Rheumatology, Department of Medicine, Duke University School of Medicine, Durham, NC USA
| | - William E. Kraus
- grid.26009.3d0000 0004 1936 7961Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Division of Cardiology, Department of Medicine, Duke University School of Medicine, Duke University, Durham, NC USA
| | - Cavin K. Ward-Caviness
- grid.418698.a0000 0001 2146 2763Center for Public Health and Environmental Assessment, US Environmental Protection Agency, Chapel Hill, NC USA
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8
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Hoffmann TJ, Lu M, Oni-Orisan A, Lee C, Risch N, Iribarren C. A large genome-wide association study of QT interval length utilizing electronic health records. Genetics 2022; 222:iyac157. [PMID: 36271874 PMCID: PMC9713425 DOI: 10.1093/genetics/iyac157] [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: 07/09/2022] [Accepted: 09/22/2022] [Indexed: 12/13/2022] Open
Abstract
QT interval length is an important risk factor for adverse cardiovascular outcomes; however, the genetic architecture of QT interval remains incompletely understood. We conducted a genome-wide association study of 76,995 ancestrally diverse Kaiser Permanente Northern California members enrolled in the Genetic Epidemiology Research on Adult Health and Aging cohort using 448,517 longitudinal QT interval measurements, uncovering 9 novel variants, most replicating in 40,537 individuals in the UK Biobank and Population Architecture using Genomics and Epidemiology studies. A meta-analysis of all 3 cohorts (n = 117,532) uncovered an additional 19 novel variants. Conditional analysis identified 15 additional variants, 3 of which were novel. Little, if any, difference was seen when adjusting for putative QT interval lengthening medications genome-wide. Using multiple measurements in Genetic Epidemiology Research on Adult Health and Aging increased variance explained by 163%, and we show that the ≈6 measurements in Genetic Epidemiology Research on Adult Health and Aging was equivalent to a 2.4× increase in sample size of a design with a single measurement. The array heritability was estimated at ≈17%, approximately half of our estimate of 36% from family correlations. Heritability enrichment was estimated highest and most significant in cardiovascular tissue (enrichment 7.2, 95% CI = 5.7-8.7, P = 2.1e-10), and many of the novel variants included expression quantitative trait loci in heart and other relevant tissues. Comparing our results to other cardiac function traits, it appears that QT interval has a multifactorial genetic etiology.
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Affiliation(s)
- Thomas J Hoffmann
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Meng Lu
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Akinyemi Oni-Orisan
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Catherine Lee
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
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Allen JP, Danoff JS, Costello MA, Hunt GL, Hellwig AF, Krol KM, Gregory SG, Giamberardino SN, Sugden K, Connelly JJ. Lifetime marijuana use and epigenetic age acceleration: A 17-year prospective examination. Drug Alcohol Depend 2022; 233:109363. [PMID: 35231715 PMCID: PMC8982677 DOI: 10.1016/j.drugalcdep.2022.109363] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/19/2022] [Accepted: 02/15/2022] [Indexed: 12/12/2022]
Abstract
AIMS This study was designed to assess links between lifetime levels of marijuana use and accelerated epigenetic aging. DESIGN Prospective longitudinal study, following participants annually from age 13 to age 30. SETTING AND PARTICIPANTS A community sample of 154 participants recruited from a small city in the Southeastern United States. MEASUREMENTS Participants completed annual assessments of marijuana use from age 13 to age 29 and provided blood samples that yielded two indices of epigenetic aging (DNAmGrimAge and DunedinPoAm) at age 30. Additional covariates examined included history of cigarette smoking, anxiety and depressive symptoms, childhood illness, gender, adolescent-era family income, and racial/ethnic minority status. FINDINGS Lifetime marijuana use predicted accelerated epigenetic aging, with effects remaining even after covarying cell counts, demographic factors and chronological age (β's = 0.32 & 0.27, p's < 0.001, 95% CI's = 0.21-0.43 & 0.16-0.39 for DNAmGrimAge and DunedinPoAm, respectively). Predictions remained after accounting for cigarette smoking (β's = 0.25 & 0.21, respectively, p's < 0.001, 95% CI's = 0.14-0.37 & 0.09-0.32 for DNAmGrimAge and DunedinPoAm, respectively). A dose-response effect was observed and there was also evidence that effects were dependent upon recency of use. Effects of marijuana use appeared to be fully mediated by hypomethylation of a site linked to effects of hydrocarbon inhalation (cg05575921). CONCLUSIONS Marijuana use predicted epigenetic changes linked to accelerated aging, with evidence suggesting that effects may be primarily due to hydrocarbon inhalation among marijuana smokers. Further research is warranted to explore mechanisms underlying this linkage.
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10
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Xia Y, Brewer A, Bell JT. DNA methylation signatures of incident coronary heart disease: findings from epigenome-wide association studies. Clin Epigenetics 2021; 13:186. [PMID: 34627379 PMCID: PMC8501606 DOI: 10.1186/s13148-021-01175-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/19/2021] [Indexed: 12/12/2022] Open
Abstract
Coronary heart disease (CHD) is a type of cardiovascular disease (CVD) that affects the coronary arteries, which provide oxygenated blood to the heart. It is a major cause of mortality worldwide. Various prediction methods have been developed to assess the likelihood of developing CHD, including those based on clinical features and genetic variation. Recent epigenome-wide studies have identified DNA methylation signatures associated with the development of CHD, indicating that DNA methylation may play a role in predicting future CHD. This narrative review summarises recent findings from DNA methylation studies of incident CHD (iCHD) events from epigenome-wide association studies (EWASs). The results suggest that DNA methylation signatures may identify new mechanisms involved in CHD progression and could prove a useful adjunct for the prediction of future CHD.
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Affiliation(s)
- Yujing Xia
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH, UK
| | - Alison Brewer
- School of Cardiovascular Medicine and Sciences, James Black Centre, King's College London British Heart Foundation Centre of Excellence, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH, UK.
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11
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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12
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Vanderlinden LA, Johnson RK, Carry PM, Dong F, DeMeo DL, Yang IV, Norris JM, Kechris K. An effective processing pipeline for harmonizing DNA methylation data from Illumina's 450K and EPIC platforms for epidemiological studies. BMC Res Notes 2021; 14:352. [PMID: 34496950 PMCID: PMC8424820 DOI: 10.1186/s13104-021-05741-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 08/16/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE Illumina BeadChip arrays are commonly used to generate DNA methylation data for large epidemiological studies. Updates in technology over time create challenges for data harmonization within and between studies, many of which obtained data from the older 450K and newer EPIC platforms. The pre-processing pipeline for DNA methylation is not trivial, and influences the downstream analyses. Incorporating different platforms adds a new level of technical variability that has not yet been taken into account by recommended pipelines. Our study evaluated the performance of various tools on different versions of platform data harmonization at each step of pre-processing pipeline, including quality control (QC), normalization, batch effect adjustment, and genomic inflation. We illustrate our novel approach using 450K and EPIC data from the Diabetes Autoimmunity Study in the Young (DAISY) prospective cohort. RESULTS We found normalization and probe filtering had the biggest effect on data harmonization. Employing a meta-analysis was an effective and easily executable method for accounting for platform variability. Correcting for genomic inflation also helped with harmonization. We present guidelines for studies seeking to harmonize data from the 450K and EPIC platforms, which includes the use of technical replicates for evaluating numerous pre-processing steps, and employing a meta-analysis.
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Affiliation(s)
- Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Randi K Johnson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Patrick M Carry
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fran Dong
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ivana V Yang
- School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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13
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Kumari N, Karmakar A, Chakrabarti S, Ganesan SK. Integrative Computational Approach Revealed Crucial Genes Associated With Different Stages of Diabetic Retinopathy. Front Genet 2020; 11:576442. [PMID: 33304382 PMCID: PMC7693709 DOI: 10.3389/fgene.2020.576442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
The increased incidence of diabetic retinopathy (DR) and the legacy effect associated with it has raised a great concern toward the need to find early diagnostic and treatment strategies. Identifying alterations in genes and microRNAs (miRNAs) is one of the most critical steps toward understanding the mechanisms by which a disease progresses, and this can be further used in finding potential diagnostic and prognostic biomarkers and treatment methods. We selected different datasets to identify altered genes and miRNAs. The integrative analysis was employed to find potential candidate genes (differentially expressed and aberrantly methylated genes that are also the target of altered miRNAs) and early genes (genes showing altered expression and methylation pattern during early stage of DR) for DR. We constructed a protein-protein interaction (PPI) network to find hub genes (potential candidate genes showing a greater number of interactions) and modules. Gene ontologies and pathways associated with the identified genes were analyzed to determine their role in DR progression. A total of 271 upregulated-hypomethylated genes, 84 downregulated-hypermethylated genes, 11 upregulated miRNA, and 30 downregulated miRNA specific to DR were identified. 40 potential candidate genes and 9 early genes were also identified. PPI network analysis revealed 7 hub genes (number of interactions >5) and 1 module (score = 5.67). Gene ontology and pathway analysis predicted enrichment of genes in oxidoreductase activity, binding to extracellular matrix, immune responses, leukocyte migration, cell adhesion, PI3K-Akt signaling pathway, ECM receptor interaction, etc., and thus their association with DR pathogenesis. In conclusion, we identified 7 hub genes and 9 early genes that could act as a potential prognostic, diagnostic, or therapeutic target for DR, and a few early genes could also play a role in metabolic memory phenomena.
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Affiliation(s)
- Nidhi Kumari
- Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditi Karmakar
- Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Saikat Chakrabarti
- Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Senthil Kumar Ganesan
- Department of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,CSIR-IICB Translational Research Unit of Excellence (TRUE), Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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14
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Genetic and epigenetic analyses of panic disorder in the post-GWAS era. J Neural Transm (Vienna) 2020; 127:1517-1526. [PMID: 32388794 PMCID: PMC7578165 DOI: 10.1007/s00702-020-02205-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/03/2020] [Indexed: 02/07/2023]
Abstract
Panic disorder (PD) is a common and debilitating neuropsychiatric disorder characterized by panic attacks coupled with excessive anxiety. Both genetic factors and environmental factors play an important role in PD pathogenesis and response to treatment. However, PD is clinically heterogeneous and genetically complex, and the exact genetic or environmental causes of this disorder remain unclear. Various approaches for detecting disease-causing genes have recently been made available. In particular, genome-wide association studies (GWAS) have attracted attention for the identification of disease-associated loci of multifactorial disorders. This review introduces GWAS of PD, followed by a discussion about the limitations of GWAS and the major challenges facing geneticists in the post-GWAS era. Alternative strategies to address these challenges are then proposed, such as epigenome-wide association studies (EWAS) and rare variant association studies (RVAS) using next-generation sequencing. To date, however, few reports have described these analyses, and the evidence remains insufficient to confidently identify or exclude rare variants or epigenetic changes in PD. Further analyses are therefore required, using sample sizes in the tens of thousands, extensive functional annotations, and highly targeted hypothesis testing.
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15
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Abdulrahim JW, Kwee LC, Grass E, Siegler IC, Williams R, Karra R, Kraus WE, Gregory SG, Shah SH. Epigenome-Wide Association Study for All-Cause Mortality in a Cardiovascular Cohort Identifies Differential Methylation in Castor Zinc Finger 1 ( CASZ1). J Am Heart Assoc 2019; 8:e013228. [PMID: 31642367 PMCID: PMC6898816 DOI: 10.1161/jaha.119.013228] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023]
Abstract
Background DNA methylation is implicated in many chronic diseases and may contribute to mortality. Therefore, we conducted an epigenome-wide association study (EWAS) for all-cause mortality with whole-transcriptome data in a cardiovascular cohort (CATHGEN [Catheterization Genetics]). Methods and Results Cases were participants with mortality≥7 days postcatheterization whereas controls were alive with≥2 years of follow-up. The Illumina Human Methylation 450K and EPIC arrays (Illumina, San Diego, CA) were used for the discovery and validation sets, respectively. A linear model approach with empirical Bayes estimators adjusted for confounders was used to assess difference in methylation (Δβ). In the discovery set (55 cases, 49 controls), 25 629 (6.5%) probes were differently methylated (P<0.05). In the validation set (108 cases, 108 controls), 3 probes were differentially methylated with a false discovery rate-adjusted P<0.10: cg08215811 (SLC4A9; log2 fold change=-0.14); cg17845532 (MATK; fold change=-0.26); and cg17944110 (castor zinc finger 1 [CASZ1]; FC=0.26; P<0.0001; false discovery rate-adjusted P=0.046-0.080). Meta-analysis identified 6 probes (false discovery rate-adjusted P<0.05): the 3 above, cg20428720 (intergenic), cg17647904 (NCOR2), and cg23198793 (CAPN3). Messenger RNA expression of 2 MATK isoforms was lower in cases (fold change=-0.24 [P=0.007] and fold change=-0.61 [P=0.009]). The CASZ1, NCOR2, and CAPN3 transcripts did not show differential expression (P>0.05); the SLC4A9 transcript did not pass quality control. The cg17944110 probe is located within a potential regulatory element; expression of predicted targets (using GeneHancer) of the regulatory element, UBIAD1 (P=0.01) and CLSTN1 (P=0.03), were lower in cases. Conclusions We identified 6 novel methylation sites associated with all-cause mortality. Methylation in CASZ1 may serve as a regulatory element associated with mortality in cardiovascular patients. Larger studies are necessary to confirm these observations.
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Affiliation(s)
- Jawan W. Abdulrahim
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Lydia Coulter Kwee
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Elizabeth Grass
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Ilene C. Siegler
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNC
| | - Redford Williams
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNC
| | - Ravi Karra
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
| | - William E. Kraus
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
| | - Simon G. Gregory
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
| | - Svati H. Shah
- Duke Molecular Physiology InstituteDuke University School of MedicineDuke UniversityDurhamNC
- Division of CardiologyDepartment of MedicineDuke University School of MedicineDurhamNC
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