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Alcaráz N, Salcedo-Tello P, González-Barrios R, Torres-Arciga K, Guzmán-Ramos K. Underlying Mechanisms of the Protective Effects of Lifestyle Factors in the Prevention of Age-Related Diseases. Arch Med Res 2024; 55:103014. [PMID: 38861840 DOI: 10.1016/j.arcmed.2024.103014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/15/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024]
Abstract
The rise in life expectancy has significantly increased the occurrence of age-related chronic diseases, leading to escalating expenses for both society and individuals. Among the main factors influencing health and lifespan, lifestyle takes a forefront position. Specifically, nutrition, mental activity, and physical exercise influence the molecular and functional mechanisms that contribute to the prevention of major age-related diseases. Gaining deeper insights into the mechanisms that drive the positive effects of healthy lifestyles is valuable for creating interventions to prevent or postpone the development of chronic degenerative diseases. This review summarizes the main mechanisms that underlie the positive effect of lifestyle factors in counteracting the major age-related diseases involving brain health, musculoskeletal function, cancer, frailty, and cardiovascular diseases, among others. This knowledge will help to identify high-risk populations for targeted intervention trials and discover new biomarkers associated with healthy aging.
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Affiliation(s)
- Nicolás Alcaráz
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pamela Salcedo-Tello
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo González-Barrios
- Instituto Nacional de Cancerología, Laboratorio de regulación de la cromatina y genómica, Mexico City, México
| | - Karla Torres-Arciga
- Instituto Nacional de Cancerología, Laboratorio de regulación de la cromatina y genómica, Mexico City, México; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kioko Guzmán-Ramos
- Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana, Unidad Lerma, Mexico State, Mexico.
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2
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Herzog C, Jones A, Evans I, Raut JR, Zikan M, Cibula D, Wong A, Brenner H, Richmond RC, Widschwendter M. Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis. Cancer Res 2024; 84:1898-1914. [PMID: 38503267 PMCID: PMC11148547 DOI: 10.1158/0008-5472.can-23-2957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
Tobacco use is a major modifiable risk factor for adverse health outcomes, including cancer, and elicits profound epigenetic changes thought to be associated with long-term cancer risk. While electronic cigarettes (e-cigarettes) have been advocated as harm reduction alternatives to tobacco products, recent studies have revealed potential detrimental effects, highlighting the urgent need for further research into the molecular and health impacts of e-cigarettes. Here, we applied computational deconvolution methods to dissect the cell- and tissue-specific epigenetic effects of tobacco or e-cigarette use on DNA methylation (DNAme) in over 3,500 buccal/saliva, cervical, or blood samples, spanning epithelial and immune cells at directly and indirectly exposed sites. The 535 identified smoking-related DNAme loci [cytosine-phosphate-guanine sites (CpG)] clustered into four functional groups, including detoxification or growth signaling, based on cell type and anatomic site. Loci hypermethylated in buccal epithelial cells of smokers associated with NOTCH1/RUNX3/growth factor receptor signaling also exhibited elevated methylation in cancer tissue and progressing lung carcinoma in situ lesions, and hypermethylation of these sites predicted lung cancer development in buccal samples collected from smokers up to 22 years prior to diagnosis, suggesting a potential role in driving carcinogenesis. Alarmingly, these CpGs were also hypermethylated in e-cigarette users with a limited smoking history. This study sheds light on the cell type-specific changes to the epigenetic landscape induced by smoking-related products. SIGNIFICANCE The use of both cigarettes and e-cigarettes elicits cell- and exposure-specific epigenetic effects that are predictive of carcinogenesis, suggesting caution when broadly recommending e-cigarettes as aids for smoking cessation.
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Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Innsbruck, Austria
- Research Institute for Biomedical Aging, Universität Innsbruck, Innsbruck, Austria
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, United Kingdom
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, United Kingdom
| | - Janhavi R Raut
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michal Zikan
- Department of Gynecology and Obstetrics, First Faculty of Medicine and Hospital Na Bulovce, Charles University in Prague, Prague, Czech Republic
| | - David Cibula
- Gynecologic Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Innsbruck, Austria
- Research Institute for Biomedical Aging, Universität Innsbruck, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, London, United Kingdom
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
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Shorey-Kendrick LE, McEvoy CT, Milner K, Harris J, Brownsberger J, Tepper RS, Park B, Gao L, Vu A, Morris CD, Spindel ER. Improvements in lung function following vitamin C supplementation to pregnant smokers are associated with buccal DNA methylation at 5 years of age. Clin Epigenetics 2024; 16:35. [PMID: 38413986 PMCID: PMC10900729 DOI: 10.1186/s13148-024-01644-8] [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: 10/17/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND We previously reported in the "Vitamin C to Decrease the Effects of Smoking in Pregnancy on Infant Lung Function" randomized clinical trial (RCT) that vitamin C (500 mg/day) supplementation to pregnant smokers is associated with improved respiratory outcomes that persist through 5 years of age. The objective of this study was to assess whether buccal cell DNA methylation (DNAm), as a surrogate for airway epithelium, is associated with vitamin C supplementation, improved lung function, and decreased occurrence of wheeze. METHODS We conducted epigenome-wide association studies (EWAS) using Infinium MethylationEPIC arrays and buccal DNAm from 158 subjects (80 placebo; 78 vitamin C) with pulmonary function testing (PFT) performed at the 5-year visit. EWAS were performed on (1) vitamin C treatment, (2) forced expiratory flow between 25 and 75% of expired volume (FEF25-75), and (3) offspring wheeze. Models were adjusted for sex, race, study site, gestational age at randomization (≤ OR > 18 weeks), proportion of epithelial cells, and latent covariates in addition to child length at PFT in EWAS for FEF25-75. We considered FDR p < 0.05 as genome-wide significant and nominal p < 0.001 as candidates for downstream analyses. Buccal DNAm measured in a subset of subjects at birth and near 1 year of age was used to determine whether DNAm signatures originated in utero, or emerged with age. RESULTS Vitamin C treatment was associated with 457 FDR significant (q < 0.05) differentially methylated CpGs (DMCs; 236 hypermethylated; 221 hypomethylated) and 53 differentially methylated regions (DMRs; 26 hyper; 27 hypo) at 5 years of age. FEF25-75 was associated with one FDR significant DMC (cg05814800), 1,468 candidate DMCs (p < 0.001), and 44 DMRs. Current wheeze was associated with 0 FDR-DMCs, 782 candidate DMCs, and 19 DMRs (p < 0.001). In 365/457 vitamin C FDR significant DMCs at 5 years of age, there was no significant interaction between time and treatment. CONCLUSIONS Vitamin C supplementation to pregnant smokers is associated with buccal DNA methylation in offspring at 5 years of age, and most methylation signatures appear to be persistent from the prenatal period. Buccal methylation at 5 years was also associated with current lung function and occurrence of wheeze, and these functionally associated loci are enriched for vitamin C associated loci. Clinical trial registration ClinicalTrials.gov, NCT01723696 and NCT03203603.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
| | - Cindy T McEvoy
- Department of Pediatrics, Pape Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Kristin Milner
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Julia Harris
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Julie Brownsberger
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Robert S Tepper
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byung Park
- Biostatistics Shared Resources, Knight Cancer Institute, Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland State University School of Public Health, Portland, OR, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland State University School of Public Health, Portland, OR, USA
| | - Annette Vu
- Oregon Clinical & Translational Research Institute, Oregon Health and Science; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Cynthia D Morris
- Oregon Clinical & Translational Research Institute, Oregon Health and Science; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
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Sterling J, Policastro C, Elyaguov J, Simhan J, Nikolavsky D. How and why tobacco use affects reconstructive surgical practice: a contemporary narrative review. Transl Androl Urol 2023; 12:112-127. [PMID: 36760864 PMCID: PMC9906109 DOI: 10.21037/tau-22-427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/24/2022] [Indexed: 01/05/2023] Open
Abstract
Background and Objective The overall negative impact of tobacco use on an individual's health has been well documented but the literature on tobacco's impact on post-surgical outcomes, specifically the outcomes after urologic surgery, is not as clear cut. The aim of this narrative review is to provide urologists with the information needed to have a nuanced pre-operative counseling conversation with patients about tobacco use. Here we combine publications on the histologic and physiologic changes induced by nicotine and tobacco use with publications from the wider surgical literature on post-operative outcomes in tobacco users. Methods A literature search of PubMed, Google Scholar and Medline was performed using iterations of the following terms: tobacco, nicotine, changes, physiologic, histology, post-operative, and surgical. Non-English publications and abstracts were excluded. Inclusion required agreement from all authors and preference was given to human specimens over animal models for the basic science manuscripts and large database and meta-analyses over single institution experiences. Key Content and Findings Tobacco use results in measurable changes in nearly every organ system in the body. While smokers have increased wound complications, there is no evidence that reconstructive surgery using grafts or flaps fail more frequently in tobacco users. Smokers have an increased risk of respiratory complications following endotracheal intubation. Conclusions Surgeries should not be canceled due to a patient's inability to cease tobacco use. Urologists and patients should engage in joint decision making regarding the timing and pursuit of elective operations.
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Affiliation(s)
- Joshua Sterling
- SUNY Upstate Medical University, Department of Urology, Syracuse, NY, USA;,Yale School of Medicine, Department of Urology, New Haven, CT, USA
| | - Connor Policastro
- SUNY Upstate Medical University, Department of Urology, Syracuse, NY, USA
| | - Jason Elyaguov
- SUNY Upstate Medical University, Department of Urology, Syracuse, NY, USA
| | - Jay Simhan
- Fox Chase Cancer Center, Division of Urologic Oncology and Urology, Philadelphia, PA, USA
| | - Dmitriy Nikolavsky
- SUNY Upstate Medical University, Department of Urology, Syracuse, NY, USA
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Reale A, Tagliatesta S, Zardo G, Zampieri M. Counteracting aged DNA methylation states to combat ageing and age-related diseases. Mech Ageing Dev 2022; 206:111695. [PMID: 35760211 DOI: 10.1016/j.mad.2022.111695] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation (DNAm) overwrites information about multiple extrinsic factors on the genome. Age is one of these factors. Age causes characteristic DNAm changes that are thought to be not only major drivers of normal ageing but also precursors to diseases, cancer being one of these. Although there is still much to learn about the relationship between ageing, age-related diseases and DNAm, we now know how to interpret some of the effects caused by age in the form of changes in methylation marks at specific loci. In fact, these changes form the basis of the so called "epigenetic clocks", which translate the genomic methylation profile into an "epigenetic age". Epigenetic age does not only estimate chronological age but can also predict the risk of chronic diseases and mortality. Epigenetic age is believed to be one of the most accurate metrics of biological age. Initial evidence has recently been gathered pointing to the possibility that the rate of epigenetic ageing can be slowed down or even reversed. In this review, we discuss some of the most relevant advances in this field. Expected outcome is that this approach can provide insights into how to preserve health and reduce the impact of ageing diseases in humans.
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Affiliation(s)
- Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Stefano Tagliatesta
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00161 Rome, Italy.
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
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6
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Konigsberg IR, Yang IV. Differential Methylation of COPD Lung Macrophage Genes Sheds Light on Disease Pathogenesis. Am J Respir Cell Mol Biol 2022; 66:589-590. [PMID: 35377834 PMCID: PMC9163643 DOI: 10.1165/rcmb.2022-0125ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Iain R Konigsberg
- University of Colorado Denver School of Medicine, 12225, Department of Medicine, Aurora, Colorado, United States
| | - Ivana V Yang
- University of Colorado Denver School of Medicine, 12225, Medicine, Aurora, Colorado, United States;
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7
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Genetic risk factors for colorectal cancer in multiethnic Indonesians. Sci Rep 2021; 11:9988. [PMID: 33976257 PMCID: PMC8113452 DOI: 10.1038/s41598-021-88805-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/14/2021] [Indexed: 11/09/2022] Open
Abstract
Colorectal cancer is a common cancer in Indonesia, yet it has been understudied in this resource-constrained setting. We conducted a genome-wide association study focused on evaluation and preliminary discovery of colorectal cancer risk factors in Indonesians. We administered detailed questionnaires and collecting blood samples from 162 colorectal cancer cases throughout Makassar, Indonesia. We also established a control set of 193 healthy individuals frequency matched by age, sex, and ethnicity. A genome-wide association analysis was performed on 84 cases and 89 controls passing quality control. We evaluated known colorectal cancer genetic variants using logistic regression and established a genome-wide polygenic risk model using a Bayesian variable selection technique. We replicate associations for rs9497673, rs6936461 and rs7758229 on chromosome 6; rs11255841 on chromosome 10; and rs4779584, rs11632715, and rs73376930 on chromosome 15. Polygenic modeling identified 10 SNP associated with colorectal cancer risk. This work helps characterize the relationship between variants in the SCL22A3, SCG5, GREM1, and STXBP5-AS1 genes and colorectal cancer in a diverse Indonesian population. With further biobanking and international research collaborations, variants specific to colorectal cancer risk in Indonesians will be identified.
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8
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DeMeo DL. Sex and Gender Omic Biomarkers in Men and Women With COPD: Considerations for Precision Medicine. Chest 2021; 160:104-113. [PMID: 33745988 DOI: 10.1016/j.chest.2021.03.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
Sex and gender differences in lung health and disease are imperative to consider and study if precision pulmonary medicine is to be achieved. The development of reliable COPD biomarkers has been elusive, and the translation of biomarkers to clinical care has been limited. Useful and effective biomarkers must be developed with attention to clinical heterogeneity of COPD; inherent heterogeneity exists related to grouping women and men together in the studies of COPD. Considering sex and gender differences and influences related to -omics may represent progress in susceptibility, diagnostic, prognostic, and therapeutic biomarker development and clinical innovation to improve the lung health of men and women.
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Affiliation(s)
- Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
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Chen YC, Tsai YH, Wang CC, Liu SF, Chen TW, Fang WF, Lee CP, Hsu PY, Chao TY, Wu CC, Wei YF, Chang HC, Tsen CC, Chang YP, Lin MC. Epigenome-wide association study on asthma and chronic obstructive pulmonary disease overlap reveals aberrant DNA methylations related to clinical phenotypes. Sci Rep 2021; 11:5022. [PMID: 33658578 PMCID: PMC7930096 DOI: 10.1038/s41598-021-83185-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
We hypothesized that epigenetics is a link between smoking/allergen exposures and the development of Asthma and chronic obstructive pulmonary disease (ACO). A total of 75 of 228 COPD patients were identified as ACO, which was independently associated with increased exacerbations. Microarray analysis identified 404 differentially methylated loci (DML) in ACO patients, and 6575 DML in those with rapid lung function decline in a discovery cohort. In the validation cohort, ACO patients had hypermethylated PDE9A (+ 30,088)/ZNF323 (− 296), and hypomethylated SEPT8 (− 47) genes as compared with either pure COPD patients or healthy non-smokers. Hypermethylated TIGIT (− 173) gene and hypomethylated CYSLTR1 (+ 348)/CCDC88C (+ 125,722)/ADORA2B (+ 1339) were associated with severe airflow limitation, while hypomethylated IFRD1 (− 515) gene with frequent exacerbation in all the COPD patients. Hypermethylated ZNF323 (− 296) / MPV17L (+ 194) and hypomethylated PTPRN2 (+ 10,000) genes were associated with rapid lung function decline. In vitro cigarette smoke extract and ovalbumin concurrent exposure resulted in specific DNA methylation changes of the MPV17L / ZNF323 genes, while 5-aza-2′-deoxycytidine treatment reversed promoter hypermethylation-mediated MPV17L under-expression accompanied with reduced apoptosis and decreased generation of reactive oxygen species. Aberrant DNA methylations may constitute a determinant for ACO, and provide a biomarker of airflow limitation, exacerbation, and lung function decline.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan. .,Medical Department, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Ying-Huang Tsai
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chin-Chou Wang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Chang Gung University of Science and Technology, Chia-Yi, Taiwan
| | - Shih-Feng Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Wen-Feng Fang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Chang Gung University of Science and Technology, Chia-Yi, Taiwan
| | - Chiu-Ping Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Po-Yuan Hsu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Tung-Ying Chao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chao-Chien Wu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Yu-Feng Wei
- Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Huang-Chih Chang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chia-Cheng Tsen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Yu-Ping Chang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan. .,Medical Department, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Cai J, Xu Y, Zhang W, Ding S, Sun Y, Lyu J, Duan M, Liu S, Huang L, Zhou F. A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear. Brief Bioinform 2020; 22:5921981. [PMID: 33048108 DOI: 10.1093/bib/bbaa253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/10/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin architectures. Such modifications in the promoter regions will inactivate some tumor-suppressor genes. DNA methylation within the coding region may significantly reduce the transcription elongation efficiency. The gene function may be tuned through some cytosines are methylated. METHODS This study hypothesizes that the overall methylation level across a gene may have a better association with the sample labels like diseases than the methylations of individual cytosines. The gene methylation level is formulated as a regression model using the methylation levels of all the cytosines within this gene. A comprehensive evaluation of various feature selection algorithms and classification algorithms is carried out between the gene-level and residue-level methylation levels. RESULTS A comprehensive evaluation was conducted to compare the gene and cytosine methylation levels for their associations with the sample labels and classification performances. The unsupervised clustering was also improved using the gene methylation levels. Some genes demonstrated statistically significant associations with the class label, even when no residue-level methylation features have statistically significant associations with the class label. So in summary, the trained gene methylation levels improved various methylome-based machine learning models. Both methodology development of regression algorithms and experimental validation of the gene-level methylation biomarkers are worth of further investigations in the future studies. The source code, example data files and manual are available at http://www.healthinformaticslab.org/supp/.
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DNA Methylation in Chronic Obstructive Pulmonary Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:83-98. [PMID: 32949392 DOI: 10.1007/978-981-15-4494-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a lung disease affected by both genetic and environmental factors. Therefore, the role of epigenetics in the pathogenesis of COPD has attracted much attention. As one of the three epigenetic mechanisms, DNA methylation has been extensively studied in COPD. The present review aims at overviewing the effect of DNA methylation on etiology, pathogenesis, pathophysiological changes, and complications of COPD. The clarification of aberrant methylation of target genes, which play important roles in the initiation and progression of COPD, will provide new disease-specific biomarker and targets for early diagnosis and therapy.
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Avram GE, Marcu A, Moatar A, Samoila C, Podariu A, Seclaman E, Marian C. Changes in global DNA methylation and hydroxymethylation in oral mucosa according to tobacco smoke exposure. J Int Med Res 2020; 48:300060520954677. [PMID: 32938281 PMCID: PMC7503033 DOI: 10.1177/0300060520954677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE This prospective clinical study comparatively investigated the effects of tobacco smoking on global methylation and hydroxymethylation in oral epithelial cells. METHODS Buccal cells from the inside of the cheeks were collected from 47 individuals, including smokers, former smokers, and never smokers. DNA was extracted using dedicated kits. Methylated and hydroxymethylated DNA fractions were measured using assays similar to enzyme-linked immunosorbent assays. The levels of methylation and hydroxymethylation were compared among groups using unpaired two-tailed t-tests or the Mann-Whitney U test; P < 0.05 was considered statistically significant. RESULTS There was no statistically significant difference in the average number of cigarettes between smoker and former smoker groups. Although methylation levels were lower for smokers (3.1%) and former smokers (2.16%), compared with never smokers (4.16%), these differences were not statistically significant. There was a two-fold increase in hydroxymethylation level in never smokers, compared with smokers. CONCLUSIONS Our findings suggest that smoking leads to global reductions in both methylation and hydroxymethylation levels in oral epithelial cells in a manner influenced by the intensity and length of exposure to tobacco smoke.
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Affiliation(s)
- Gabriela-Emilia Avram
- Doctoral School, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania.,Department of Maxillofacial Surgery, Faculty of Dentistry, "Vasile Goldis" Western University of Arad, Arad, Romania
| | - Anca Marcu
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Alexandra Moatar
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Corina Samoila
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Angela Podariu
- Department of Preventive Dentistry, Community and Oral Health, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Edward Seclaman
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry & Pharmacology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
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13
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Morrow JD, Make B, Regan E, Han M, Hersh CP, Tal-Singer R, Quackenbush J, Choi AMK, Silverman EK, DeMeo DL. DNA Methylation Is Predictive of Mortality in Current and Former Smokers. Am J Respir Crit Care Med 2020; 201:1099-1109. [PMID: 31995399 DOI: 10.1164/rccm.201902-0439oc] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rationale: Smoking results in at least a decade lower life expectancy. Mortality among current smokers is two to three times as high as never smokers. DNA methylation is an epigenetic modification of the human genome that has been associated with both cigarette smoking and mortality.Objectives: We sought to identify DNA methylation marks in blood that are predictive of mortality in a subset of the COPDGene (Genetic Epidemiology of COPD) study, representing 101 deaths among 667 current and former smokers.Methods: We assayed genome-wide DNA methylation in non-Hispanic white smokers with and without chronic obstructive pulmonary disease (COPD) using blood samples from the COPDGene enrollment visit. We tested whether DNA methylation was associated with mortality in models adjusted for COPD status, age, sex, current smoking status, and pack-years of cigarette smoking. Replication was performed in a subset of 231 individuals from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) study.Measurements and Main Results: We identified seven CpG sites associated with mortality (false discovery rate < 20%) that replicated in the ECLIPSE cohort (P < 0.05). None of these marks were associated with longitudinal lung function decline in survivors, smoking history, or current smoking status. However, differential methylation of two replicated PIK3CD (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta) sites were associated with lung function at enrollment (P < 0.05). We also observed associations between DNA methylation and gene expression for the PIK3CD sites.Conclusions: This study is the first to identify variable DNA methylation associated with all-cause mortality in smokers with and without COPD. Evaluating predictive epigenomic marks of smokers in peripheral blood may allow for targeted risk stratification and aid in delivery of future tailored therapeutic interventions.
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Affiliation(s)
| | - Barry Make
- National Jewish Health, Denver, Colorado
| | | | - MeiLan Han
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Craig P Hersh
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; and
| | - Augustine M K Choi
- Department of Medicine, NewYork-Presbyterian/Weill Cornell Medical Center, New York, New York
| | - Edwin K Silverman
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Dawn L DeMeo
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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14
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Regan EA, Hersh CP, Castaldi PJ, DeMeo DL, Silverman EK, Crapo JD, Bowler RP. Omics and the Search for Blood Biomarkers in Chronic Obstructive Pulmonary Disease. Insights from COPDGene. Am J Respir Cell Mol Biol 2020; 61:143-149. [PMID: 30874442 DOI: 10.1165/rcmb.2018-0245ps] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There is an unmet need for blood biomarkers in diagnosis and prognosis of chronic obstructive pulmonary disease (COPD). The search for these biomarkers has been revolutionized by high-throughput sequencing techniques and multiplex platforms that can measure thousands of gene transcripts, proteins, or metabolites. We review COPDGene (Genetic Epidemiology of COPD) project publications that include DNA methylation, transcriptomic, proteomic, and metabolomic blood biomarkers and discuss their impact on COPD. Key contributions from COPDGene include identification of DNA methylation effects from smoking and genetic variation, new transcriptomic signatures in the blood, identification of protein biomarkers associated with severity and progression (e.g., sRAGE [soluble receptor for advanced glycosylation end products], inflammatory cytokines IL-6 and IL-8), and identification of small molecules (ceramides and sphingomyelin) that may be pathogenic. COPDGene studies have revealed that some of the COPD genome-wide association study polymorphisms are strongly associated with blood biomarkers (e.g., rs2070600 in AGER is a pQTL [protein quantitative trait locus] for sRAGE), underscoring the importance of combining omics results. Investigators have developed molecular networks identifying lower CD4+ resting memory cells associated with COPD. Genes, proteins, and metabolite networks are particularly important because the explanatory value of any single molecule is small (1-10%) compared with panels of multiple markers. COPDGene has been a useful resource in the identification and validation of multiple biomarkers for COPD. These biomarkers, either combined in multiple biomarker panels or integrated with other omics data types, may lead to novel diagnostic and prognostic tests for COPD phenotypes and may be relevant for assessing novel therapies.
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Affiliation(s)
- Elizabeth A Regan
- 1Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Craig P Hersh
- 2Channing Division of Network Medicine and.,3Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Peter J Castaldi
- 2Channing Division of Network Medicine and.,3Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Dawn L DeMeo
- 2Channing Division of Network Medicine and.,3Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Edwin K Silverman
- 2Channing Division of Network Medicine and.,3Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - James D Crapo
- 1Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Russell P Bowler
- 1Department of Medicine, National Jewish Health, Denver, Colorado; and
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15
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Whole-genome methylation profiling from PBMCs in acute-exacerbation COPD patients with good and poor responses to corticosteroid treatment. Genomics 2019; 111:1381-1386. [DOI: 10.1016/j.ygeno.2018.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 01/09/2023]
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16
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van Rooij J, Mandaviya PR, Claringbould A, Felix JF, van Dongen J, Jansen R, Franke L, 't Hoen PAC, Heijmans B, van Meurs JBJ. Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies. Genome Biol 2019; 20:235. [PMID: 31727104 PMCID: PMC6857161 DOI: 10.1186/s13059-019-1878-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 11/02/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A large number of analysis strategies are available for DNA methylation (DNAm) array and RNA-seq datasets, but it is unclear which strategies are best to use. We compare commonly used strategies and report how they influence results in large cohort studies. RESULTS We tested the associations of DNAm and RNA expression with age, BMI, and smoking in four different cohorts (n = ~ 2900). By comparing strategies against the base model on the number and percentage of replicated CpGs for DNAm analyses or genes for RNA-seq analyses in a leave-one-out cohort replication approach, we find the choice of the normalization method and statistical test does not strongly influence the results for DNAm array data. However, adjusting for cell counts or hidden confounders substantially decreases the number of replicated CpGs for age and increases the number of replicated CpGs for BMI and smoking. For RNA-seq data, the choice of the normalization method, gene expression inclusion threshold, and statistical test does not strongly influence the results. Including five principal components or excluding correction of technical covariates or cell counts decreases the number of replicated genes. CONCLUSIONS Results were not influenced by the normalization method or statistical test. However, the correction method for cell counts, technical covariates, principal components, and/or hidden confounders does influence the results.
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Affiliation(s)
- Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Pooja R Mandaviya
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Annique Claringbould
- Faculty of Medical Sciences, University of Groningen, Groningen, the Netherlands
| | - Janine F Felix
- The Generation R Study Group, Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- The Generation R Study Group, Department of Pediatrics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Amsterdam, the Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, Groningen, the Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, the Netherlands
| | - Bas Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands.
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17
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Yu M, Hazelton WD, Luebeck GE, Grady WM. Epigenetic Aging: More Than Just a Clock When It Comes to Cancer. Cancer Res 2019; 80:367-374. [PMID: 31694907 DOI: 10.1158/0008-5472.can-19-0924] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/26/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022]
Abstract
The incidence of cancer, adjusted for secular trends, is directly related to age, and advanced chronologic age is one of the most significant risk factors for cancer. Organismal aging is associated with changes at the molecular, cellular, and tissue levels and is affected by both genetic and environmental factors. The specific mechanisms through which these age-associated molecular changes contribute to the increased risk of aging-related disease, such as cancer, are incompletely understood. DNA methylation, a prominent epigenetic mark, also changes over a lifetime as part of an "epigenetic aging" process. Here, we give an update and review of epigenetic aging, in particular, the phenomena of epigenetic drift and epigenetic clock, with regard to its implication in cancer etiology. We discuss the discovery of the DNA methylation-based biomarkers for biological tissue age and the construction of various epigenetic age estimators for human clinical outcomes and health/life span. Recent studies in various types of cancer point to the significance of epigenetic aging in tumorigenesis and its potential use for cancer risk prediction. Future studies are needed to assess the potential clinical impact of strategies focused on lowering cancer risk by preventing premature aging or promoting healthy aging.
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Affiliation(s)
- Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
| | - William D Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Georg E Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. .,Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington.,GI Cancer Prevention Program, Seattle Cancer Care Alliance, Seattle, Washington
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18
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Sao T, Yoshino Y, Yamazaki K, Ozaki Y, Mori Y, Ochi S, Yoshida T, Mori T, Iga JI, Ueno SI. TREM1 mRNA Expression in Leukocytes and Cognitive Function in Japanese Patients with Alzheimer's Disease. J Alzheimers Dis 2019; 64:1275-1284. [PMID: 30010135 DOI: 10.3233/jad-180418] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Triggering receptor expressed on myeloid cells 2 (TREM2) activates the innate immune system, promotes phagocytosis by microglia, and is associated with Alzheimer's disease (AD). The possible role of a related molecule, TREM1, in AD remains unknown. OBJECTIVE We investigated a possible role for TREM1 in AD by determining the gene expression and methylation levels of TREM1 in leukocytes from AD patients. METHODS Fifty patients with AD and 50 age-matched healthy controls were enrolled. AD patients underwent a battery of neuropsychiatric tests. Peripheral blood samples were obtained from each participant, RNA and DNA were extracted, and samples were assessed for TREM1 mRNA expression and methylation rates at three CpG sites in the TREM1 promoter. RESULTS TREM1 mRNA expression levels in AD patients were significantly higher than those in controls (p = 0.008). TREM1 mRNA expression levels were not correlated with sex, age, duration of illness, APOE genotype, donepezil treatment, or scores of most neuropsychiatric tests. TREM1 mRNA expression levels in AD patients were correlated with the total score of the Montgomery-Åsberg Depression Rating Scale (p = 0.047, r = - 0.344). Methylation rates at the three CpG sites were significantly lower in AD patients than in controls. We also found a significant correlation between TREM1 mRNA expression and TREM1 DNA methylation rates (p < 0.001). CONCLUSION TREM1 may be associated with the immune responses in AD, and along with hypomethylation at CpG sites in the TREM1 promoter, may become part of a biomarker panel for AD pathogenesis.
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Affiliation(s)
- Tomoko Sao
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Taku Yoshida
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
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19
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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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20
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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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21
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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: 29] [Impact Index Per Article: 4.8] [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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22
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Morrow JD, Glass K, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci. Am J Respir Crit Care Med 2018; 197:1275-1284. [PMID: 29313708 PMCID: PMC5955059 DOI: 10.1164/rccm.201707-1434oc] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/03/2018] [Indexed: 12/23/2022] Open
Abstract
RATIONALE As the third leading cause of death in the United States, the impact of chronic obstructive pulmonary disease (COPD) makes identification of its molecular mechanisms of great importance. Genome-wide association studies (GWASs) have identified multiple genomic regions associated with COPD. However, genetic variation only explains a small fraction of the susceptibility to COPD, and sub-genome-wide significant loci may play a role in pathogenesis. OBJECTIVES Regulatory annotation with epigenetic evidence may give priority for further investigation, particularly for GWAS associations in noncoding regions. We performed integrative genomics analyses using DNA methylation profiling and genome-wide SNP genotyping from lung tissue samples from 90 subjects with COPD and 36 control subjects. METHODS We performed methylation quantitative trait loci (mQTL) analyses, testing for SNPs associated with percent DNA methylation and assessed the colocalization of these results with previous COPD GWAS findings using Bayesian methods in the R package coloc to highlight potential regulatory features of the loci. MEASUREMENTS AND MAIN RESULTS We identified 942,068 unique SNPs and 33,996 unique CpG sites among the significant (5% false discovery rate) cis-mQTL results. The genome-wide significant and subthreshold (P < 10-4) GWAS SNPs were enriched in the significant mQTL SNPs (hypergeometric test P < 0.00001). We observed enrichment for sites located in CpG shores and shelves, but not CpG islands. Using Bayesian colocalization, we identified loci in regions near KCNK3, EEFSEC, PIK3CD, DCDC2C, TCERG1L, FRMD4B, and IL27. CONCLUSIONS Colocalization of mQTL and GWAS loci provides regulatory characterization of significant and subthreshold GWAS findings, supporting a role for genetic control of methylation in COPD pathogenesis.
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Affiliation(s)
| | | | - Michael H. Cho
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Craig P. Hersh
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | | | | | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, Pennsylvania
| | - Gerard Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, Pennsylvania
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, and
| | - Augustine M. K. Choi
- Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, New York; and
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edwin K. Silverman
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Dawn L. DeMeo
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
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23
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Nedeljkovic I, Carnero-Montoro E, Lahousse L, van der Plaat DA, de Jong K, Vonk JM, van Diemen CC, Faiz A, van den Berge M, Obeidat M, Bossé Y, Nickle DC, Consortium B, Uitterlinden AG, van Meurs JJB, Stricker BCH, Brusselle GG, Postma DS, Boezen HM, van Duijn CM, Amin N. Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics. Eur J Hum Genet 2018; 26:709-722. [PMID: 29422661 PMCID: PMC5945654 DOI: 10.1038/s41431-017-0089-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 11/06/2017] [Accepted: 12/19/2017] [Indexed: 12/25/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a major health burden in adults and cigarette smoking is considered the most important environmental risk factor of COPD. Chromosome 15q25.1 locus is associated with both COPD and smoking. Our study aims at understanding the mechanism underlying the association of chromosome 15q25.1 with COPD through epigenetic and transcriptional variation in a population-based setting. To assess if COPD-associated variants in 15q25.1 are methylation quantitative trait loci, epigenome-wide association analysis of four genetic variants, previously associated with COPD (P < 5 × 10-8) in the 15q25.1 locus (rs12914385:C>T-CHRNA3, rs8034191:T>C-HYKK, rs13180:C>T-IREB2 and rs8042238:C>T-IREB2), was performed in the Rotterdam study (n = 1489). All four variants were significantly associated (P < 1.4 × 10-6) with blood DNA methylation of IREB2, CHRNA3 and PSMA4, of which two, including IREB2 and PSMA4, were also differentially methylated in COPD cases and controls (P < 0.04). Further additive and multiplicative effects of smoking were evaluated and no significant effect was observed. To evaluate if these four genetic variants are expression quantitative trait loci, transcriptome-wide association analysis was performed in 1087 lung samples. All four variants were also significantly associated with differential expression of the IREB2 3'UTR in lung tissues (P < 5.4 × 10-95). We conclude that regulatory mechanisms affecting the expression of IREB2 gene, such as DNA methylation, may explain the association between genetic variants in chromosome 15q25.1 and COPD, largely independent of smoking.
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Affiliation(s)
- Ivana Nedeljkovic
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Elena Carnero-Montoro
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Pfizer University of Granada, GENYO Centre for Genomics and Oncological Research, Andalusian Region Government, Granada, Spain
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Bioanalysis Pharmaceutical Care Unit, Ghent University Hospital, Ghent, Belgium
| | - Diana A van der Plaat
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Kim de Jong
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec, QC, Canada
| | - David C Nickle
- Genetics and Pharmacogenomics (GpGx), Merck Research Laboratories, Seattle, WA, USA
| | | | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Joyce J B van Meurs
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Bruno C H Stricker
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Bioanalysis Pharmaceutical Care Unit, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
- Department of Pulmonology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands.
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24
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Whole-genome methylation profiling of peripheral blood mononuclear cell for acute exacerbations of chronic obstructive pulmonary disease treated with corticosteroid. Pharmacogenet Genomics 2018; 28:78-85. [DOI: 10.1097/fpc.0000000000000325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Widschwendter M, Jones A, Evans I, Reisel D, Dillner J, Sundström K, Steyerberg EW, Vergouwe Y, Wegwarth O, Rebitschek FG, Siebert U, Sroczynski G, de Beaufort ID, Bolt I, Cibula D, Zikan M, Bjørge L, Colombo N, Harbeck N, Dudbridge F, Tasse AM, Knoppers BM, Joly Y, Teschendorff AE, Pashayan N. Epigenome-based cancer risk prediction: rationale, opportunities and challenges. Nat Rev Clin Oncol 2018; 15:292-309. [PMID: 29485132 DOI: 10.1038/nrclinonc.2018.30] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The incidence of cancer is continuing to rise and risk-tailored early diagnostic and/or primary prevention strategies are urgently required. The ideal risk-predictive test should: integrate the effects of both genetic and nongenetic factors and aim to capture these effects using an approach that is both biologically stable and technically reproducible; derive a score from easily accessible biological samples that acts as a surrogate for the organ in question; and enable the effectiveness of risk-reducing measures to be monitored. Substantial evidence has accumulated suggesting that the epigenome and, in particular, DNA methylation-based tests meet all of these requirements. However, the development and implementation of DNA methylation-based risk-prediction tests poses considerable challenges. In particular, the cell type specificity of DNA methylation and the extensive cellular heterogeneity of the easily accessible surrogate cells that might contain information relevant to less accessible tissues necessitates the use of novel methods in order to account for these confounding issues. Furthermore, the engagement of the scientific community with health-care professionals, policymakers and the public is required in order to identify and address the organizational, ethical, legal, social and economic challenges associated with the routine use of epigenetic testing.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Allison Jones
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Iona Evans
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Daniel Reisel
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ewout W Steyerberg
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands.,Department of Biomedical Data Sciences, LUMC, Leiden, Netherlands
| | - Yvonne Vergouwe
- Center for Medical Decision Sciences, Department of Public Health, Erasmus MC, Rotterdam, Netherlands
| | - Odette Wegwarth
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany.,Max Planck Institute for Human Development, Center for Adaptive Rationality, Berlin, Germany
| | - Felix G Rebitschek
- Max Planck Institute for Human Development, Harding Center for Risk Literacy, Berlin, Germany
| | - Uwe Siebert
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria.,Harvard T. C. Chan School of Public Health, Center for Health Decision Science, Department of Health Policy and Management, Boston, MA, USA.,Oncotyrol: Center for Personalized Medicine, Innsbruck, Austria
| | - Gaby Sroczynski
- Institute of Public Health, Medical Decision Making and Health Technology Assessment, Department of Public Health, Health Services Research, and HTA, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
| | - Inez D de Beaufort
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ineke Bolt
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - David Cibula
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Michal Zikan
- Department of Obstetrics and Gynaecology, First Medical Faculty of the Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, and Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nicoletta Colombo
- European Institute of Oncology and University Milan-Bicocca, Milan, Italy
| | - Nadia Harbeck
- Breast Center, Department of Gynaecology and Obstetrics, University of Munich (LMU), Munich, Germany
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anne-Marie Tasse
- Public Population Project in Genomics and Society, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | | | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Andrew E Teschendorff
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Nora Pashayan
- Department of Applied Health Research, Institute of Epidemiology and Healthcare, University College London, UK
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26
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North CM, Allen JG, Okello S, Sentongo R, Kakuhikire B, Ryan ET, Tsai AC, Christiani DC, Siedner MJ. HIV Infection, Pulmonary Tuberculosis, and COPD in Rural Uganda: A Cross-Sectional Study. Lung 2018; 196:49-57. [PMID: 29260309 PMCID: PMC6261662 DOI: 10.1007/s00408-017-0080-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/15/2017] [Indexed: 10/18/2022]
Abstract
PURPOSE HIV is associated with chronic obstructive pulmonary disease (COPD) in high resource settings. Similar relationships are less understood in low resource settings. We aimed to estimate the association between HIV infection, tuberculosis, and COPD in rural Uganda. METHODS The Uganda Non-communicable Diseases and Aging Cohort study observes people 40 years and older living with HIV (PLWH) on antiretroviral therapy, and population-based HIV-uninfected controls in rural Uganda. Participants completed respiratory questionnaires and post-bronchodilator spirometry. RESULTS Among 269 participants with spirometry, median age was 52 (IQR 48-55), 48% (n = 130) were ever-smokers, and few (3%, n = 9) reported a history of COPD or asthma. All participants with prior tuberculosis (7%, n = 18) were PLWH. Among 143 (53%) PLWH, median CD4 count was 477 cells/mm3 and 131 (92%) were virologically suppressed. FEV1 was lower among older individuals (- 0.5%pred/year, 95% CI 0.2-0.8, p < 0.01) and those with a history of tuberculosis (- 14.4%pred, 95% CI - 23.5 to - 5.3, p < 0.01). COPD was diagnosed in 9 (4%) participants, eight of whom (89%) were PLWH, six of whom (67%) had a history of tuberculosis, and all of whom (100%) were men. Among 287 participants with complete symptom questionnaires, respiratory symptoms were more likely among women (AOR 3.9, 95% CI 2.0-7.7, p < 0.001) and those in homes cooking with charcoal (AOR 3.2, 95% CI 1.4-7.4, p = 0.008). CONCLUSION In rural Uganda, COPD may be more prevalent among PLWH, men, and those with prior tuberculosis. Future research is needed to confirm these findings and evaluate their broader impacts on health.
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Affiliation(s)
- Crystal M North
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, 55 Fruit Street, BUL-148, Boston, MA, 02114, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Joseph G Allen
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Samson Okello
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ruth Sentongo
- Mbarara University of Science and Technology, Mbarara, Uganda
| | | | - Edward T Ryan
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alexander C Tsai
- Harvard Medical School, Boston, MA, USA
- Chester M. Pierce, MD Division of Global Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - David C Christiani
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, 55 Fruit Street, BUL-148, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark J Siedner
- Harvard Medical School, Boston, MA, USA
- Mbarara University of Science and Technology, Mbarara, Uganda
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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27
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Huan T, Joehanes R, Schurmann C, Schramm K, Pilling LC, Peters MJ, Mägi R, DeMeo D, O'Connor GT, Ferrucci L, Teumer A, Homuth G, Biffar R, Völker U, Herder C, Waldenberger M, Peters A, Zeilinger S, Metspalu A, Hofman A, Uitterlinden AG, Hernandez DG, Singleton AB, Bandinelli S, Munson PJ, Lin H, Benjamin EJ, Esko T, Grabe HJ, Prokisch H, van Meurs JBJ, Melzer D, Levy D. A whole-blood transcriptome meta-analysis identifies gene expression signatures of cigarette smoking. Hum Mol Genet 2018; 25:4611-4623. [PMID: 28158590 DOI: 10.1093/hmg/ddw288] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/21/2016] [Accepted: 08/25/2016] [Indexed: 01/03/2023] Open
Abstract
Cigarette smoking is a leading modifiable cause of death worldwide. We hypothesized that cigarette smoking induces extensive transcriptomic changes that lead to target-organ damage and smoking-related diseases. We performed a meta-analysis of transcriptome-wide gene expression using whole blood-derived RNA from 10,233 participants of European ancestry in six cohorts (including 1421 current and 3955 former smokers) to identify associations between smoking and altered gene expression levels. At a false discovery rate (FDR) <0.1, we identified 1270 differentially expressed genes in current vs. never smokers, and 39 genes in former vs. never smokers. Expression levels of 12 genes remained elevated up to 30 years after smoking cessation, suggesting that the molecular consequence of smoking may persist for decades. Gene ontology analysis revealed enrichment of smoking-related genes for activation of platelets and lymphocytes, immune response, and apoptosis. Many of the top smoking-related differentially expressed genes, including LRRN3 and GPR15, have DNA methylation loci in promoter regions that were recently reported to be hypomethylated among smokers. By linking differential gene expression with smoking-related disease phenotypes, we demonstrated that stroke and pulmonary function show enrichment for smoking-related gene expression signatures. Mediation analysis revealed the expression of several genes (e.g. ALAS2) to be putative mediators of the associations between smoking and inflammatory biomarkers (IL6 and C-reactive protein levels). Our transcriptomic study provides potential insights into the effects of cigarette smoking on gene expression in whole blood and their relations to smoking-related diseases. The results of such analyses may highlight attractive targets for treating or preventing smoking-related health effects.
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Affiliation(s)
- Tianxiao Huan
- Boston University’s Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Roby Joehanes
- Boston University’s Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA.,Hebrew SeniorLife, Harvard Medical School, Boston, MA, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,Genetics of Obesity & Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Schramm
- Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Luke C Pilling
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Marjolein J Peters
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands.,The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Reedik Mägi
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | | | - George T O'Connor
- Boston University School of Medicine and School of Public Health, Boston, MA, USA
| | - Luigi Ferrucci
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Alexander Teumer
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Reiner Biffar
- Department of Prosthetic Dentistry, Gerostomatology and Dental Materials, Center of Oral Health, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Christian Herder
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sonja Zeilinger
- Institute of Epidemiology II, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Andres Metspalu
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands.,The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands.,The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Albert Hofman
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands.,The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center Rotterdam, The Netherlands
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Peter J Munson
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, MD, USA
| | - Honghuang Lin
- Boston University School of Medicine and School of Public Health, Boston, MA, USA
| | - Emelia J Benjamin
- Boston University’s Framingham Heart Study, Framingham, MA, USA.,The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands.,The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands.,Boston University School of Medicine and School of Public Health, Boston, MA, USA.,The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Tõnu Esko
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands.,Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.,German Center for Neurodegenerative Diseases DZNE, Site Rostock/Greifswald, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands.,The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - David Melzer
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Daniel Levy
- Boston University’s Framingham Heart Study, Framingham, MA, USA.,The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
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28
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Zhang Y, Petropoulos S, Liu J, Cheishvili D, Zhou R, Dymov S, Li K, Li N, Szyf M. The signature of liver cancer in immune cells DNA methylation. Clin Epigenetics 2018; 10:8. [PMID: 29375724 PMCID: PMC5774119 DOI: 10.1186/s13148-017-0436-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
Background The idea that changes to the host immune system are critical for cancer progression was proposed a century ago and recently regained experimental support. Results Herein, the hypothesis that hepatocellular carcinoma (HCC) leaves a molecular signature in the host peripheral immune system was tested by profiling DNA methylation in peripheral blood mononuclear cells (PBMC) and T cells from a discovery cohort (n = 69) of healthy controls, chronic hepatitis, and HCC using Illumina 450K platform and was validated in two validation sets (n = 80 and n = 48) using pyrosequencing. Conclusions The study reveals a broad signature of hepatocellular carcinoma in PBMC and T cells DNA methylation which discriminates early HCC stage from chronic hepatitis B and C and healthy controls, intensifies with progression of HCC, and is highly enriched in immune function-related genes such as PD-1, a current cancer immunotherapy target. These data also support the feasibility of using these profiles for early detection of HCC.
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Affiliation(s)
- Yonghong Zhang
- 1Beijing Youan Hospital, Capital Medical School, Beijing, China
| | - Sophie Petropoulos
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada.,3Deparment of Clinical Science, Karolinska Institutet, Alfred Nobels Allé 8, 141 52 Huddinge, Sweden
| | - Jinhua Liu
- 1Beijing Youan Hospital, Capital Medical School, Beijing, China
| | - David Cheishvili
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada.,Montreal EpiTerapia Inc., 4567 Cecile, H9K1N2, Montreal, QC Canada
| | - Rudy Zhou
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada
| | - Sergiy Dymov
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada
| | - Kang Li
- 1Beijing Youan Hospital, Capital Medical School, Beijing, China
| | - Ning Li
- 1Beijing Youan Hospital, Capital Medical School, Beijing, China
| | - Moshe Szyf
- 2Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G 1Y6 Canada
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Parker MM, Chase RP, Lamb A, Reyes A, Saferali A, Yun JH, Himes BE, Silverman EK, Hersh CP, Castaldi PJ. RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking. BMC Med Genomics 2017; 10:58. [PMID: 28985737 PMCID: PMC6225866 DOI: 10.1186/s12920-017-0295-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/02/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cigarette smoking is the leading modifiable risk factor for disease and death worldwide. Previous studies quantifying gene-level expression have documented the effect of smoking on mRNA levels. Using RNA sequencing, it is possible to analyze the impact of smoking on complex regulatory phenomena (e.g. alternative splicing, differential isoform usage) leading to a more detailed understanding of the biology underlying smoking-related disease. METHODS We used whole-blood RNA sequencing to describe gene and exon-level expression differences between 229 current and 286 former smokers in the COPDGene study. We performed differential gene expression and differential exon usage analyses using the voom/limma and DEXseq R packages. Samples from current and former smokers were compared while controlling for age, gender, race, lifetime smoke exposure, cell counts, and technical covariates. RESULTS At an adjusted p-value <0.05, 171 genes were differentially expressed between current and former smokers. Differentially expressed genes included 7 long non-coding RNAs that have not been previously associated with smoking: LINC00599, LINC01362, LINC00824, LINC01624, RP11-563D10.1, RP11-98G13.1, AC004791.2. Secondary analysis of acute smoking (having smoked within 2-h) revealed 5 of the 171 smoking genes demonstrated an acute response above the baseline effect of chronic smoking. Exon-level analyses identified 9 exons from 8 genes with significant differential usage by smoking status, suggesting smoking-induced changes in isoform expression. CONCLUSIONS Transcriptomic changes at the gene and exon levels from whole blood can refine our understanding of the molecular mechanisms underlying the response to smoking.
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Affiliation(s)
- Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA
| | - Andrew Lamb
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA
| | - Alejandro Reyes
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
- Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA.
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30
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Ozaki Y, Yoshino Y, Yamazaki K, Sao T, Mori Y, Ochi S, Yoshida T, Mori T, Iga JI, Ueno SI. DNA methylation changes at TREM2 intron 1 and TREM2 mRNA expression in patients with Alzheimer's disease. J Psychiatr Res 2017; 92:74-80. [PMID: 28412600 DOI: 10.1016/j.jpsychires.2017.04.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/23/2017] [Accepted: 04/10/2017] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Recent genome-wide association studies revealed that Triggering receptor expressed on myeloid cells 2 (TREM2) was associated with Alzheimer's disease (AD) and other neurodegenerative diseases. We previously reported that TREM2 mRNA is highly expressed in leukocytes of AD patients compared to those in healthy controls. However, the mechanism of TREM2 expression change is still not known. In this study, we examined the involvement of the DNA methylation status of TREM2 in its high gene expression. MATERIALS AND METHODS Fifty AD subjects and age- and sex-matched control subjects were recruited (25 males, 25 females; 79.9 ± 5.27 and 79.4 ± 3.92 years old, respectively). TREM2 mRNA expression and the percentage of DNA methylation at four CpG sites in intron 1 of TREM2 were studied using their peripheral leukocytes. RESULTS We confirmed that TREM2 mRNA expression in leukocytes was significantly higher in AD patients than in controls (p = 0.007). The percentage methylation at three CpG sites in TREM2 intron 1 was significantly lower in AD subjects than in control: CpG1, 9.4 ± 3.2 vs 11.9 ± 4.0 (p = 0.001); CpG2, 15.4 ± 4.9 vs 19.1 ± 4.8 (p = 0.001); CpG3, 20.8 ± 5.5 vs 25.5 ± 5.4 (p < 0.001); and the average percentage methylation of all CpG sites: 13.5 ± 3.7 vs 16.1 ± 3.8 (p = 0.002), respectively. In addition, there were significant negative correlations between TREM2 mRNA expression and the percentage DNA methylation of each of CpG sites (CpG1, r = -0.416, p < 0.001; CpG2, r = -0.510, p < 0.001; CpG3, r = -0.504, p < 0.001; CpG4, r = -0.356, p < 0.001). CONCLUSIONS Lower DNA methylation at TREM2 intron 1 caused higher TREM2 mRNA expression in the leukocytes of AD subjects versus controls and may be a biomarker for AD.
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Affiliation(s)
- Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Tomoko Sao
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Taku Yoshida
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan.
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
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Kan M, Shumyatcher M, Himes BE. Using omics approaches to understand pulmonary diseases. Respir Res 2017; 18:149. [PMID: 28774304 PMCID: PMC5543452 DOI: 10.1186/s12931-017-0631-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/26/2017] [Indexed: 12/24/2022] Open
Abstract
Omics approaches are high-throughput unbiased technologies that provide snapshots of various aspects of biological systems and include: 1) genomics, the measure of DNA variation; 2) transcriptomics, the measure of RNA expression; 3) epigenomics, the measure of DNA alterations not involving sequence variation that influence RNA expression; 4) proteomics, the measure of protein expression or its chemical modifications; and 5) metabolomics, the measure of metabolite levels. Our understanding of pulmonary diseases has increased as a result of applying these omics approaches to characterize patients, uncover mechanisms underlying drug responsiveness, and identify effects of environmental exposures and interventions. As more tissue- and cell-specific omics data is analyzed and integrated for diverse patients under various conditions, there will be increased identification of key mechanisms that underlie pulmonary biological processes, disease endotypes, and novel therapeutics that are efficacious in select individuals. We provide a synopsis of how omics approaches have advanced our understanding of asthma, chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS), idiopathic pulmonary fibrosis (IPF), and pulmonary arterial hypertension (PAH), and we highlight ongoing work that will facilitate pulmonary disease precision medicine.
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Affiliation(s)
- Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Maya Shumyatcher
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Blanca E. Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
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Miller RL, Zhang H, Jezioro J, De Planell Saguer M, Lovinsky-Desir S, Liu X, Perzanowski M, Divjan A, Phipatanakul W, Matsui EC. Reduced mouse allergen is associated with epigenetic changes in regulatory genes, but not mouse sensitization, in asthmatic children. ENVIRONMENTAL RESEARCH 2017; 156:619-624. [PMID: 28454014 PMCID: PMC5503684 DOI: 10.1016/j.envres.2017.04.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 03/06/2017] [Accepted: 04/20/2017] [Indexed: 06/07/2023]
Abstract
Chronic exposure to mouse allergen may contribute greatly to the inner-city asthma burden. We hypothesized that reducing mouse allergen exposure may modulate the immunopathology underlying symptomatic pediatric allergic asthma, and that this occurs through epigenetic regulation. To test this hypothesis, we studied a cohort of mouse sensitized, persistent asthmatic inner-city children undergoing mouse allergen-targeted integrated pest management (IPM) vs education in a randomized controlled intervention trial. We found that decreasing mouse allergen exposure, but not cockroach, was associated with reduced FOXP3 buccal DNA promoter methylation, but this was unrelated to mouse specific IgE production. This finding suggests that the environmental epigenetic regulation of an immunomodulatory gene may occur following changing allergen exposures in some highly exposed cohorts. Given the clinical and public health importance of inner-city pediatric asthma and the potential impact of environmental interventions, further studies will be needed to corroborate changes in epigenetic regulation following changing exposures over time, and determine their impact on asthma morbidity in susceptible children.
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Affiliation(s)
- Rachel L Miller
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA; Department of Environmental Health Sciences, Columbia University, 722 W 168th St, 11th Floor, New York City, NY, 10032, USA.
| | - Hanjie Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA
| | - Jacqueline Jezioro
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA
| | - Mariangels De Planell Saguer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, PH8E-101B, 630 W. 168th St., New York City, NY 10032, USA
| | - Stephanie Lovinsky-Desir
- Division of Pulmonary, Department of Pediatrics, Columbia University Medical Center, 3959 Broadway, CHC 7-701, New York City, NY 10032, USA
| | - Xinhua Liu
- Department of Biostatistics, Columbia University Medical Center, 722 W 168 St, 6 Floor, New York City, NY, 10032, USA
| | - Matthew Perzanowski
- Department of Environmental Health Sciences, Columbia University, 722 W 168th St, 11th Floor, New York City, NY, 10032, USA
| | - Adnan Divjan
- Department of Environmental Health Sciences, Columbia University, 722 W 168th St, 11th Floor, New York City, NY, 10032, USA
| | - Wanda Phipatanakul
- Division of Pediatric Allergy/Immunology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Elizabeth C Matsui
- Division of Pediatric Allergy/Immunology, Johns Hopkins School of Medicine, CMSC 1102, 600 N. Wolfe Street, Baltimore, MD 21287, USA
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Lee DH, Hwang SH, Lim MK, Oh JK, Song DY, Yun EH, Park EY. Performance of urine cotinine and hypomethylation of AHRR and F2RL3 as biomarkers for smoking exposure in a population-based cohort. PLoS One 2017; 12:e0176783. [PMID: 28453567 PMCID: PMC5409156 DOI: 10.1371/journal.pone.0176783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/17/2017] [Indexed: 12/11/2022] Open
Abstract
There is a growing body of evidence demonstrating an association between smoking and DNA methylation. Accordingly, DNA methylation is now considered a promising biomarker of smoking exposure. We evaluated the relationship between methylation markers (AHRR and F2RL3) and urine cotinine as well as self-reported smoking status. DNA methylation levels of AHRR and F2RL3 in blood as well as urine cotinine were measured in 330 adults (46 to 87 years of age). Pyrosequencing was performed to measure DNA methylation of AHRR and F2RL3 associated with smoking exposure. The lung cancer risk associated with DNA methylation and urine cotinine was analyzed using logistic regression analysis. The AHRR and F2RL3 genes were significantly hypomethylated in current smokers compared to in individuals who have never smoked. An inverse relationship was observed between urine cotinine and methylation levels. Methylation of AHRR and F2RL3 distinguished current smokers from never-smokers with high accuracy. Logistic multivariate analysis showed that AHRR methylation is significantly associated with the risk of lung cancer (OR = 0.96, P = 0.011). Our study validated the smoking-associated DNA methylation markers reported in a Korean population-based cohort. In conclusion, DNA methylation of AHRR and F2RL3 provided accurate measures for smoking exposure. Methylation markers reflecting the long-term effect of smoking on the risk of lung cancer showed better performance in distinguishing former smokers from never-smokers.
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Affiliation(s)
- Do-Hoon Lee
- Department of Laboratory Medicine, Center for Diagnostic Oncology, Research Institute and Hospital, National Cancer Center, Goyang-si, Gyeinggi-do, Republic of Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, Center for Diagnostic Oncology, Research Institute and Hospital, National Cancer Center, Goyang-si, Gyeinggi-do, Republic of Korea
- Hematologic Malignancy Branch, Research Institute and Hospital, National Cancer Center, Goyang-si, Gyeinggi-do, Republic of Korea
- * E-mail:
| | - Min Kyung Lim
- Department of Cancer Control Policy, Graduate School of Cancer Science and Policy, and National Cancer Control Institute, National Cancer Center, Goyang, Gyeinggi-do, Republic of Korea
- Cancer Risk Appraisal and Prevention Branch, National Cancer Control Institute, National Cancer Center, Goyang-si, Gyeinggi-do, Republic of Korea
| | - Jin-Kyoung Oh
- Department of Cancer Control Policy, Graduate School of Cancer Science and Policy, and National Cancer Control Institute, National Cancer Center, Goyang, Gyeinggi-do, Republic of Korea
- Cancer Risk Appraisal and Prevention Branch, National Cancer Control Institute, National Cancer Center, Goyang-si, Gyeinggi-do, Republic of Korea
| | - Da Young Song
- Cancer Risk Appraisal and Prevention Branch, National Cancer Control Institute, National Cancer Center, Goyang-si, Gyeinggi-do, Republic of Korea
| | - E. Hwa Yun
- Department of Cancer Control Policy, Graduate School of Cancer Science and Policy, and National Cancer Control Institute, National Cancer Center, Goyang, Gyeinggi-do, Republic of Korea
- Cancer Risk Appraisal and Prevention Branch, National Cancer Control Institute, National Cancer Center, Goyang-si, Gyeinggi-do, Republic of Korea
| | - Eun Young Park
- Carcinogenic Hazard Branch, National Cancer Control Institute, National Cancer Center, Goyang-si, Gyeinggi-do, Republic of Korea
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Sundar IK, Yin Q, Baier BS, Yan L, Mazur W, Li D, Susiarjo M, Rahman I. DNA methylation profiling in peripheral lung tissues of smokers and patients with COPD. Clin Epigenetics 2017; 9:38. [PMID: 28416970 PMCID: PMC5391602 DOI: 10.1186/s13148-017-0335-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/29/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Epigenetics changes have been shown to be affected by cigarette smoking. Cigarette smoke (CS)-mediated DNA methylation can potentially affect several cellular and pathophysiological processes, acute exacerbations, and comorbidity in the lungs of patients with chronic obstructive pulmonary disease (COPD). We sought to determine whether genome-wide lung DNA methylation profiles of smokers and patients with COPD were significantly different from non-smokers. We isolated DNA from parenchymal lung tissues of patients including eight lifelong non-smokers, eight current smokers, and eight patients with COPD and analyzed the samples using Illumina's Infinium HumanMethylation450 BeadChip. RESULTS Our data revealed that the differentially methylated genes were related to top canonical pathways (e.g., G beta gamma signaling, mechanisms of cancer, and nNOS signaling in neurons), disease and disorders (organismal injury and abnormalities, cancer, and respiratory disease), and molecular and cellular functions (cell death and survival, cellular assembly and organization, cellular function and maintenance) in patients with COPD. The genome-wide DNA methylation analysis identified suggestive genes, such as NOS1AP, TNFAIP2, BID, GABRB1, ATXN7, and THOC7 with DNA methylation changes in COPD lung tissues that were further validated by pyrosequencing. Pyrosequencing validation confirmed hyper-methylation in smokers and patients with COPD as compared to non-smokers. However, we did not detect significant differences in DNA methylation for TNFAIP2, ATXN7, and THOC7 genes in smokers and COPD groups despite the changes observed in the genome-wide analysis. CONCLUSIONS Our study suggests that DNA methylation in suggestive genes, such as NOS1AP, BID, and GABRB1 may be used as epigenetic signatures in smokers and patients with COPD if the same is validated in a larger cohort. Future studies are required to correlate DNA methylation status with transcriptomics of selective genes identified in this study and elucidate their role and involvement in the progression of COPD and its exacerbations.
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Affiliation(s)
- Isaac K Sundar
- Department of Environmental Medicine, University of Rochester Medical Center, Box 850, 601 Elmwood Avenue, Rochester, 14642 NY USA
| | - Qiangzong Yin
- Department of Environmental Medicine, University of Rochester Medical Center, Box 850, 601 Elmwood Avenue, Rochester, 14642 NY USA
| | - Brian S Baier
- Department of Environmental Medicine, University of Rochester Medical Center, Box 850, 601 Elmwood Avenue, Rochester, 14642 NY USA
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY USA
| | - Witold Mazur
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Dongmei Li
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY USA
| | - Martha Susiarjo
- Department of Environmental Medicine, University of Rochester Medical Center, Box 850, 601 Elmwood Avenue, Rochester, 14642 NY USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Box 850, 601 Elmwood Avenue, Rochester, 14642 NY USA
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35
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San-Cristobal R, Navas-Carretero S, Milagro FI, Riezu-Boj JI, Guruceaga E, Celis-Morales C, Livingstone KM, Brennan L, Lovegrove JA, Daniel H, Saris WH, Traczyk I, Manios Y, Gibney ER, Gibney MJ, Mathers JC, Martinez JA. Gene methylation parallelisms between peripheral blood cells and oral mucosa samples in relation to overweight. J Physiol Biochem 2017; 73:465-474. [DOI: 10.1007/s13105-017-0560-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/16/2017] [Indexed: 01/08/2023]
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36
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Vineis P, Chatziioannou A, Cunliffe VT, Flanagan JM, Hanson M, Kirsch-Volders M, Kyrtopoulos S. Epigenetic memory in response to environmental stressors. FASEB J 2017; 31:2241-2251. [PMID: 28280003 DOI: 10.1096/fj.201601059rr] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022]
Abstract
Exposure to environmental stressors, toxicants, and nutrient deficiencies can affect DNA in several ways. Some exposures cause damage and alter the structure of DNA, but there is increasing evidence that the same or other environmental exposures, including those that occur during fetal development in utero, can cause epigenetic effects that modulate DNA function and gene expression. Some epigenetic changes to DNA that affect gene transcription are at least partially reversible (i.e., they can be enzymatically reversed after cessation of exposure to environmental agents), but some epigenetic modifications seem to persist, even for decades. To explain the effects of early life experiences (such as famine and exposures to other stressors) on the long-term persistence of specific patterns of epigenetic modifications, such as DNA methylation, we propose an analogy with immune memory. We propose that an epigenetic memory can be established and maintained in self-renewing stem cell compartments. We suggest that the observations on early life effects on adult diseases and the persistence of methylation changes in smokers support our hypothesis, for which a mechanistic basis, however, needs to be further clarified. We outline a new model based on methylation changes. Although these changes seem to be mainly adaptive, they are also implicated in the pathogenesis and onset of diseases, depending on individual genotypic background and types of subsequent exposures. Elucidating the relationships between the adaptive and maladaptive consequences of the epigenetic modifications that result from complex environmental exposures is a major challenge for current and future research in epigenetics.-Vineis, P., Chatziioannou, A., Cunliffe, V. T., Flanagan, J. M., Hanson, M., Kirsch-Volders, M., Kyrtopoulos, S. Epigenetic memory in response to environmental stressors.
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Affiliation(s)
- Paolo Vineis
- Medical Research Council-Public Health England Center for Environment and Health, Imperial College London, London, United Kingdom;
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Vincent T Cunliffe
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - James M Flanagan
- Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Mark Hanson
- Institute of Developmental Sciences, University Hospital Southampton, University of Southampton, United Kingdom
| | | | - Soterios Kyrtopoulos
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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37
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Walters MS, Salit J, Ju JH, Staudt MR, Kaner RJ, Rogalski AM, Sodeinde TB, Rahim R, Strulovici-Barel Y, Mezey JG, Almulla AM, Sattar H, Mahmoud M, Crystal RG. Waterpipe smoking induces epigenetic changes in the small airway epithelium. PLoS One 2017; 12:e0171112. [PMID: 28273093 PMCID: PMC5342191 DOI: 10.1371/journal.pone.0171112] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/16/2017] [Indexed: 01/01/2023] Open
Abstract
Waterpipe (also called hookah, shisha, or narghile) smoking is a common form of tobacco use in the Middle East. Its use is becoming more prevalent in Western societies, especially among young adults as an alternative form of tobacco use to traditional cigarettes. While the risk to cigarette smoking is well documented, the risk to waterpipe smoking is not well defined with limited information on its health impact at the epidemiologic, clinical and biologic levels with respect to lung disease. Based on the knowledge that airway epithelial cell DNA methylation is modified in response to cigarette smoke and in cigarette smoking-related lung diseases, we assessed the impact of light-use waterpipe smoking on DNA methylation of the small airway epithelium (SAE) and whether changes in methylation were linked to the transcriptional output of the cells. Small airway epithelium was obtained from 7 nonsmokers and 7 light-use (2.6 ± 1.7 sessions/wk) waterpipe-only smokers. Genome-wide comparison of SAE DNA methylation of waterpipe smokers to nonsmokers identified 727 probesets differentially methylated (fold-change >1.5, p<0.05) representing 673 unique genes. Dominant pathways associated with these epigenetic changes include those linked to G-protein coupled receptor signaling, aryl hydrocarbon receptor signaling and xenobiotic metabolism signaling, all of which have been associated with cigarette smoking and lung disease. Of the genes differentially methylated, 11.3% exhibited a corresponding significant (p<0.05) change in gene expression with enrichment in pathways related to regulation of mRNA translation and protein synthesis (eIF2 signaling and regulation of eIF4 and p70S6K signaling). Overall, these data demonstrate that light-use waterpipe smoking is associated with epigenetic changes and related transcriptional modifications in the SAE, the cell population demonstrating the earliest pathologic abnormalities associated with chronic cigarette smoking.
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Affiliation(s)
- Matthew S. Walters
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jin Hyun Ju
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Michelle R. Staudt
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Robert J. Kaner
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Allison M. Rogalski
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Teniola B. Sodeinde
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Riyaad Rahim
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Yael Strulovici-Barel
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | | | - Hisham Sattar
- Pulmonary Section, Hamad Medical Corporation, Doha, Qatar
| | - Mai Mahmoud
- Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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Costa LDA, da Silva ICB, Mariz BALA, da Silva MB, Freitas-Ribeiro GM, de Oliveira NFP. Influence of smoking on methylation and hydroxymethylation levels in global DNA and specific sites of KRT14 , KRT19 , MIR-9-3 and MIR-137 genes of oral mucosa. Arch Oral Biol 2016; 72:56-65. [DOI: 10.1016/j.archoralbio.2016.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 06/08/2016] [Accepted: 08/10/2016] [Indexed: 12/14/2022]
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Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics 2016; 11:730-739. [PMID: 27564456 PMCID: PMC5094634 DOI: 10.1080/15592294.2016.1226451] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/05/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a smoking-related disease characterized by genetic and phenotypic heterogeneity. Although association studies have identified multiple genomic regions with replicated associations to COPD, genetic variation only partially explains the susceptibility to lung disease, and suggests the relevance of epigenetic investigations. We performed genome-wide DNA methylation profiling in homogenized lung tissue samples from 46 control subjects with normal lung function and 114 subjects with COPD, all former smokers. The differentially methylated loci were integrated with previous genome-wide association study results. The top 535 differentially methylated sites, filtered for a minimum mean methylation difference of 5% between cases and controls, were enriched for CpG shelves and shores. Pathway analysis revealed enrichment for transcription factors. The top differentially methylated sites from the intersection with previous GWAS were in CHRM1, GLT1D1, and C10orf11; sorted by GWAS P-value, the top sites included FRMD4A, THSD4, and C10orf11. Epigenetic association studies complement genetic association studies to identify genes potentially involved in COPD pathogenesis. Enrichment for genes implicated in asthma and lung function and for transcription factors suggests the potential pathogenic relevance of genes identified through differential methylation and the intersection with a broader range of GWAS associations.
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Affiliation(s)
- Jarrett D. Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H. Cho
- 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
| | - 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
| | | | - Bartolome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Gerard Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Augustine M. K. Choi
- Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 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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40
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Joehanes R, Just AC, Marioni RE, Pilling LC, Reynolds LM, Mandaviya PR, Guan W, Xu T, Elks CE, Aslibekyan S, Moreno-Macias H, Smith JA, Brody JA, Dhingra R, Yousefi P, Pankow JS, Kunze S, Shah S, McRae AF, Lohman K, Sha J, Absher DM, Ferrucci L, Zhao W, Demerath EW, Bressler J, Grove ML, Huan T, Liu C, Mendelson MM, Yao C, Kiel DP, Peters A, Wang-Sattler R, Visscher PM, Wray NR, Starr JM, Ding J, Rodriguez CJ, Wareham NJ, Irvin MR, Zhi D, Barrdahl M, Vineis P, Ambatipudi S, Uitterlinden AG, Hofman A, Schwartz J, Colicino E, Hou L, Vokonas PS, Hernandez DG, Singleton AB, Bandinelli S, Turner ST, Ware EB, Smith AK, Klengel T, Binder EB, Psaty BM, Taylor KD, Gharib SA, Swenson BR, Liang L, DeMeo DL, O'Connor GT, Herceg Z, Ressler KJ, Conneely KN, Sotoodehnia N, Kardia SLR, Melzer D, Baccarelli AA, van Meurs JBJ, Romieu I, Arnett DK, Ong KK, Liu Y, Waldenberger M, Deary IJ, Fornage M, Levy D, London SJ. Epigenetic Signatures of Cigarette Smoking. CIRCULATION. CARDIOVASCULAR GENETICS 2016; 9:436-447. [PMID: 27651444 PMCID: PMC5267325 DOI: 10.1161/circgenetics.116.001506] [Citation(s) in RCA: 532] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 08/16/2016] [Indexed: 01/19/2023]
Abstract
BACKGROUND DNA methylation leaves a long-term signature of smoking exposure and is one potential mechanism by which tobacco exposure predisposes to adverse health outcomes, such as cancers, osteoporosis, lung, and cardiovascular disorders. METHODS AND RESULTS To comprehensively determine the association between cigarette smoking and DNA methylation, we conducted a meta-analysis of genome-wide DNA methylation assessed using the Illumina BeadChip 450K array on 15 907 blood-derived DNA samples from participants in 16 cohorts (including 2433 current, 6518 former, and 6956 never smokers). Comparing current versus never smokers, 2623 cytosine-phosphate-guanine sites (CpGs), annotated to 1405 genes, were statistically significantly differentially methylated at Bonferroni threshold of P<1×10-7 (18 760 CpGs at false discovery rate <0.05). Genes annotated to these CpGs were enriched for associations with several smoking-related traits in genome-wide studies including pulmonary function, cancers, inflammatory diseases, and heart disease. Comparing former versus never smokers, 185 of the CpGs that differed between current and never smokers were significant P<1×10-7 (2623 CpGs at false discovery rate <0.05), indicating a pattern of persistent altered methylation, with attenuation, after smoking cessation. Transcriptomic integration identified effects on gene expression at many differentially methylated CpGs. CONCLUSIONS Cigarette smoking has a broad impact on genome-wide methylation that, at many loci, persists many years after smoking cessation. Many of the differentially methylated genes were novel genes with respect to biological effects of smoking and might represent therapeutic targets for prevention or treatment of tobacco-related diseases. Methylation at these sites could also serve as sensitive and stable biomarkers of lifetime exposure to tobacco smoke.
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Affiliation(s)
- Roby Joehanes
- Inst for Aging Research, Hebrew SeniorLife, Dept of Medicine Beth Israel Deaconess Medical Center & Harvard Medical School, Boston
- Population Sciences Branch, National Heart, Lung, and Blood Inst, National Insts of Health, Bethesda, MD & Framingham Heart Study, Framingham, MA
| | - Allan C. Just
- Dept of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing & Cognitive Epidemiology, Edinburgh, UK
- Centre for Genomic & Experimental Medicine, Inst of Genetics & Molecular Medicine, Univ of Edinburgh, Edinburgh, UK
- Queensland Brain Inst, Univ of Queensland, Brisbane, Australia
| | - Luke C. Pilling
- Epidemiology & Public Health Group, Inst of Biomedical & Clinical Science, Univ of Exeter Medical School, Exeter, UK
| | - Lindsay M. Reynolds
- Dept of Epidemiology & Prevention, Public Health Sciences, Winston-Salem, NC
| | - Pooja R. Mandaviya
- Dept of Internal Medicine, Erasmus Univ Medical Center, Rotterdam, the Netherlands
- Dept of Clinical Chemistry, Erasmus Univ Medical Center, Rotterdam, the Netherlands
| | - Weihua Guan
- Division of Biostatistics, Univ of Minnesota, Minneapolis, MN
| | - Tao Xu
- Research Unit of Molecular Epidemiology, Inst of Epidemiology II, Helmhotz Zentrum Muenchen, Munich, Germany
| | - Cathy E. Elks
- MRC Epidemiology Unit, Inst of Metabolic Science, Univ of Cambridge, Cambridge, UK
| | | | - Hortensia Moreno-Macias
- Autonomous Metropolitan Univ-Iztapalapa, Mexico City, Mexico
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Jennifer A. Smith
- Dept of Epidemiology, School of Public Health, Univ of Michigan, Ann Arbor, MI
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Dept of Medicine, Epidemiology, & Health Services, Univ of Washington, Seattle, WA
| | - Radhika Dhingra
- Dept of Environmental Health, Rollins School of Public Health, Emory Univ, Atlanta, GA
| | - Paul Yousefi
- School of Public Health, Univ of California, Berkeley, CA
| | - James S. Pankow
- Division of Epidemiology & Community Health, School of Public Health, Univ of Minnesota, Minneapolis, MN
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Inst of Epidemiology II, Helmhotz Zentrum Muenchen, Munich, Germany
| | - Sonia Shah
- Queensland Brain Inst, Univ of Queensland, Brisbane, Australia
- Univ of Queensland Diamantina Inst, Translational Research Inst, Univ of Queensland, Brisbane, Australia
| | - Allan F. McRae
- Queensland Brain Inst, Univ of Queensland, Brisbane, Australia
- Univ of Queensland Diamantina Inst, Translational Research Inst, Univ of Queensland, Brisbane, Australia
| | - Kurt Lohman
- Dept of Biostatistical Sciences, Division of Public Health Sciences, Winston-Salem, NC
| | - Jin Sha
- Dept of Epidemiology, Univ of Alabama at Birmingham, Birmingham, AL
| | | | - Luigi Ferrucci
- Clinical Research Branch, National Inst on Aging, Baltimore, MD
| | - Wei Zhao
- Dept of Epidemiology, School of Public Health, Univ of Michigan, Ann Arbor, MI
| | | | - Jan Bressler
- Human Genetics Center, School of Public Health, The Univ of Texas Health Science Center at Houston, Houston, TX
| | - Megan L. Grove
- Human Genetics Center, School of Public Health, The Univ of Texas Health Science Center at Houston, Houston, TX
| | - Tianxiao Huan
- Population Sciences Branch, National Heart, Lung, and Blood Inst, National Insts of Health, Bethesda, MD & Framingham Heart Study, Framingham, MA
| | - Chunyu Liu
- Population Sciences Branch, National Heart, Lung, and Blood Inst, National Insts of Health, Bethesda, MD & Framingham Heart Study, Framingham, MA
| | - Michael M. Mendelson
- Population Sciences Branch, National Heart, Lung, and Blood Inst, National Insts of Health, Bethesda, MD & Framingham Heart Study, Framingham, MA
- Children's Hospital, Boston, MA
| | - Chen Yao
- Population Sciences Branch, National Heart, Lung, and Blood Inst, National Insts of Health, Bethesda, MD & Framingham Heart Study, Framingham, MA
| | - Douglas P. Kiel
- Inst for Aging Research, Hebrew SeniorLife, Dept of Medicine Beth Israel Deaconess Medical Center & Harvard Medical School, Boston
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Inst of Epidemiology II, Helmhotz Zentrum Muenchen, Munich, Germany
| | - Rui Wang-Sattler
- Research Unit of Molecular Epidemiology, Inst of Epidemiology II, Helmhotz Zentrum Muenchen, Munich, Germany
| | - Peter M. Visscher
- Centre for Cognitive Ageing & Cognitive Epidemiology, Edinburgh, UK
- Queensland Brain Inst, Univ of Queensland, Brisbane, Australia
- Univ of Queensland Diamantina Inst, Translational Research Inst, Univ of Queensland, Brisbane, Australia
| | - Naomi R. Wray
- Queensland Brain Inst, Univ of Queensland, Brisbane, Australia
| | - John M. Starr
- Centre for Cognitive Ageing & Cognitive Epidemiology, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, Univ of Edinburgh, Edinburgh, UK
| | - Jingzhong Ding
- Dept of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - Carlos J. Rodriguez
- Dept of Epidemiology & Prevention, Public Health Sciences, Winston-Salem, NC
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Inst of Metabolic Science, Univ of Cambridge, Cambridge, UK
| | | | - Degui Zhi
- School of Biomedical Informatics & School of Public Health, The Univ of Texas Health Science Center at Houston, Houston, TX
| | - Myrto Barrdahl
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Paolo Vineis
- MRC/PHE Centre for Environment & Health, School of Public Health, Imperial College London, UK
- HuGeF Foundation, Torino, Italy
| | | | | | - Albert Hofman
- Dept of Epidemiology, Erasmus Univ Medical Center, Rotterdam, The Netherlands
| | - Joel Schwartz
- Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Elena Colicino
- Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lifang Hou
- Dept of Preventive Medicine and the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern Univ, Chicago, IL
| | - Pantel S. Vokonas
- VA Normative Aging Study, VA Boston Healthcare System & Dept of Medicine, Boston Univ School of Medicine, Boston, MA
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Inst on Aging, National Insts of Health, Bethesda, MD
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Inst on Aging, National Insts of Health, Bethesda, MD
| | | | | | - Erin B. Ware
- Dept of Epidemiology, School of Public Health, Univ of Michigan, Ann Arbor, MI
- Research Center for Group Dynamics, Inst for Social Research, Univ of Michigan, Ann Arbor, MI
| | - Alicia K. Smith
- Psychiatry & Behavioral Sciences, Emory Univ School of Medicine, Atlanta, GA
| | - Torsten Klengel
- Dept of Translational Research in Psychiatry, Max-Planck Inst of Psychiatry, Munich, Germany
- Division of Depression & Anxiety Disorders, McLean Hospital, Belmont, MA
| | - Elisabeth B. Binder
- Dept of Translational Research in Psychiatry, Max-Planck Inst of Psychiatry, Munich, Germany
- Dept of Psychiatry and Behavioral Sciences, Emory Univ School of Medicine, Atlanta, GA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Dept of Medicine, Epidemiology, & Health Services, Univ of Washington, Seattle, WA
- Inst for Translational Genomics & Population Sciences, Los Angeles BioMedical Research Inst
| | - Kent D. Taylor
- Inst for Translational Genomics & Population Sciences, Los Angeles BioMedical Research Inst
- Division of Genomic Outcomes, Dept of Pediatrics, Harbor-UCLA Medical Center, Torrance
- Depts of Pediatrics, Medicine, and Human Genetics, UCLA, Los Angeles, CA
| | - Sina A. Gharib
- Center for Lung Biology, Division of Pulmonary & Critical Care Medicine, Dept of Medicine, Univ of Washington, Seattle, WA
| | - Brenton R. Swenson
- Cardiovascular Health Research Unit, Dept of Medicine, Epidemiology, & Health Services, Univ of Washington, Seattle, WA
| | | | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham & Women's Hospital, Harvard Medical School
| | | | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Kerry J. Ressler
- Psychiatry & Behavioral Sciences, Emory Univ School of Medicine, Atlanta, GA
- Division of Depression & Anxiety Disorders, McLean Hospital, Belmont, MA
- Dept of Psychiatry, Harvard Medical School
| | | | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, Dept of Epidemiology, Univ of Washington, Seattle, WA
| | - Sharon L. R. Kardia
- Dept of Epidemiology, School of Public Health, Univ of Michigan, Ann Arbor, MI
| | - David Melzer
- Epidemiology & Public Health Group, Inst of Biomedical & Clinical Science, Univ of Exeter Medical School, Exeter, UK
| | - Andrea A. Baccarelli
- Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
- Dept of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA
| | | | - Isabelle Romieu
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Donna K. Arnett
- Dept of Epidemiology, Univ of Alabama at Birmingham, Birmingham, AL
| | - Ken K. Ong
- MRC Epidemiology Unit, Inst of Metabolic Science, Univ of Cambridge, Cambridge, UK
| | - Yongmei Liu
- Dept of Epidemiology & Prevention, Public Health Sciences, Winston-Salem, NC
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Inst of Epidemiology II, Helmhotz Zentrum Muenchen, Munich, Germany
| | - Ian J. Deary
- Centre for Cognitive Ageing & Cognitive Epidemiology, Edinburgh, UK
- Dept of Psychology, Univ of Edinburgh, Edinburgh, UK
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, The Univ of Texas Health Science Center at Houston, Houston, TX
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Inst, National Insts of Health, Bethesda, MD & Framingham Heart Study, Framingham, MA
| | - Stephanie J. London
- Epidemiology Branch, National Inst of Environmental Health Sciences, National Insts of Health, Dept of Health and Human Services, Research Triangle Park, NC
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41
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Joubert BR, Felix JF, Yousefi P, Bakulski KM, Just AC, Breton C, Reese SE, Markunas CA, Richmond RC, Xu CJ, Küpers LK, Oh SS, Hoyo C, Gruzieva O, Söderhäll C, Salas LA, Baïz N, Zhang H, Lepeule J, Ruiz C, Ligthart S, Wang T, Taylor JA, Duijts L, Sharp GC, Jankipersadsing SA, Nilsen RM, Vaez A, Fallin MD, Hu D, Litonjua AA, Fuemmeler BF, Huen K, Kere J, Kull I, Munthe-Kaas MC, Gehring U, Bustamante M, Saurel-Coubizolles MJ, Quraishi BM, Ren J, Tost J, Gonzalez JR, Peters MJ, Håberg SE, Xu Z, van Meurs JB, Gaunt TR, Kerkhof M, Corpeleijn E, Feinberg AP, Eng C, Baccarelli AA, Benjamin Neelon SE, Bradman A, Merid SK, Bergström A, Herceg Z, Hernandez-Vargas H, Brunekreef B, Pinart M, Heude B, Ewart S, Yao J, Lemonnier N, Franco OH, Wu MC, Hofman A, McArdle W, Van der Vlies P, Falahi F, Gillman MW, Barcellos LF, Kumar A, Wickman M, Guerra S, Charles MA, Holloway J, Auffray C, Tiemeier HW, Smith GD, Postma D, Hivert MF, Eskenazi B, Vrijheid M, Arshad H, Antó JM, Dehghan A, Karmaus W, Annesi-Maesano I, Sunyer J, Ghantous A, Pershagen G, Holland N, Murphy SK, DeMeo DL, Burchard EG, Ladd-Acosta C, Snieder H, Nystad W, Koppelman GH, Relton CL, Jaddoe VWV, Wilcox A, Melén E, London SJ. DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis. Am J Hum Genet 2016; 98:680-96. [PMID: 27040690 PMCID: PMC4833289 DOI: 10.1016/j.ajhg.2016.02.019] [Citation(s) in RCA: 573] [Impact Index Per Article: 71.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/20/2016] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences. The mechanisms are largely unknown, but epigenetics most likely plays a role. We formed the Pregnancy And Childhood Epigenetics (PACE) consortium and meta-analyzed, across 13 cohorts (n = 6,685), the association between maternal smoking in pregnancy and newborn blood DNA methylation at over 450,000 CpG sites (CpGs) by using the Illumina 450K BeadChip. Over 6,000 CpGs were differentially methylated in relation to maternal smoking at genome-wide statistical significance (false discovery rate, 5%), including 2,965 CpGs corresponding to 2,017 genes not previously related to smoking and methylation in either newborns or adults. Several genes are relevant to diseases that can be caused by maternal smoking (e.g., orofacial clefts and asthma) or adult smoking (e.g., certain cancers). A number of differentially methylated CpGs were associated with gene expression. We observed enrichment in pathways and processes critical to development. In older children (5 cohorts, n = 3,187), 100% of CpGs gave at least nominal levels of significance, far more than expected by chance (p value < 2.2 × 10(-16)). Results were robust to different normalization methods used across studies and cell type adjustment. In this large scale meta-analysis of methylation data, we identified numerous loci involved in response to maternal smoking in pregnancy with persistence into later childhood and provide insights into mechanisms underlying effects of this important exposure.
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Affiliation(s)
- Bonnie R Joubert
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - Paul Yousefi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Kelly M Bakulski
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Allan C Just
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carrie Breton
- University of Southern California, Los Angeles, CA 90032, USA
| | - Sarah E Reese
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Christina A Markunas
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Cheng-Jian Xu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Leanne K Küpers
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Cathrine Hoyo
- Department of Biological Sciences and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695-7633, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 141 83, Sweden
| | - Lucas A Salas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Nour Baïz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Saint-Antoine Medical School, F75012 Paris, France
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Johanna Lepeule
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Institut Albert Bonniot, Institut National de la Santé et de le Recherche Médicale, University of Grenoble Alpes, Centre Hospitalier Universitaire de Grenoble, F-38000 Grenoble, France
| | - Carlos Ruiz
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Symen Ligthart
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Tianyuan Wang
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jack A Taylor
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Liesbeth Duijts
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands; Division of Neonatology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands; Division of Respiratory Medicine, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Soesma A Jankipersadsing
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Roy M Nilsen
- Department of Global Public Health and Primary Care, University of Bergen, Bergen 5018, Norway
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; School of Medicine, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - M Daniele Fallin
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bernard F Fuemmeler
- Department of Community and Family Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Karen Huen
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 141 83, Sweden
| | - Inger Kull
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | | | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, the Netherlands
| | - Mariona Bustamante
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Center for Genomic Regulation (CRG), Barcelona 08003, Spain
| | | | - Bilal M Quraishi
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Jie Ren
- University of Southern California, Los Angeles, CA 90032, USA
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, 91000 Evry, France
| | - Juan R Gonzalez
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Marjolein J Peters
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Siri E Håberg
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo 0403, Norway
| | - Zongli Xu
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Joyce B van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Marjan Kerkhof
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Andrew P Feinberg
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Asa Bradman
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3508 TD, the Netherlands
| | - Mariona Pinart
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Barbara Heude
- INSERM, UMR 1153, Early Origin of the Child's Health And Development (ORCHAD) Team, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Université Paris Descartes, 94807 Villejuif, France
| | - Susan Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jin Yao
- University of Southern California, Los Angeles, CA 90032, USA
| | - Nathanaël Lemonnier
- Centre National de la Recherche Scientifique-École Normale Supérieure de Lyon-Université Claude Bernard (Lyon 1), Université de Lyon, European Institute for Systems Biology and Medicine 69007 Lyon, France
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Michael C Wu
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Wendy McArdle
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Pieter Van der Vlies
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Fahimeh Falahi
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Matthew W Gillman
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Lisa F Barcellos
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Department of Public Health Epidemiology, Unit of Chronic Disease Epidemiology, Swiss Tropical and Public Health Institute, Basel 4051, Switzerland; University of Basel, Basel 4001, Switzerland
| | - Magnus Wickman
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Sachs' Children's Hospital and Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm 171 77, Sweden
| | - Stefano Guerra
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain
| | - Marie-Aline Charles
- INSERM, UMR 1153, Early Origin of the Child's Health And Development (ORCHAD) Team, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Université Paris Descartes, 94807 Villejuif, France
| | - John Holloway
- Faculty of Medicine, Clinical & Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK; Faculty of Medicine, Human Development & Health, University of Southampton, Southampton SO16 6YD, UK
| | - Charles Auffray
- Centre National de la Recherche Scientifique-École Normale Supérieure de Lyon-Université Claude Bernard (Lyon 1), Université de Lyon, European Institute for Systems Biology and Medicine 69007 Lyon, France
| | - Henning W Tiemeier
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Dirkje Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Marie-France Hivert
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Martine Vrijheid
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Hasan Arshad
- Faculty of Medicine, Clinical & Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Josep M Antó
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Isabella Annesi-Maesano
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Saint-Antoine Medical School, F75012 Paris, France
| | - Jordi Sunyer
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Nina Holland
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Susan K Murphy
- Departments of Obstetrics and Gynecology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Christine Ladd-Acosta
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Wenche Nystad
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo 0403, Norway
| | - Gerard H Koppelman
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - Allen Wilcox
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Sachs' Children's Hospital and Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm 171 77, Sweden
| | - Stephanie J London
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
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Current and Future Prospects for Epigenetic Biomarkers of Substance Use Disorders. Genes (Basel) 2015; 6:991-1022. [PMID: 26473933 PMCID: PMC4690026 DOI: 10.3390/genes6040991] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 01/30/2023] Open
Abstract
Substance abuse has an enormous impact on economic and quality of life measures throughout the world. In more developed countries, overutilization of the most common forms of substances of abuse, alcohol and tobacco, is addressed primarily through prevention of substance use initiation and secondarily through the treatment of those with substance abuse or dependence. In general, these therapeutic approaches to substance abuse are deemed effective. However, there is a broad consensus that the development of additional tools to aid diagnosis, prioritize treatment selection and monitor treatment response could have substantial impact on the effectiveness of both substance use prevention and treatment. The recent demonstrations by a number of groups that substance use exposure is associated with robust changes in DNA methylation signatures of peripheral blood cells suggests the possibility that methylation assessments of blood or saliva could find broad clinical applications. In this article, we review recent progress in epigenetic approaches to substance use assessment with a particular emphasis on smoking (and alcohol) related applications. In addition, we highlight areas, such as the epigenetics of psychostimulant, opioid and cannabis abuse, which are markedly understudied and could benefit from intensified collaborative efforts to define epigenetic biomarkers of abuse and dependence.
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