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Awada Z, Cahais V, Cuenin C, Akika R, Silva Almeida Vicente AL, Makki M, Tamim H, Herceg Z, Khoueiry Zgheib N, Ghantous A. Waterpipe and cigarette epigenome analysis reveals markers implicated in addiction and smoking type inference. ENVIRONMENT INTERNATIONAL 2023; 182:108260. [PMID: 38006773 PMCID: PMC10716859 DOI: 10.1016/j.envint.2023.108260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 11/27/2023]
Abstract
Waterpipe smoking is frequent in the Middle East and Africa with emerging prevalence worldwide. The epigenome acts as a molecular sensor to exposures and a crucial driver in several diseases. With the widespread use of waterpipe smoking, it is timely to investigate its epigenomic markers and their role in addiction, as a central player in disease prevention and therapeutic strategies. DNA methylome-wide profiling was performed on an exposure-rich population from the Middle East, constituting of 216 blood samples split equally between never, cigarette-only and waterpipe-only smokers. Waterpipe smokers showed predominantly distinct epigenetic markers from cigarette smokers, even though both smoking forms are tobacco-based. Moreover, each smoking form could be accurately (∼90 %) inferred from the DNA methylome using machine learning. Top markers showed dose-response relationship with extent of smoking and were validated using independent technologies and additional samples (total N = 284). Smoking markers were enriched in regulatory regions and several biological pathways, primarily addiction. The epigenetically altered genes were not associated with genetic etiology of tobacco use, and the methylation levels of addiction genes, in particular, were more likely to reverse after smoking cessation. In contrast, other epigenetic markers continued to feature smoking exposure after cessation, which may explain long-term health effects observed in former smokers. This study reports, for the first time, blood epigenome-wide markers of waterpipe smokers and reveals new markers of cigarette smoking, with implications in mechanisms of addiction and the capacity to discriminate between different smoking types. These markers may offer actionable targets to reverse the epigenetic memory of addiction and can guide future prevention strategies for tobacco smoking as the most preventable cause of illnesses worldwide.
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Affiliation(s)
- Zainab Awada
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Reem Akika
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Anna Luiza Silva Almeida Vicente
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France; Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Maha Makki
- Clinical Research Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hani Tamim
- Clinical Research Institute, American University of Beirut Medical Center, Beirut, Lebanon; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Khoueiry Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France.
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2
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Perez MF, Yurieva M, Poddutoori S, Mortensen EM, Crotty Alexander LE, Williams A. Transcriptomic responses in the blood and sputum of cigarette smokers compared to e-cigarette vapers. Respir Res 2023; 24:134. [PMID: 37208747 PMCID: PMC10196320 DOI: 10.1186/s12931-023-02438-x] [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: 07/14/2022] [Accepted: 04/27/2023] [Indexed: 05/21/2023] Open
Abstract
RATIONALE Electronic (e)-cigarettes are popular among youth and cigarette smokers attempting to quit. Studies to date have focused on the utility of e-cigarettes as a smoking cessation tool, but the biological effects are largely unknown. OBJECTIVES To identify transcriptomic differences in the blood and sputum of e-cigarette users compared to conventional cigarettes smokers and healthy controls and describe biological pathways affected by these tobacco products. METHODS Cross-sectional analysis of whole blood and sputum RNA-sequencing data from 8 smokers, 9 e-cigarette users (e-cigs) and 4 controls. Weighted gene co-network analysis (WGCNA) identified gene module associations. Ingenuity Pathway Analysis (IPA) identified canonical pathways associated with tobacco products. MAIN RESULTS In blood, a three-group comparison showed 16 differentially expressed genes (DEGs); pair-wise comparison showed 7 DEGs between e-cigs and controls, 35 DEGs between smokers and controls, and 13 DEGs between smokers and e-cigs. In sputum, 438 DEGs were in the three-group comparison. In pair-wise comparisons, there were 2 DEGs between e-cigs and controls, 270 DEGs between smokers and controls, and 468 DEGs between smokers and e-cigs. Only 2 genes in the smokers vs. control comparison overlapped between blood and sputum. Most gene modules identified through WGCNA associated with tobacco product exposures also were associated with cotinine and exhaled CO levels. IPA showed more canonical pathways altered by conventional cigarette smoking than by e-cigarette use. CONCLUSION Cigarette smoking and e-cigarette use led to transcriptomic changes in both blood and sputum. However, conventional cigarettes induced much stronger transcriptomic responses in both compartments.
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Affiliation(s)
- Mario F Perez
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Connecticut School of Medicine, Farmington, CT, USA.
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Eric M Mortensen
- Department of Pulmonary, Critical Care and Sleep Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Laura E Crotty Alexander
- Division of Pulmonary Critical Care, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Fernández-Carrión R, Sorlí JV, Asensio EM, Pascual EC, Portolés O, Alvarez-Sala A, Francès F, Ramírez-Sabio JB, Pérez-Fidalgo A, Villamil LV, Tinahones FJ, Estruch R, Ordovas JM, Coltell O, Corella D. DNA-Methylation Signatures of Tobacco Smoking in a High Cardiovascular Risk Population: Modulation by the Mediterranean Diet. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3635. [PMID: 36834337 PMCID: PMC9964856 DOI: 10.3390/ijerph20043635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Biomarkers based on DNA methylation are relevant in the field of environmental health for precision health. Although tobacco smoking is one of the factors with a strong and consistent impact on DNA methylation, there are very few studies analyzing its methylation signature in southern European populations and none examining its modulation by the Mediterranean diet at the epigenome-wide level. We examined blood methylation smoking signatures on the EPIC 850 K array in this population (n = 414 high cardiovascular risk subjects). Epigenome-wide methylation studies (EWASs) were performed analyzing differential methylation CpG sites by smoking status (never, former, and current smokers) and the modulation by adherence to a Mediterranean diet score was explored. Gene-set enrichment analysis was performed for biological and functional interpretation. The predictive value of the top differentially methylated CpGs was analyzed using receiver operative curves. We characterized the DNA methylation signature of smoking in this Mediterranean population by identifying 46 differentially methylated CpGs at the EWAS level in the whole population. The strongest association was observed at the cg21566642 (p = 2.2 × 10-32) in the 2q37.1 region. We also detected other CpGs that have been consistently reported in prior research and discovered some novel differentially methylated CpG sites in subgroup analyses. In addition, we found distinct methylation profiles based on the adherence to the Mediterranean diet. Particularly, we obtained a significant interaction between smoking and diet modulating the cg5575921 methylation in the AHRR gene. In conclusion, we have characterized biomarkers of the methylation signature of tobacco smoking in this population, and suggest that the Mediterranean diet can increase methylation of certain hypomethylated sites.
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Affiliation(s)
- Rebeca Fernández-Carrión
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José V. Sorlí
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eva M. Asensio
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Olga Portolés
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Andrea Alvarez-Sala
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Francesc Francès
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Alejandro Pérez-Fidalgo
- Department of Medical Oncology, University Clinic Hospital of Valencia, 46010 Valencia, Spain
- Biomedical Research Networking Centre on Cancer (CIBERONC), Health Institute Carlos III, 28029 Madrid, Spain
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Laura V. Villamil
- Department of Physiology, School of Medicine, University Antonio Nariño, Bogotá 111511, Colombia
| | - Francisco J. Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, 29590 Málaga, Spain
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Internal Medicine, Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
| | - Jose M. Ordovas
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
- Nutritional Control of the Epigenome Group, Precision Nutrition and Obesity Program, IMDEA Food, UAM + CSIC, 28049 Madrid, Spain
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain
| | - Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
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Fernández-Pérez I, Jiménez-Balado J, Lazcano U, Giralt-Steinhauer E, Rey Álvarez L, Cuadrado-Godia E, Rodríguez-Campello A, Macias-Gómez A, Suárez-Pérez A, Revert-Barberá A, Estragués-Gázquez I, Soriano-Tarraga C, Roquer J, Ois A, Jiménez-Conde J. Machine Learning Approximations to Predict Epigenetic Age Acceleration in Stroke Patients. Int J Mol Sci 2023; 24:ijms24032759. [PMID: 36769083 PMCID: PMC9917369 DOI: 10.3390/ijms24032759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Age acceleration (Age-A) is a useful tool that is able to predict a broad range of health outcomes. It is necessary to determine DNA methylation levels to estimate it, and it is known that Age-A is influenced by environmental, lifestyle, and vascular risk factors (VRF). The aim of this study is to estimate the contribution of these easily measurable factors to Age-A in patients with cerebrovascular disease (CVD), using different machine learning (ML) approximations, and try to find a more accessible model able to predict Age-A. We studied a CVD cohort of 952 patients with information about VRF, lifestyle habits, and target organ damage. We estimated Age-A using Hannum's epigenetic clock, and trained six different models to predict Age-A: a conventional linear regression model, four ML models (elastic net regression (EN), K-Nearest neighbors, random forest, and support vector machine models), and one deep learning approximation (multilayer perceptron (MLP) model). The best-performing models were EN and MLP; although, the predictive capability was modest (R2 0.358 and 0.378, respectively). In conclusion, our results support the influence of these factors on Age-A; although, they were not enough to explain most of its variability.
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Affiliation(s)
- Isabel Fernández-Pérez
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
| | - Joan Jiménez-Balado
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
- Correspondence: (J.J.-B.); (J.J.-C.)
| | - Uxue Lazcano
- Unidad de Investigación AP-OSIs Guipúzcoa, 20014 Donostia, Spain
| | - Eva Giralt-Steinhauer
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
| | - Lucía Rey Álvarez
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
| | - Elisa Cuadrado-Godia
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Ana Rodríguez-Campello
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Adrià Macias-Gómez
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
| | - Antoni Suárez-Pérez
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
| | - Anna Revert-Barberá
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
| | - Isabel Estragués-Gázquez
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
| | - Carolina Soriano-Tarraga
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jaume Roquer
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Angel Ois
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Jordi Jiménez-Conde
- Neurovascular Research Group, Department of Neurology, IMIM-Hospital del Mar (Institut Hospital del Mar d’Investigacions Mèdiques), 08003 Barcelona, Spain
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
- Correspondence: (J.J.-B.); (J.J.-C.)
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5
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Nagamatsu ST, Pietrzak RH, Xu K, Krystal JH, Gelernter J, Montalvo-Ortiz JL. Dissecting the epigenomic differences between smoking and nicotine dependence in a veteran cohort. Addict Biol 2023; 28:e13259. [PMID: 36577721 DOI: 10.1111/adb.13259] [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: 01/14/2022] [Revised: 08/26/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022]
Abstract
Smoking is a serious public health issue linked to more than 8 million deaths per year worldwide and may lead to nicotine dependence (ND). Although the epigenomic literature on smoking is well established, studies evaluating the role of epigenetics in ND are limited. In this study, we examined the epigenomic signatures of ND and how these differ from smoking exposure to identify biomarkers specific to ND. We investigated the peripheral epigenetic profile of smoking status (SS) and ND in a US male veteran cohort. DNA from saliva was collected from 1135 European American (EA) male US military veterans. DNAm was assessed using the Illumina Infinium Human MethylationEPIC BeadChip array. SS was evaluated as current smokers (n = 137; 12.1%) and non-current smokers (never and former; n = 998; 87.9%). NDFTND was assessed as a continuous variable using the Fagerström Test for ND (FTND; n = 1135; mean = 2.54 ± 2.29). Epigenome-wide association studies (EWAS) and co-methylation analyses were conducted for SS and NDFTND . A total of 450 and 22 genome-wide significant differentially methylated sites (DMS) were associated with SS and NDFTND , respectively (15 overlapped DMS). We identified 97 DMS (43 genes) in SS-EWAS previously reported in the literature, including AHRR and F2RL3 genes (p-value: 1.95 × 10-83 to 4.55 × 10-33 ). NDFTND novel DMS mapped to NEUROG1, ANPEP, and SLC29A1. Co-methylation analysis identified 386 modules (11 SS-related and 19 NDFTND -related). SS-related modules showed enrichment for alcoholism, while NDFTND -related modules were enriched for nicotine addiction. This study confirms previous findings associated with SS and identifies novel and-potentially specific-epigenetic biomarkers of ND that may inform prognosis and novel treatment strategies.
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Affiliation(s)
- Sheila Tiemi Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
| | - Robert H Pietrzak
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| | - Ke Xu
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| | - John H Krystal
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
| | - Janitza Liz Montalvo-Ortiz
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- VA CT Healthcare Center, West Haven, Connecticut, USA
- Clinical Neurosciences Division, U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder, West Haven, Connecticut, USA
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Epigenetics and Gut Microbiota Crosstalk: A potential Factor in Pathogenesis of Cardiovascular Disorders. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120798. [PMID: 36551003 PMCID: PMC9774431 DOI: 10.3390/bioengineering9120798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Cardiovascular diseases (CVD) are the leading cause of mortality, morbidity, and "sudden death" globally. Environmental and lifestyle factors play important roles in CVD susceptibility, but the link between environmental factors and genetics is not fully established. Epigenetic influence during CVDs is becoming more evident as its direct involvement has been reported. The discovery of epigenetic mechanisms, such as DNA methylation and histone modification, suggested that external factors could alter gene expression to modulate human health. These external factors also influence our gut microbiota (GM), which participates in multiple metabolic processes in our body. Evidence suggests a high association of GM with CVDs. Although the exact mechanism remains unclear, the influence of GM over the epigenetic mechanisms could be one potential pathway in CVD etiology. Both epigenetics and GM are dynamic processes and vary with age and environment. Changes in the composition of GM have been found to underlie the pathogenesis of metabolic diseases via modulating epigenetic changes in the form of DNA methylation, histone modifications, and regulation of non-coding RNAs. Several metabolites produced by the GM, including short-chain fatty acids, folates, biotin, and trimethylamine-N-oxide, have the potential to regulate epigenetics, apart from playing a vital role in normal physiological processes. The role of GM and epigenetics in CVDs are promising areas of research, and important insights in the field of early diagnosis and therapeutic approaches might appear soon.
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7
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Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics 2022; 297:1451-1466. [PMID: 35969270 DOI: 10.1007/s00438-022-01935-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
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8
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Cullell N, Soriano-Tárraga C, Gallego-Fábrega C, Cárcel-Márquez J, Torres-Águila NP, Muiño E, Lledós M, Llucià-Carol L, Esteller M, Castro de Moura M, Montaner J, Fernández-Sanlés A, Elosua R, Delgado P, Martí-Fábregas J, Krupinski J, Roquer J, Jiménez-Conde J, Fernández-Cadenas I. DNA Methylation and Ischemic Stroke Risk: An Epigenome-Wide Association Study. Thromb Haemost 2022; 122:1767-1778. [PMID: 35717949 DOI: 10.1055/s-0042-1749328] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND Ischemic stroke (IS) risk heritability is partly explained by genetics. Other heritable factors, such as epigenetics, could explain an unknown proportion of the IS risk. The objective of this study is to evaluate DNA methylation association with IS using epigenome-wide association studies (EWAS). METHODS We performed a two-stage EWAS comprising 1,156 subjects. Differentially methylated positions (DMPs) and differentially methylated regions (DMRs) were assessed using the Infinium 450K and EPIC BeadChip in the discovery cohort (252 IS and 43 controls). Significant DMPs were replicated in an independent cohort (618 IS and 243 controls). Stroke subtype associations were also evaluated. Differentially methylated cell-type (DMCT) was analyzed in the replicated CpG sites using EpiDISH. We additionally performed pathway enrichment analysis and causality analysis with Mendelian randomization for the replicated CpG sites. RESULTS A total of 957 CpG sites were epigenome-wide-significant (p ≤ 10-7) in the discovery cohort, being CpG sites in the top signals (logFC = 0.058, p = 2.35 × 10-22; logFC = 0.035, p = 3.22 × 10-22, respectively). ZFHX3 and MAP3K1 were among the most significant DMRs. In addition, 697 CpG sites were replicated considering Bonferroni-corrected p-values (p < 5.22 × 10-5). All the replicated DMPs were associated with risk of cardioembolic, atherothrombotic, and undetermined stroke. The DMCT analysis demonstrated that the significant associations were driven by natural killer cells. The pathway enrichment analysis showed overrepresentation of genes belonging to certain pathways including oxidative stress. ZFHX3 and MAP3K1 methylation was causally associated with specific stroke-subtype risk. CONCLUSION Specific DNA methylation pattern is causally associated with IS risk. These results could be useful for specifically predicting stroke occurrence and could potentially be evaluated as therapeutic targets.
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Affiliation(s)
- Natalia Cullell
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain.,Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Carolina Soriano-Tárraga
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain.,Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, Missouri, United States
| | | | - Jara Cárcel-Márquez
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Nuria P Torres-Águila
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Evolutionary Developmental Genomics Research Group, The Scottish Oceans Institute, University of St Andrews, St Andrews, United Kingdom
| | - Elena Muiño
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Miquel Lledós
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Laia Llucià-Carol
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Centro de Investigación Biomédica en Red Cancer, Barcelona, Spain
| | | | - Joan Montaner
- Department of Neurology, Hospital Universitario Virgen Macarena, Institute of Biomedicine of Seville/Hospital Universitario Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain.,CIBER Cardiovascular Diseases, Instituto Carlos III, Barcelona, Spain.,School of Medicine, University of Vic-Central University of Catalonia, Barcelona, Spain
| | - Pilar Delgado
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Barcelona, Spain
| | - Joan Martí-Fábregas
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jerzy Krupinski
- Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain.,Centre for Bioscience, School of HealthCare Science, Manchester Metropolitan University, Manchester, England
| | - Jaume Roquer
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Jiménez-Conde
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Israel Fernández-Cadenas
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain
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9
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Do WL, Gohar J, McCullough LE, Galaviz KI, Conneely KN, Narayan KMV. Examining the association between adiposity and DNA methylation: A systematic review and meta-analysis. Obes Rev 2021; 22:e13319. [PMID: 34278703 DOI: 10.1111/obr.13319] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/26/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022]
Abstract
Obesity is associated with widespread differential DNA methylation (DNAm) patterns, though there have been limited overlap in the obesity-associated cytosine-guanine nucleotide pair (CpG) sites that have been identified in the literature. We systematically searched four databases for studies published until January 2020. Eligible studies included cross-sectional, longitudinal, or intervention studies examining adiposity and genome-wide DNAm in non-pregnant adults aged 18-75 in all tissue types. Study design and results were extracted in the descriptive review. Blood-based DNAm results in body mass index (BMI) and waist circumference (WC) were meta-analyzed using weighted sum of Z-score meta-analysis. Of the 10,548 studies identified, 46 studies were included in the systematic review with 18 and nine studies included in the meta-analysis of BMI and WC, respectively. In the blood, 77 and four CpG sites were significant in three or more studies of BMI and WC, respectively. Using a genome-wide threshold for significance, 52 blood-based CpG sites were significantly associated with BMI. These sites have previously been associated with many obesity-related diseases including type 2 diabetes, cardiovascular disease, Crohn's disease, and depression. Our study shows that DNAm at 52 CpG sites represent potential mediators of obesity-associated chronic diseases and may be novel intervention or therapeutic targets to protect against obesity-associated chronic diseases.
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Affiliation(s)
- Whitney L Do
- Nutrition and Health Sciences Program, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Jazib Gohar
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Lauren E McCullough
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Karla I Galaviz
- Department of Applied Health Science, School of Public Health, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - K M Venkat Narayan
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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10
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Kucher AN, Babushkina NP, Sleptcov AA, Nazarenko MS. Genetic Control of Human Infection with SARS-CoV-2. RUSS J GENET+ 2021; 57:627-641. [PMID: 34248311 PMCID: PMC8254434 DOI: 10.1134/s1022795421050057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/26/2020] [Accepted: 08/25/2020] [Indexed: 01/21/2023]
Abstract
In 2019, the SARS-CoV-2 beta-coronavirus, which caused a pandemic of severe acute respiratory viral infection COVID-19 (from COronaVIrus Disease 2019), was first detected. The susceptibility to SARS-CoV-2 and the nature of the course of the COVID-19 clinical picture are determined by many factors, including genetic characteristics of both the pathogen and the human. The SARS-CoV-2 genome has a similarity to the genomes of other coronaviruses, which are pathogenic for humans and cause a severe course of infection: 79% to the SARS-CoV genome and 50% to the MERS-CoV genome. The most significant differences between SARS-CoV-2 and other coronaviruses are recorded in the structure of the gene of the S protein, a key protein responsible for the virus binding to the receptor of the host organism cells. In particular, substitutions in the S protein of SARS-CoV-2, leading to the formation of the furin cleavage site that is absent in other SARS-like coronaviruses, were identified, which may explain the high pathogenicity of SARS-CoV-2. In humans, the genes that are significant for the initial stages of infection include ACE2, ANPEP, DPP4 (encode receptors for coronavirus binding); TMPRSS2, FURIN, TMPRSS11D, CTSL, CTSB (encode proteases involved in the entry of the coronavirus into the cell); DDX1 (the gene of ATP-dependent RNA helicase DDX1, which promotes replication of coronaviruses); and IFITM1, IFITM2, and IFITM3 (encode interferon-induced transmembrane proteins with an antiviral effect). These genes are expressed in many tissues (including those susceptible to the effects of SARS-CoV-2); rare and frequent variants that affect the structure of the encoded protein and its properties and expression level are described in them. A number of common genetic variants with proven functional significance are characterized by the variability in the allele frequency in the world's populations, which can determine interpopulation differences in the prevalence of COVID-19 and in the clinical features of the course of this pathology. The expression level of genes that are important for the formation of the susceptibility to SARS-CoV-2 is affected by epigenetic modifications, comorbidities at the time of infection, taking medications, and bad habits.
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Affiliation(s)
- A. N. Kucher
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - N. P. Babushkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - A. A. Sleptcov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - M. S. Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
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11
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Xiao C, Yi S, Huang D. Genome-wide identification of age-related CpG sites for age estimation from blood DNA of Han Chinese individuals. Electrophoresis 2021; 42:1488-1496. [PMID: 33978960 DOI: 10.1002/elps.202000367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/07/2021] [Accepted: 05/05/2021] [Indexed: 11/11/2022]
Abstract
Age-related CpG (AR-CpG) sites are currently the most promising molecular markers for forensic age estimation. However, the AR-CpG sites of Han Chinese population remains to be systematically characterized. In this study, we performed genome-wide methylation analyses on 42 whole blood DNA from healthy Han Chinese volunteers (aged from 18 to 62 years) using the Illumina MethylationEPIC BeadChip microarray. As expected, both known and novel AR-CpG sites were identified. Considering the sex difference in aging rate, we then separately selected AR-CpG candidates and built pyrosequencing-based multiple linear regression models for age estimation of males and females. The model constructed from the male sample group (n = 167, aged from 1.50 to 85.71 years) explained 95.22% of variation in age using five AR-CpG sites (chr6:11044864 ELOVL2, chr1:207997068 C1orf132, cg19283806 CCDC102B, cg17740900, and chr10:73740306 CHST3) and yielded a mean absolute error (MAE) of 2.79 years. The model constructed from the female sample group (n = 141, aged from 3.33 to 80.38 years) explained 94.90% of variation in age with six AR-CpG sites (chr6:11044867 ELOVL2, chr1:207997060 C1orf132, chr2:106015757 FHL2, cg26947034, chr16: 67184108 B3GNT9, and chr20:44658203 SLC12A5) and yielded an MAE of 2.53 years. Besides, the estimated age was highly correlated with the actual age (R > 0.97). The robustness of these AR-CpG markers was demonstrated by 10-fold cross-validations. In conclusion, we updated the AR-CpG sites of Han Chinese population and provided two sets of AR-CpG sites for accurate age estimation.
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Affiliation(s)
- Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, P. R. China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, P. R. China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, P. R. China
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12
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Koo HK, Morrow J, Kachroo P, Tantisira K, Weiss ST, Hersh CP, Silverman EK, DeMeo DL. Sex-specific associations with DNA methylation in lung tissue demonstrate smoking interactions. Epigenetics 2021; 16:692-703. [PMID: 32962511 PMCID: PMC8143227 DOI: 10.1080/15592294.2020.1819662] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/08/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cigarette smoking impacts DNA methylation, but the investigation of sex-specific features of lung tissue DNA methylation in smokers has been limited. Women appear more susceptible to cigarette smoke, and often develop more severe lung disease at an earlier age with less smoke exposure. We aimed to analyse whether there are sex differences in DNA methylation in lung tissue and whether these DNA methylation marks interact with smoking. We collected lung tissue samples from former smokers who underwent lung tissue resection. One hundred thirty samples from white subjects were included for this analysis. Regression models for sex as a predictor of methylation were adjusted for age, presence of COPD, smoking variables and technical batch variables revealed 710 associated sites. 294 sites demonstrated robust sex-specific methylation associations in foetal lung tissue. Pathway analysis identified 6 nominally significant pathways including the mitophagy pathway. Three CpG sites demonstrated a suggested interaction between sex and pack-years of smoking: GPR132, ANKRD44 and C19orf60. All of them were nominally significant in both male- and female-specific models, and the effect estimates were in opposite directions for male and female; GPR132 demonstrated significant association between DNA methylation and gene expression in lung tissue (P < 0.05). Sex-specific associations with DNA methylation in lung tissue are wide-spread and may reveal genes and pathways relevant to sex differences for lung damaging effects of cigarette smoking.
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Affiliation(s)
- Hyeon-Kyoung Koo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Ilsan Paik Hospital, Inje University College of Medicine, Ilsan, Republic of Korea
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
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13
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Fernández-Sanlés A, Sayols-Baixeras S, Subirana I, Sentí M, Pérez-Fernández S, de Castro Moura M, Esteller M, Marrugat J, Elosua R. DNA methylation biomarkers of myocardial infarction and cardiovascular disease. Clin Epigenetics 2021; 13:86. [PMID: 33883000 PMCID: PMC8061080 DOI: 10.1186/s13148-021-01078-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The epigenetic landscape underlying cardiovascular disease (CVD) is not completely understood and the clinical value of the identified biomarkers is still limited. We aimed to identify differentially methylated loci associated with acute myocardial infarction (AMI) and assess their validity as predictive and causal biomarkers. RESULTS We designed a case-control, two-stage, epigenome-wide association study on AMI (ndiscovery = 391, nvalidation = 204). DNA methylation was assessed using the Infinium MethylationEPIC BeadChip. We performed a fixed-effects meta-analysis of the two samples. 34 CpGs were associated with AMI. Only 12 of them were available in two independent cohort studies (n ~ 1800 and n ~ 2500) with incident coronary and cardiovascular disease (CHD and CVD, respectively). The Infinium HumanMethylation450 BeadChip was used in those two studies. Four of the 12 CpGs were validated in association with incident CHD: AHRR-mapping cg05575921, PTCD2-mapping cg25769469, intergenic cg21566642 and MPO-mapping cg04988978. We then assessed whether methylation risk scores based on those CpGs improved the predictive capacity of the Framingham risk function, but they did not. Finally, we aimed to study the causality of those associations using a Mendelian randomization approach but only one of the CpGs had a genetic influence and therefore the results were not conclusive. CONCLUSIONS We have identified 34 CpGs related to AMI. These loci highlight the relevance of smoking, lipid metabolism, and inflammation in the biological mechanisms related to AMI. Four were additionally associated with incident CHD and CVD but did not provide additional predictive information.
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Affiliation(s)
- Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003, Barcelona, Catalonia, Spain.,Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain.,Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003, Barcelona, Catalonia, Spain.,CIBER Cardiovascular Diseases (CIBERCV), Madrid, Spain.,Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Isaac Subirana
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003, Barcelona, Catalonia, Spain.,CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Mariano Sentí
- Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain
| | - S Pérez-Fernández
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003, Barcelona, Catalonia, Spain.,CIBER Cardiovascular Diseases (CIBERCV), Madrid, Spain
| | | | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Catalonia, Spain.,CIBER Oncology (CIBERONC), Madrid, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Jaume Marrugat
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003, Barcelona, Catalonia, Spain.,CIBER Cardiovascular Diseases (CIBERCV), Madrid, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003, Barcelona, Catalonia, Spain. .,CIBER Cardiovascular Diseases (CIBERCV), Madrid, Spain. .,Medicine Department, Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Catalonia, Spain.
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14
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Silva CP, Kamens HM. Cigarette smoke-induced alterations in blood: A review of research on DNA methylation and gene expression. Exp Clin Psychopharmacol 2021; 29:116-135. [PMID: 32658533 PMCID: PMC7854868 DOI: 10.1037/pha0000382] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Worldwide, smoking remains a threat to public health, causing preventable diseases and premature mortality. Cigarette smoke is a powerful inducer of DNA methylation and gene expression alterations, which have been associated with negative health consequences. Here, we review the current knowledge on smoking-related changes in DNA methylation and gene expression in human blood samples. We identified 30 studies focused on the association between active smoking, DNA methylation modifications, and gene expression alterations. Overall, we identified 1,758 genes with differentially methylated sites (DMS) and differentially expressed genes (DEG) between smokers and nonsmokers, of which 261 were detected in multiple studies (≥4). The most frequently (≥10 studies) reported genes were AHRR, GPR15, GFI1, and RARA. Functional enrichment analysis of the 261 genes identified the aryl hydrocarbon receptor repressor and T cell pathways (T helpers 1 and 2) as influenced by smoking status. These results highlight specific genes for future mechanistic and translational research that may be associated with cigarette smoke exposure and smoking-related diseases. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
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Affiliation(s)
- Constanza P. Silva
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States of America
| | - Helen M. Kamens
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States of America.,Correspondence concerning this article should be addressed to Helen M. Kamens, 228 Biobehavioral Health Building, The Pennsylvania State University, University Park, PA 16802; ; Phone number: 814-865-1269; Fax number: 814-863-7525
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15
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Mulder RH, Neumann A, Cecil CAM, Walton E, Houtepen LC, Simpkin AJ, Rijlaarsdam J, Heijmans BT, Gaunt TR, Felix JF, Jaddoe VWV, Bakermans-Kranenburg MJ, Tiemeier H, Relton CL, van IJzendoorn MH, Suderman M. Epigenome-wide change and variation in DNA methylation in childhood: trajectories from birth to late adolescence. Hum Mol Genet 2021; 30:119-134. [PMID: 33450751 PMCID: PMC8033147 DOI: 10.1093/hmg/ddaa280] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/03/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
DNA methylation (DNAm) is known to play a pivotal role in childhood health and development, but a comprehensive characterization of genome-wide DNAm trajectories across this age period is currently lacking. We have therefore performed a series of epigenome-wide association studies in 5019 blood samples collected at multiple time-points from birth to late adolescence from 2348 participants of two large independent cohorts. DNAm profiles of autosomal CpG sites (CpGs) were generated using the Illumina Infinium HumanMethylation450 BeadChip. Change over time was widespread, observed at over one-half (53%) of CpGs. In most cases, DNAm was decreasing (36% of CpGs). Inter-individual variation in linear trajectories was similarly widespread (27% of CpGs). Evidence for non-linear change and inter-individual variation in non-linear trajectories was somewhat less common (11 and 8% of CpGs, respectively). Very little inter-individual variation in change was explained by sex differences (0.4% of CpGs) even though sex-specific DNAm was observed at 5% of CpGs. DNAm trajectories were distributed non-randomly across the genome. For example, CpGs with decreasing DNAm were enriched in gene bodies and enhancers and were annotated to genes enriched in immune-developmental functions. In contrast, CpGs with increasing DNAm were enriched in promoter regions and annotated to genes enriched in neurodevelopmental functions. These findings depict a methylome undergoing widespread and often non-linear change throughout childhood. They support a developmental role for DNA methylation that extends beyond birth into late adolescence and has implications for understanding life-long health and disease. DNAm trajectories can be visualized at http://epidelta.mrcieu.ac.uk.
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Affiliation(s)
- Rosa H Mulder
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Institute of Education and Child Studies, Leiden University, Leiden, The Netherlands
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Psychology, Institute of Psychology, Psychiatry and Neuroscience, King's College London, London, UK
| | - Esther Walton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,Department of Psychology, University of Bath, Bath, UK
| | - Lotte C Houtepen
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew J Simpkin
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Jolien Rijlaarsdam
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Social and Behavioral Science, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, The Netherlands.,School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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16
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Current status of development of methylation biomarkers for in vitro diagnostic IVD applications. Clin Epigenetics 2020; 12:100. [PMID: 32631437 PMCID: PMC7336678 DOI: 10.1186/s13148-020-00886-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
A significant volume of research clearly shows that disease-related methylation changes can be used as biomarkers at all stages of clinical disease management, including risk assessment and predisposition screening through early diagnostics to personalization of patient care and monitoring of the relapse and chronic disease. Thus disease-related methylation changes are an attractive source of the biomarkers that can have significant impact on precision medicine. However, the translation of the research findings in methylation biomarkers field to clinical practice is at the very least not satisfactory. That is mainly because the evidence generated in research studies indicating the utility of the disease-related methylation change to predict clinical outcome is in majority of the cases not sufficient to postulate the diagnostic use of the biomarker. The research studies need to be followed by well-designed and systematic investigations of clinical utility of the biomarker that produce data of sufficient quality to meet regulatory approval for the test to be used to make clinically valid decision. In this review, we describe methylation-based IVD tests currently approved for IVD use or at the advanced stages of the development for the diagnostic use. For each of those tests, we analyze the technologies that the test utilizes for methylation detection as well as describe the types of the clinical studies that were performed to show clinical validity of the test and warrant regulatory approval. The examples reviewed here should help with planning of clinical investigations and delivery of the clinical evidence required for the regulatory approval of potential methylation biomarker based IVD tests.
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17
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Andersson C, Lin H, Liu C, Levy D, Mitchell GF, Larson MG, Vasan RS. Integrated Multiomics Approach to Identify Genetic Underpinnings of Heart Failure and Its Echocardiographic Precursors. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 12:e002489. [DOI: 10.1161/circgen.118.002489] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background:
Heart failure (HF) may arise from alterations in metabolic, structural, and signaling pathways, but its genetic architecture is incompletely understood. To elucidate potential genetic contributors to cardiac remodeling and HF, we integrated genome-wide single-nucleotide polymorphisms, gene expression, and DNA methylation using a transomics analytical approach.
Methods:
We used robust rank aggregation (where the position of a certain gene in a rank order list [based on statistical significance level] is tested against a randomly shuffled rank order list) to derive an integrative transomic score for each annotated gene associated with a HF trait.
Results:
We evaluated ≤8372 FHS (Framingham Heart Study) participants (54% women; mean age, 55±17 years). Of these, 62 (0.7%) and 35 (0.4%) had prevalent HF with reduced ejection fraction and HF with preserved left ventricular ejection fraction, respectively. During a mean follow-up of 8.5 years (minimum–maximum, 0.005–18.6 years), 223 (2.7%) and 234 (2.8%) individuals developed incident HF with reduced ejection fraction and HF with reduced ejection fraction, respectively. Top genes included
MMP20
and
MTSS1
(promotes actin assembly at intercellular junctions) for left ventricular systolic function;
ITGA9
(receptor for
VCAM1
[vascular cell protein 1]) and
C5
for left ventricular remodeling;
NUP210
(expressed during myogenic differentiation) and
ANK1
(cytoskeletal protein) for diastolic function;
TSPAN16
and
RAB11FIP3
(involved in regulation of actin cytoskeleton) for prevalent HF with reduced ejection fraction;
ANKRD13D
and
TRIM69
for incident HF with reduced ejection fraction;
HPCAL1
and
PTTG1IP
for prevalent HF with reduced ejection fraction; and
ZNF146
(close to the
COX7A1
enzyme) and
ZFP3
(close to
SLC52A1
—the riboflavin transporter) for incident HF with reduced ejection fraction. We tested the HF-related top single-nucleotide polymorphisms in the UK biobank, where
rs77059055
in
TPM1
(minor allele frequency, 0.023; odds ratio, 0.83;
P
=0.002) remained statistically significant upon Bonferroni correction.
Conclusions:
Our integrative transomics approach offers insights into potential molecular and genetic contributors to HF and its precursors. Although several of our candidate genes have been implicated in HF in animal models, independent replication is warranted.
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Affiliation(s)
- Charlotte Andersson
- Framingham Heart Study, MA (C.A., H.L., C.L., D.L., M.G.L., R.S.V.)
- Department of Cardiology, Herlev and Gentofte Hospital, Herlev, Denmark (C.A.)
| | - Honghuang Lin
- Framingham Heart Study, MA (C.A., H.L., C.L., D.L., M.G.L., R.S.V.)
- Section of Computational Biomedicine, Department of Medicine (H.L.), Boston University School of Medicine, MA
| | - Chunyu Liu
- Framingham Heart Study, MA (C.A., H.L., C.L., D.L., M.G.L., R.S.V.)
- Department of Biostatistics (C.L., M.G.L.), Boston University School of Public Health, MA
| | - Daniel Levy
- Framingham Heart Study, MA (C.A., H.L., C.L., D.L., M.G.L., R.S.V.)
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD (D.L.)
| | | | - Martin G. Larson
- Framingham Heart Study, MA (C.A., H.L., C.L., D.L., M.G.L., R.S.V.)
- Department of Biostatistics (C.L., M.G.L.), Boston University School of Public Health, MA
| | - Ramachandran S. Vasan
- Framingham Heart Study, MA (C.A., H.L., C.L., D.L., M.G.L., R.S.V.)
- Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine (R.S.V.), Boston University School of Medicine, MA
- Department of Epidemiology (R.S.V.), Boston University School of Public Health, MA
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18
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Fernández-Sanlés A, Sayols-Baixeras S, Castro DE Moura M, Esteller M, Subirana I, Torres-Cuevas S, Pérez-Fernández S, Aslibekyan S, Marrugat J, Elosua R. Physical Activity and Genome-wide DNA Methylation: The REgistre GIroní del COR Study. Med Sci Sports Exerc 2019; 52:589-597. [PMID: 31652233 DOI: 10.1249/mss.0000000000002174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION DNA methylation may be one of the biological mechanisms underlying the health benefits of physical activity (PA). Our objective was to determine the association between PA and genome-wide DNA methylation at CpG level. METHODS We designed a two-stage epigenome wide association study. In the discovery stage, we used 619 individuals from the REgistre GIroní del COR cohort. Next, we validated the CpG suggestively associated with PA (P < 10) in two independent populations (n = 1735 and 190, respectively). Physical activity was assessed with validated questionnaires and classified as light PA (LPA), moderate PA, vigorous PA, moderate-vigorous PA (MVPA) and total PA. We examined linear and nonlinear associations and meta-analyzed the results in the three populations. The linear associations were meta-analyzed with a fixed-effects model and the P values of the nonlinear associations with the Stouffer and Fisher methods. We established a P value threshold that fulfilled Bonferroni criteria over the number of CpG analyzed (0.05/421,940 = 1.185 × 10). RESULTS In the meta-analyses, two CpG sites had a statistically significant nonlinear association with MVPA. cg24155427 (P = 1.19 × 10), located in an intergenic region in chromosome 1, has been previously associated with smoking, lupus, and aging. cg09565397 (P = 1.59 × 10), located within DGAT1 in chromosome 8, which encodes an enzyme involved in triacylglycerol synthesis. CONCLUSIONS This population-based study identified two new, differentially methylated CpG sites with a nonlinear dose-response relationship to MVPA. These associations must be additionally validated and may be considered for further research on the biological mechanisms underlying health benefits of PA.
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Affiliation(s)
| | | | - Manuel Castro DE Moura
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, SPAIN
| | | | | | | | | | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
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19
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Epigenome-wide association study of depression symptomatology in elderly monozygotic twins. Transl Psychiatry 2019; 9:214. [PMID: 31477683 PMCID: PMC6718679 DOI: 10.1038/s41398-019-0548-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 02/15/2019] [Accepted: 06/20/2019] [Indexed: 12/11/2022] Open
Abstract
Depression is a severe and debilitating mental disorder diagnosed by evaluation of affective, cognitive and physical depression symptoms. Severity of these symptoms strongly impacts individual's quality of life and is influenced by a combination of genetic and environmental factors. One of the molecular mechanisms allowing for an interplay between these factors is DNA methylation, an epigenetic modification playing a pivotal role in regulation of brain functioning across lifespan. The aim of this study was to investigate if there are DNA methylation signatures associated with depression symptomatology in order to identify molecular mechanisms contributing to pathophysiology of depression. We performed an epigenome-wide association study (EWAS) of continuous depression symptomatology score measured in a cohort of 724 monozygotic Danish twins (346 males, 378 females). Through EWAS analyses adjusted for sex, age, flow-cytometry based blood cell composition, and twin relatedness structure in the data we identified depression symptomatology score to be associated with blood DNA methylation levels in promoter regions of neuropsin (KLK8, p-value = 4.7 × 10-7) and DAZ associated protein 2 (DAZAP2, p-value = 3.13 × 10-8) genes. Other top associated probes were located in gene bodies of MAD1L1 (p-value = 5.16 × 10-6), SLC29A2 (p-value = 6.15 × 10-6) and AKT1 (p-value = 4.47 × 10-6), all genes associated before with development of depression. Additionally, the following three measures (a) DNAmAge (calculated with Horvath and Hannum epigenetic clock estimators) adjusted for chronological age, (b) difference between DNAmAge and chronological age, and (c) DNAmAge acceleration were not associated with depression symptomatology score in our cohort. In conclusion, our data suggests that depression symptomatology score is associated with DNA methylation levels of genes implicated in response to stress, depressive-like behaviors, and recurrent depression in patients, but not with global DNA methylation changes across the genome.
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20
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Sayols-Baixeras S, Fernández-Sanlés A, Prats-Uribe A, Subirana I, Plusquin M, Künzli N, Marrugat J, Basagaña X, Elosua R. Association between long-term air pollution exposure and DNA methylation: The REGICOR study. ENVIRONMENTAL RESEARCH 2019; 176:108550. [PMID: 31260916 DOI: 10.1016/j.envres.2019.108550] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 05/17/2023]
Abstract
INTRODUCTION Limited evidence suggests that epigenetic mechanisms may partially mediate the adverse effects of air pollution on health. Our aims were to identify new genomic loci showing differential DNA methylation associated with long-term exposure to air pollution and to replicate loci previously identified in other studies. METHODS A two-stage epigenome-wide association study was designed: 630 individuals from the REGICOR study were included in the discovery and 454 participants of the EPIC-Italy study in the validation stage. DNA methylation was assessed using the Infinium HumanMethylation450 BeadChip. NOX, NO2, PM10, PM2.5, PMcoarse, traffic intensity and traffic load exposure were measured according to the ESCAPE protocol. A systematic review was undertaken to identify those cytosine-phosphate-guanine (CpGs) associated with air pollution in previous studies and we screened for them in the discovery study. RESULTS In the discovery stage of the epigenome-wide association study, 81 unique CpGs were associated with air pollution (p-value <10-5) but none of them were validated in the replication sample. Furthermore, we identified 15 CpGs in the systematic review showing differential methylation with a p-value fulfilling the Bonferroni criteria and 1673 CpGs fulfilling the false discovery rate criteria, all of which were related to PM2.5 or NO2. None of them was replicated in the discovery study, in which the top hits were located in an intergenic region on chromosome 1 (cg10893043, p-value = 6.79·10-5) and in the LRRC45 and PXK genes (cg05088605, p-value = 2.15·10-04; cg16560256, p-value = 2.23·10-04). CONCLUSIONS Neither new genomic loci associated with long-term air pollution were identified, nor previously identified loci were replicated. Continued efforts to test this potential association are warranted.
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Affiliation(s)
- Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Albert Prats-Uribe
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Preventive Medicine and Public Health Training Unit, Parc de Salut Mar-Universitat Pompeu Fabra-Agència de Salut Pública de Barcelona (UDMPiSP PSMar-UPF-ASPB), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Isaac Subirana
- CIBER Epidemiology and Public Health (CIBERESP), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Michelle Plusquin
- Department of Epidemiology and Biostatics, The School of Public Health, Imperial College London, Medical School Building, St Mary's Hospital, Norfolk Place, London, W2 1PG, United Kingdom; Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, St Mary's Campus, Imperial College, Paddington, London, W2 1PG, United Kingdom; Centre for Environmental Sciences, Hasselt University, Campus Hasselt, Martelarenlaan 42, BE3500, Hasselt, Belgium
| | - Nino Künzli
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland; University of Basel, Klingelbergstrasse 61, 4056, Basel, Switzerland
| | - Jaume Marrugat
- REGICOR Research Group, IMIM (Hospital del Mar Medical Research Institute), DR Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Xavier Basagaña
- ISGlobal (Institute for Global Health), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Epidemiology and Public Health (CIBERESP), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Carretera de Roda 70, 08500 Vic, Catalonia, Spain.
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21
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Richter GM, Kruppa J, Munz M, Wiehe R, Häsler R, Franke A, Martins O, Jockel-Schneider Y, Bruckmann C, Dommisch H, Schaefer AS. A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers. Clin Epigenetics 2019; 11:105. [PMID: 31331382 PMCID: PMC6647091 DOI: 10.1186/s13148-019-0697-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/18/2019] [Indexed: 01/08/2023] Open
Abstract
Background The oral mucosa has an important role in maintaining barrier integrity at the gateway to the gastrointestinal and respiratory tracts. Smoking is a strong environmental risk factor for the common oral inflammatory disease periodontitis and oral cancer. Cigarette smoke affects gene methylation and expression in various tissues. This is the first epigenome-wide association study (EWAS) that aimed to identify biologically active methylation marks of the oral masticatory mucosa that are associated with smoking. Results Ex vivo biopsies of 18 current smokers and 21 never smokers were analysed with the Infinium Methylation EPICBeadChip and combined with whole transcriptome RNA sequencing (RNA-Seq; 16 mio reads per sample) of the same samples. We analysed the associations of CpG methylation values with cigarette smoking and smoke pack year (SPY) levels in an analysis of covariance (ANCOVA). Nine CpGs were significantly associated with smoking status, with three CpGs mapping to the genetic region of CYP1B1 (cytochrome P450 family 1 subfamily B member 1; best p = 5.5 × 10−8) and two mapping to AHRR (aryl-hydrocarbon receptor repressor; best p = 5.9 × 10−9). In the SPY analysis, 61 CpG sites at 52 loci showed significant associations of the quantity of smoking with changes in methylation values. Here, the most significant association located to the gene CYP1B1, with p = 4.0 × 10−10. RNA-Seq data showed significantly increased expression of CYP1B1 in smokers compared to non-smokers (p = 2.2 × 10−14), together with 13 significantly upregulated transcripts. Six transcripts were significantly downregulated. No differential expression was observed for AHRR. In vitro studies with gingival fibroblasts showed that cigarette smoke extract directly upregulated the expression of CYP1B1. Conclusion This study validated the established role of CYP1B1 and AHRR in xenobiotic metabolism of tobacco smoke and highlights the importance of epigenetic regulation for these genes. For the first time, we give evidence of this role for the oral masticatory mucosa. Electronic supplementary material The online version of this article (10.1186/s13148-019-0697-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gesa M Richter
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Aßmannshauser Str. 4-6, 14197, Berlin, Germany.
| | - Jochen Kruppa
- Institute for Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Matthias Munz
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Aßmannshauser Str. 4-6, 14197, Berlin, Germany.,Medical Systems Biology Group, Institute of Experimental Dermatology, Institute for Cardiogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Ricarda Wiehe
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Aßmannshauser Str. 4-6, 14197, Berlin, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Orlando Martins
- Institute of Periodontology, Dentistry Department, Faculty of Medicine, University of Coimbra, Av. Bissaya Barreto, Bloco de Celas, 3000-075, Coimbra, Portugal
| | - Yvonne Jockel-Schneider
- Department of Periodontology, Clinic of Preventive Dentistry and Periodontology, University Medical Center of the Julius-Maximilians-University, Pleicherwall, 97070, Würzburg, Germany
| | - Corinna Bruckmann
- Department of Conservative Dentistry and Periodontology, Medical University Vienna, School of Dentistry, Sensengasse 2a, 1090, Vienna, Austria
| | - Henrik Dommisch
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Aßmannshauser Str. 4-6, 14197, Berlin, Germany
| | - Arne S Schaefer
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Aßmannshauser Str. 4-6, 14197, Berlin, Germany
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22
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Freudenheim JL, Shields PG, Song MA, Smiraglia D. DNA Methylation and Smoking: Implications for Understanding Effects of Electronic Cigarettes. CURR EPIDEMIOL REP 2019. [DOI: 10.1007/s40471-019-00191-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Fragou D, Pakkidi E, Aschner M, Samanidou V, Kovatsi L. Smoking and DNA methylation: Correlation of methylation with smoking behavior and association with diseases and fetus development following prenatal exposure. Food Chem Toxicol 2019; 129:312-327. [PMID: 31063835 DOI: 10.1016/j.fct.2019.04.059] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Among epigenetic mechanisms, DNA methylation has been widely studied with respect to many environmental factors. Smoking is a common factor which affects both global and gene-specific DNA methylation. It is supported that smoking directly affects DNA methylation, and these effects contribute to the development and progression of various diseases, such as cancer, lung and cardiovascular diseases and male infertility. In addition, prenatal smoking influences the normal development of the fetus via DNA methylation changes. The DNA methylation profile and its smoking-induced alterations helps to distinguish current from former smokers and non-smokers and can be used to predict the risk for the development of a disease. This review summarizes the DNA methylation changes induced by smoking, their correlation with smoking behavior and their association with various diseases and fetus development.
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Affiliation(s)
- Domniki Fragou
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece
| | - Eleni Pakkidi
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece
| | - Michael Aschner
- Departments of Molecular Pharmacology, Neuroscience, and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Victoria Samanidou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece.
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24
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Gupta R, van Dongen J, Fu Y, Abdellaoui A, Tyndale RF, Velagapudi V, Boomsma DI, Korhonen T, Kaprio J, Loukola A, Ollikainen M. Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci. Clin Epigenetics 2019; 11:1. [PMID: 30611298 PMCID: PMC6321663 DOI: 10.1186/s13148-018-0606-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/21/2018] [Indexed: 01/10/2023] Open
Abstract
Background DNA methylation alteration extensively associates with smoking and is a plausible link between smoking and adverse health. We examined the association between epigenome-wide DNA methylation and serum cotinine levels as a proxy of nicotine exposure and smoking quantity, assessed the role of SNPs in these associations, and evaluated molecular mediation by methylation in a sample of biochemically verified current smokers (N = 310). Results DNA methylation at 50 CpG sites was associated (FDR < 0.05) with cotinine levels, 17 of which are novel associations. As cotinine levels are influenced not only by nicotine intake but also by CYP2A6-mediated nicotine metabolism rate, we performed secondary analyses adjusting for genetic risk score of nicotine metabolism rate and identified five additional novel associations. We further assessed the potential role of genetic variants in the detected association between methylation and cotinine levels observing 124 cis and 3898 trans methylation quantitative trait loci (meQTLs). Nineteen of these SNPs were also associated with cotinine levels (FDR < 0.05). Further, at seven CpG sites, we observed a trend (P < 0.05) that altered DNA methylation mediates the effect of SNPs on nicotine exposure rather than a direct consequence of smoking. Finally, we performed replication of our findings in two independent cohorts of biochemically verified smokers (N = 450 and N = 79). Conclusions Using cotinine, a biomarker of nicotine exposure, we replicated and extended identification of novel epigenetic associations in smoking-related genes. We also demonstrated that DNA methylation in some of the identified loci is driven by the underlying genotype and may mediate the causal effect of genotype on cotinine levels. Electronic supplementary material The online version of this article (10.1186/s13148-018-0606-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richa Gupta
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Yu Fu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Abdel Abdellaoui
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, and Departments of Pharmacology & Toxicology and Psychiatry, University of Toronto, Toronto, Canada
| | - Vidya Velagapudi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Tellervo Korhonen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
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25
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Prince C, Hammerton G, Taylor AE, Anderson EL, Timpson NJ, Davey Smith G, Munafò MR, Relton CL, Richmond RC. Investigating the impact of cigarette smoking behaviours on DNA methylation patterns in adolescence. Hum Mol Genet 2019; 28:155-165. [PMID: 30215712 PMCID: PMC6298233 DOI: 10.1093/hmg/ddy316] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/02/2018] [Accepted: 09/03/2018] [Indexed: 01/09/2023] Open
Abstract
Smoking usually begins in adolescence, and early onset of smoking has been linked to increased risk of later life disease. There is a need to better understand the biological impact of cigarette smoking behaviours in adolescence. DNA methylation profiles related to smoking behaviours and cessation in adulthood have been previously identified, but alterations arising from smoking initiation have not been thoroughly investigated. We aimed to investigate DNA methylation in the Avon Longitudinal Study of Parents and Children in relation to (1) different smoking measures, (2) time since smoking initiation and frequency of smoke exposure and (3) latent classes of smoking behaviour. Using 2620 CpG sites previously associated with cigarette smoking, we investigated DNA methylation change in relation to own smoking measures, smoke exposure duration and frequency, and using longitudinal latent class analysis of different smoking behaviour patterns in 968 adolescents. Eleven CpG sites located in seven gene regions were differentially methylated in relation to smoking in adolescence. While only AHRR (cg05575921) showed a robust pattern of methylation in relation to weekly smoking, several CpGs showed differences in methylation among individuals who had tried smoking compared with non-smokers. In relation to smoke exposure duration and frequency, cg05575921 showed a strong dose-response relationship, while there was evidence for more immediate methylation change at other sites. Our findings illustrate the impact of cigarette smoking behaviours on DNA methylation at some smoking-responsive CpG sites, even among individuals with a short smoking history.
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Affiliation(s)
| | - Gemma Hammerton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Amy E Taylor
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Emma L Anderson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Nicholas J Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - George Davey Smith
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Tobacco and Alcohol Research Group, School of Experimental Psychology, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Rebecca C Richmond
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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26
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Murphy SE, Park SL, Balbo S, Haiman CA, Hatsukami DK, Patel Y, Peterson LA, Stepanov I, Stram DO, Tretyakova N, Hecht SS, Le Marchand L. Tobacco biomarkers and genetic/epigenetic analysis to investigate ethnic/racial differences in lung cancer risk among smokers. NPJ Precis Oncol 2018; 2:17. [PMID: 30155522 PMCID: PMC6105591 DOI: 10.1038/s41698-018-0057-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
The Multiethnic Cohort Study has demonstrated that African Americans and Native Hawaiians have a higher risk for lung cancer due to cigarette smoking than Whites while Latinos and Japanese Americans have a lower risk. These findings are consistent with other epidemiologic studies in the literature. In this review, we summarize tobacco carcinogen and toxicant biomarker studies and genetic analyses which partially explain these differences. As determined by measurement of total nicotine equivalents in urine, which account for about 85% of the nicotine dose, African Americans take up greater amounts of nicotine than Whites per cigarette while Japanese Americans take up less. There are corresponding differences in the uptake of tobacco smoke carcinogens such as tobacco-specific nitrosamines, polycyclic aromatic hydrocarbons, 1,3-butadiene, and other toxic volatiles. The lower nicotine uptake of Japanese Americans is clearly linked to the preponderance of low activity forms of the primary nicotine metabolizing enzyme CYP2A6 in this ethnic group, leading to more unchanged nicotine in the body and thus lower smoking intensity. But the relatively high risk of Native Hawaiians and the low risk of Latino smokers for lung cancer are not explained by these factors. The possible role of epigenetics in modifying lung cancer risk among smokers is also discussed here. The results of these published studies may lead to a better understanding of susceptibility factors for lung cancer in cigarette smokers thus potentially identifying biomarkers that can detect those individuals at highest risk so that preventive approaches can be initiated at an early stage of the lung cancer development process.
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Affiliation(s)
- Sharon E. Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Sungshim Lani Park
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Christopher A. Haiman
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 USA
| | | | - Yesha Patel
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 USA
| | - Lisa A. Peterson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Irina Stepanov
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Daniel O. Stram
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089 USA
| | - Natalia Tretyakova
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Stephen S. Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Loïc Le Marchand
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI 96813 USA
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27
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Li S, Wong EM, Bui M, Nguyen TL, Joo JHE, Stone J, Dite GS, Giles GG, Saffery R, Southey MC, Hopper JL. Causal effect of smoking on DNA methylation in peripheral blood: a twin and family study. Clin Epigenetics 2018; 10:18. [PMID: 29456763 PMCID: PMC5810186 DOI: 10.1186/s13148-018-0452-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Smoking has been reported to be associated with peripheral blood DNA methylation, but the causal aspects of the association have rarely been investigated. We aimed to investigate the association and underlying causation between smoking and blood methylation. Methods The methylation profile of DNA from the peripheral blood, collected as dried blood spots stored on Guthrie cards, was measured for 479 Australian women including 66 monozygotic twin pairs, 66 dizygotic twin pairs, and 215 sisters of twins from 130 twin families using the Infinium HumanMethylation450K BeadChip array. Linear regression was used to estimate associations between methylation at ~ 410,000 cytosine-guanine dinucleotides (CpGs) and smoking status. A regression-based methodology for twins, Inference about Causation through Examination of Familial Confounding (ICE FALCON), was used to assess putative causation. Results At a 5% false discovery rate, 39 CpGs located at 27 loci, including previously reported AHRR, F2RL3, 2q37.1 and 6p21.33, were found to be differentially methylated across never, former and current smokers. For all 39 CpG sites, current smokers had the lowest methylation level. Our study provides the first replication for two previously reported CpG sites, cg06226150 (SLC2A4RG) and cg21733098 (12q24.32). From the ICE FALCON analysis with smoking status as the predictor and methylation score as the outcome, a woman’s methylation score was associated with her co-twin’s smoking status, and the association attenuated towards the null conditioning on her own smoking status, consistent with smoking status causing changes in methylation. To the contrary, using methylation score as the predictor and smoking status as the outcome, a woman’s smoking status was not associated with her co-twin’s methylation score, consistent with changes in methylation not causing smoking status. Conclusions For middle-aged women, peripheral blood DNA methylation at several genomic locations is associated with smoking. Our study suggests that smoking has a causal effect on peripheral blood DNA methylation, but not vice versa. Electronic supplementary material The online version of this article (10.1186/s13148-018-0452-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuai Li
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
| | - Ee Ming Wong
- 2Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria Australia.,3Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
| | - Minh Bui
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
| | - Tuong L Nguyen
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
| | - Ji-Hoon Eric Joo
- 2Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria Australia.,3Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
| | - Jennifer Stone
- 4Centre for Genetic Origins of Health and Disease, Curtin University and the University of Western Australia, Perth, Western Australia Australia
| | - Gillian S Dite
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
| | - Graham G Giles
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia.,5Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
| | - Richard Saffery
- 6Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria Australia.,7Department of Paediatrics, University of Melbourne, Parkville, Victoria Australia
| | - Melissa C Southey
- 2Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, Victoria Australia.,3Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria Australia
| | - John L Hopper
- 1Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria Australia
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28
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Zhang X, Hu Y, Justice AC, Li B, Wang Z, Zhao H, Krystal JH, Xu K. DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty. Nat Commun 2017; 8:2243. [PMID: 29269866 PMCID: PMC5740109 DOI: 10.1038/s41467-017-02326-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/20/2017] [Indexed: 01/13/2023] Open
Abstract
Intravenous illicit drug use (IDU) and hepatitis C infection (HCV) commonly co-occur among HIV-infected individuals. These co-occurring conditions may produce interacting epigenetic effects in white blood cells that influence immune function and health outcomes. Here, we report an epigenome-wide association analysis comparing IDU+/ HCV+ and IDU-/HCV- in 386 HIV-infected individuals as a discovery sample and in 412 individuals as a replication sample. We observe 6 significant CpGs in the promoters of 4 genes, NLRC5, TRIM69, CX3CR1, and BCL9, in the discovery sample and in meta-analysis. We identify 19 differentially methylated regions on chromosome 6 harboring MHC gene clusters. Importantly, a panel of IDU+/HCV+-associated CpGs discriminated HIV frailty based upon a validated index with an area under the curve of 79.3% for high frailty and 82.3% for low frailty. These findings suggest that IDU and HCV involve epigenetic programming and that their associated methylation signatures discriminate HIV pathophysiologic frailty.
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Affiliation(s)
- Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Ying Hu
- National Cancer Institute Center for Biomedical Information & Information Technology, 9609 Medical Center Drive, Bethesda, MD, 20850, USA
| | - Amy C Justice
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
- Yale University School of Medicine, New Haven Veterans Affairs Connecticut Healthcare System, New Haven, CT, 06516, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA.
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA.
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29
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Abstract
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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