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Fitzgerald S, Bhat B, Print C, Jones GT. A validated restriction enzyme ddPCR cg05575921 (AHRR) assay to accurately assess smoking exposure. Clin Epigenetics 2024; 16:45. [PMID: 38528596 PMCID: PMC10962207 DOI: 10.1186/s13148-024-01659-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND & METHODS In this study, a novel restriction enzyme (RE) digestion-based droplet digital polymerase chain reaction (ddPCR) assay was designed for cg005575921 within the AHRR gene body and compared with matching results obtained by bisulfite conversion (BIS) ddPCR and Illumina DNA methylation array. RESULTS The RE ddPCR cg05575921 assay appeared concordant with BIS ddPCR (r2 = 0.94, P < 0.0001) and, when compared with the Illumina array, had significantly better smoking status classification performance for current versus never smoked (AUC 0.96 versus 0.93, P < 0.04) and current versus ex-smoker (AUC 0.88 versus 0.83, P < 0.04) comparisons. CONCLUSIONS The RE ddPCR cg05575921 assay accurately predicts smoking status and could be a useful component of 'precision-medicine' chronic disease risk screening tools.
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Affiliation(s)
- Sandra Fitzgerald
- Department of Molecular Medicine & Pathology, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre of Research Excellence, Auckland, New Zealand
| | - Basharat Bhat
- Vascular Research Group, Department of Surgical Sciences, Dunedin Medical School, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Cristin Print
- Department of Molecular Medicine & Pathology, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre of Research Excellence, Auckland, New Zealand
| | - Gregory T Jones
- Vascular Research Group, Department of Surgical Sciences, Dunedin Medical School, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
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Chu WM, Nishita Y, Tange C, Zhang S, Furuya K, Shimokata H, Lee MC, Arai H, Otsuka R. Effects of cigarette smoking and secondhand smoke exposure on physical frailty development among community-dwelling older adults in Japan: Evidence from a 10-year population-based cohort study. Geriatr Gerontol Int 2024; 24 Suppl 1:142-149. [PMID: 37885346 DOI: 10.1111/ggi.14708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/07/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
AIM This study explored longitudinally the relationship between smoking and secondhand smoke and the incidence of physical frailty in community-dwelling Japanese older people. METHODS Data collected from the National Institute for Longevity Sciences-Longitudinal Study of Aging database from 2002 to 2012 (third to seventh wave) among older adults aged ≥65 years were analyzed. Participants with physical frailty at baseline, as determined by the Cardiovascular Health Study criteria, missing data or who failed to attend follow ups were excluded. Data on current cigarette smoking and secondhand smoke exposure were collected from the third wave results. The generalized estimating equation model was used to examine the longitudinal relationships between smoking, secondhand smoke and subsequent frailty. RESULTS The final analysis included 540 participants with a mean age of 71.4 years (standard deviation 4.6). The generalized estimating equation analysis showed that, compared with non-smokers, smokers were at significant risk of physical frailty (odds ratio [OR] 2.39, 95% confidence interval [CI] 1.21-4.74) after adjustment for multiple covariates; especially men (OR 3.75, 95% CI 1.76-8.00) and older adults aged ≥75 years (OR 4.12, 95% CI 1.43-11.87). Participants exposed to both smoking and secondhand smoke had a higher risk of physical frailty (OR 3.47, 95% CI 1.56-7.73) than non-smokers without secondhand smoke exposure. Smokers exposed to secondhand smoke were associated with more risk of physical frailty (OR 9.03, 95% CI 2.42-33.77) compared with smokers without secondhand smoke exposure. CONCLUSIONS Smoking, especially when combined with secondhand smoke exposure, is associated with future physical frailty among older adults. Geriatr Gerontol Int 2024; 24: 142-149.
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Affiliation(s)
- Wei-Min Chu
- Department of Family Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Center for Tobacco Treatment and Management, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Epidemiology of Aging, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Yukiko Nishita
- Department of Epidemiology of Aging, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Chikako Tange
- Department of Epidemiology of Aging, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Shu Zhang
- Department of Epidemiology of Aging, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Kanae Furuya
- Department of Epidemiology of Aging, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Hiroshi Shimokata
- Graduate School of Nutritional Sciences, Nagoya University of Arts and Sciences, AIchi, Japan
| | - Meng-Chih Lee
- Department of Family Medicine, Taichung Hospital, Ministry of Health and Welfare, Taichung, Taiwan
- Institute of Population Sciences, National Health Research Institutes, Miaoli County, Taiwan
- College of Management, Chaoyang University of Technology, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Hidenori Arai
- National Center for Geriatrics and Gerontology, Obu, Japan
| | - Rei Otsuka
- Department of Epidemiology of Aging, National Center for Geriatrics and Gerontology, Obu, Japan
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Wang W, Zhao T, Geng K, Yuan G, Chen Y, Xu Y. Smoking and the Pathophysiology of Peripheral Artery Disease. Front Cardiovasc Med 2021; 8:704106. [PMID: 34513948 PMCID: PMC8429807 DOI: 10.3389/fcvm.2021.704106] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022] Open
Abstract
Smoking is one of the most important preventable factors causing peripheral artery disease (PAD). The purpose of this review is to comprehensively analyze and summarize the pathogenesis and clinical characteristics of smoking in PAD based on existing clinical, in vivo, and in vitro studies. Extensive searches and literature reviews have shown that a large amount of data exists on the pathological process underlying the effects of cigarette smoke and its components on PAD through various mechanisms. Cigarette smoke extracts (CSE) induce endothelial cell dysfunction, smooth muscle cell remodeling and macrophage phenotypic transformation through multiple molecular mechanisms. These pathological changes are the molecular basis for the occurrence and development of peripheral vascular diseases. With few discussions on the topic, we will summarize recent insights into the effect of smoking on regulating PAD through multiple pathways and its possible pathogenic mechanism.
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Affiliation(s)
- Weiming Wang
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.,Department of General Surgery (Vascular Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Tingting Zhao
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Kang Geng
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Gang Yuan
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Yue Chen
- Department of Nuclear Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Youhua Xu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
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Andersen A, Gerrard M, Gibbons FX, Beach SRH, Philibert R. An Examination of Risk Factors for Tobacco and Cannabis Smoke Exposure in Adolescents Using an Epigenetic Biomarker. Front Psychiatry 2021; 12:688384. [PMID: 34504443 PMCID: PMC8421639 DOI: 10.3389/fpsyt.2021.688384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/23/2021] [Indexed: 01/23/2023] Open
Abstract
Objective: Evolving patterns of nicotine and cannabis use by adolescents require new tools to understand the changing epidemiology of these substances. Here we describe the use of a novel epigenetic biomarker sensitive to both tobacco and cannabis smoke in a longitudinal sample of high-risk adolescents. We examine risk factors for positivity for this epigenetic biomarker in comparison to positivity for conventional serum biomarkers of nicotine and cannabis use. Method: Eastern Iowa 10th graders who had a friend or family member who smoked were eligible to participate in a longitudinal study over 10-12th grades. Subjects provided self-report data on nicotine, tobacco, and cannabis use patterns as well as blood samples that were used for serum cotinine and THC assays. DNA was prepared for analysis of methylation at the CpG cg05575921, a sensitive indicator of smoke exposure. Relationships between positivity for each these biomarkers and a variety of risk factors, including demographics, family and peer relationships, psychopathology, willingness to smoke, and perceptions of typical cigarette and cannabis users, were examined at the 10th (n = 442), 11th (n = 376), and 12th (n = 366) grade timepoints. Results: A increasing proportion of subjects were positive for cotinine (5-16%), THC (3-10%), and cg05575921 methylation (5-7%) across timepoints, with some overlap. Self-reported combusted tobacco and cannabis use was strongly correlated with all biomarkers, whereas cg05575921 methylation was not correlated with reported e-cigarette use. Dual users, defined as those positive for nicotine and THC in the 12th grade showed the greatest cumulative smoke exposure, indicated by cg05575921 methylation. Subjects reported more positive attitudes toward cannabis users than cigarette smokers, and willingness to smoke and positive perceptions of tobacco and cannabis smokers were significant risk factors for biomarker positivity across timepoints. Conclusion: We conclude that measurement of cg05575921 methylation in adolescents is a useful tool in detecting tobacco smoking in adolescents, and may be a novel tool for the detection of cannabis smoking and cannabis and tobacco co-use, though non-combusted forms of nicotine use do not appear to be detectable by this method.
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Affiliation(s)
- Allan Andersen
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
| | - Meg Gerrard
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, United States
| | - Frederick X. Gibbons
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, United States
| | - Steven R. H. Beach
- Center for Family Research, University of Georgia, Athens, GA, United States
- Department of Psychological Sciences, University of Georgia, Athens, GA, United States
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
- Behavioral Diagnostics, Coralville, IA, United States
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Fuemmeler BF, Dozmorov MG, Do EK, Zhang J(J, Grenier C, Huang Z, Maguire RL, Kollins SH, Hoyo C, Murphy SK. DNA Methylation in Babies Born to Nonsmoking Mothers Exposed to Secondhand Smoke during Pregnancy: An Epigenome-Wide Association Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:57010. [PMID: 34009014 PMCID: PMC8132610 DOI: 10.1289/ehp8099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 02/09/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Maternal smoking during pregnancy is related to altered DNA methylation in infant umbilical cord blood. The extent to which low levels of smoke exposure among nonsmoking pregnant women relates to offspring DNA methylation is unknown. OBJECTIVE This study sought to evaluate relationships between maternal prenatal plasma cotinine levels and DNA methylation in umbilical cord blood in newborns using the Infinium HumanMethylation 450K BeadChip. METHODS Participants from the Newborn Epigenetics Study cohort who reported not smoking during pregnancy had verified low levels of cotinine from maternal prenatal plasma (0 ng / mL to < 4 ng / mL ), and offspring epigenetic data from umbilical cord blood were included in this study (n = 79 ). Multivariable linear regression models were fit to the data, controlling for cell proportions, age, race, education, and parity. Estimates represent changes in response to any 1 -ng / mL unit increase in exposure. RESULTS Multivariable linear regression models yielded 29,049 CpGs that were differentially methylated in relation to increases in cotinine at a 5% false discovery rate. Top CpGs were within or near genes involved in neuronal functioning (PRKG1, DLGAP2, BSG), carcinogenesis (FHIT, HSPC157) and inflammation (AGER). Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggest cotinine was related to methylation of gene pathways controlling neuronal signaling, metabolic regulation, cell signaling and regulation, and cancer. Further, enhancers associated with transcription start sites were enriched in altered CpGs. Using an independent sample from the same study population (n = 115 ), bisulfite pyrosequencing was performed with infant cord blood DNA for two genes within our top 20 hits (AGER and PRKG1). Results from pyrosequencing replicated epigenome results for PRKG1 (cg17079497, estimate = - 1.09 , standard error ( SE ) = 0.45 , p = 0.018 ) but not for AGER (cg09199225; estimate = - 0.16 , SE = 0.21 , p = 0.44 ). DISCUSSION Secondhand smoke exposure among nonsmoking women may alter DNA methylation in regions involved in development, carcinogenesis, and neuronal functioning. These novel findings suggest that even low levels of smoke exposure during pregnancy may be sufficient to alter DNA methylation in distinct sites of mixed umbilical cord blood leukocytes in pathways that are known to be altered in cord blood from pregnant active smokers. https://doi.org/10.1289/EHP8099.
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Affiliation(s)
- Bernard F. Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, Virginia, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Elizabeth K. Do
- Department of Health Behavior and Policy, Virginia Commonwealth University, Richmond, Virginia, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Junfeng (Jim) Zhang
- Nicholas School of the Environment and Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Rachel L. Maguire
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biological Sciences, Center for Human Health and the Environment North Carolina State University, Raleigh, North Carolina, USA
| | - Scott H. Kollins
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment North Carolina State University, Raleigh, North Carolina, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
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Hannon E, Mansell G, Walker E, Nabais MF, Burrage J, Kepa A, Best-Lane J, Rose A, Heck S, Moffitt TE, Caspi A, Arseneault L, Mill J. Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology. PLoS Genet 2021; 17:e1009443. [PMID: 33739972 PMCID: PMC8011804 DOI: 10.1371/journal.pgen.1009443] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 03/31/2021] [Accepted: 02/23/2021] [Indexed: 02/01/2023] Open
Abstract
Most epigenome-wide association studies (EWAS) quantify DNA methylation (DNAm) in peripheral tissues such as whole blood to identify positions in the genome where variation is statistically associated with a trait or exposure. As whole blood comprises a mix of cell types, it is unclear whether trait-associated DNAm variation is specific to an individual cellular population. We collected three peripheral tissues (whole blood, buccal epithelial and nasal epithelial cells) from thirty individuals. Whole blood samples were subsequently processed using fluorescence-activated cell sorting (FACS) to purify five constituent cell-types (monocytes, granulocytes, CD4+ T cells, CD8+ T cells, and B cells). DNAm was profiled in all eight sample-types from each individual using the Illumina EPIC array. We identified significant differences in both the level and variability of DNAm between different sample types, and DNAm data-derived estimates of age and smoking were found to differ dramatically across sample types from the same individual. We found that for the majority of loci variation in DNAm in individual blood cell types was only weakly predictive of variance in DNAm measured in whole blood, although the proportion of variance explained was greater than that explained by either buccal or nasal epithelial samples. Covariation across sample types was much higher for DNAm sites influenced by genetic factors. Overall, we observe that DNAm variation in whole blood is additively influenced by a combination of the major blood cell types. For a subset of sites, however, variable DNAm detected in whole blood can be attributed to variation in a single blood cell type providing potential mechanistic insight about EWAS findings. Our results suggest that associations between whole blood DNAm and traits or exposures reflect differences in multiple cell types and our data will facilitate the interpretation of findings in epigenetic epidemiology. As epigenetic variation is cell-type specific, an ongoing challenge in epigenetic epidemiology is how to interpret studies performed using bulk tissue (for example, whole blood) which comprises a mix of different cell types. In this study, we identified major differences in DNA methylation (DNAm) across multiple peripheral tissues and different blood cell types, with each sample type being characterized by a unique signature across multiple genomic loci. We demonstrate how these differences influence commonly used prediction scores derived from DNAm data for age and tobacco smoking, with estimates for the same individual being highly variable across tissues and cell types. Our results enabled us to assess the extent to which variable DNAm in each individual blood cell type relates to variation measured in whole blood. We found that although individual blood cell types predict more of the variation in DNAm in whole blood compared to buccal and nasal epithelial cells, the actual proportion of variance explained is relatively small, except for at sites where DNAm is under genetic control. Our data indicate that for most sites variation in multiple blood cell types additively combines to drive variation in DNAm measured in whole blood. Of note, for a subset of sites, variation in DNAm detected in whole blood can be attributed to a specific blood cell type, potentially facilitating the interpretation of EWAS findings.
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Emma Walker
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Marta F Nabais
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Agnieszka Kepa
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Janis Best-Lane
- Section of Anaesthetics, Pain Medicine and Intensive Care Medicine, Department of Surgery and Cancer, Imperial College London and Imperial College Healthcare NHS Trust, London, United Kingdom
- Imperial Clinical Trials Unit, Imperial College London, London, United Kingdom
| | - Anna Rose
- BRC Flow Cytometry Platform, NIHR GSTT/KCL Comprehensive Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Suzanne Heck
- Biomedical Research Centre at Guy's and St Thomas' Hospitals and King's College London, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Terrie E Moffitt
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Psychology and Neuroscience, Duke University, Durham, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America
| | - Avshalom Caspi
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Psychology and Neuroscience, Duke University, Durham, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Hulls PM, de Vocht F, Bao Y, Relton CL, Martin RM, Richmond RC. DNA methylation signature of passive smoke exposure is less pronounced than active smoking: The Understanding Society study. ENVIRONMENTAL RESEARCH 2020; 190:109971. [PMID: 32745538 PMCID: PMC7536273 DOI: 10.1016/j.envres.2020.109971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/09/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
INTRODUCTION The extent of the biological impact of passive smoke exposure is unclear. We sought to investigate the association between passive smoke exposure and DNA methylation, which could serve as a biomarker of health risk. MATERIALS AND METHODS We derived passive smoke exposure from self-reported questionnaire data among smoking and non-smoking partners of participants enrolled in the UK Household Longitudinal Study 'Understanding Society' (n=769). We performed an epigenome-wide association study (EWAS) of passive smoke exposure with DNA methylation in peripheral blood measured using the Illumina Infinium Methylation EPIC array. RESULTS No CpG sites surpassed the epigenome-wide significance threshold of p<5.97 × 10-8 in relation to partner smoking, compared with 10 CpG sites identified in relation to own smoking. However, 10 CpG sites surpassed a less stringent threshold of p<1 × 10-5 in a model of partner smoking adjusted for own smoking (model 1), 7 CpG sites in a model of partner smoking restricted to non-smokers (model 2) and 16 CpGs in a model restricted to regular smokers (model 3). In addition, there was evidence for an interaction between own smoking status and partners' smoking status on DNA methylation levels at the majority of CpG sites identified in models 2 and 3. There was a clear lack of enrichment for previously identified smoking signals in the EWAS of passive smoke exposure compared with the EWAS of own smoking. CONCLUSION The DNA methylation signature associated with passive smoke exposure is much less pronounced than that of own smoking, with no positive findings for 'expected' signals. It is unlikely that changes to DNA methylation serve as an important mechanism underlying the health risks of passive smoke exposure.
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Affiliation(s)
- Paige M Hulls
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; MRC Integrative Epidemiology Unit at University of Bristol, BS8 2BN, UK.
| | - Frank de Vocht
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; NIHR Applied Research Collaboration West (NIHR ARC West), Bristol, BS1 2NT, UK.
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, CO4 3SQ, UK.
| | - Caroline L Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; MRC Integrative Epidemiology Unit at University of Bristol, BS8 2BN, UK.
| | - Richard M Martin
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; MRC Integrative Epidemiology Unit at University of Bristol, BS8 2BN, UK; NIHR Bristol Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, BS8 2BN, UK.
| | - Rebecca C Richmond
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN, UK; MRC Integrative Epidemiology Unit at University of Bristol, BS8 2BN, UK.
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Vives-Usano M, Hernandez-Ferrer C, Maitre L, Ruiz-Arenas C, Andrusaityte S, Borràs E, Carracedo Á, Casas M, Chatzi L, Coen M, Estivill X, González JR, Grazuleviciene R, Gutzkow KB, Keun HC, Lau CHE, Cadiou S, Lepeule J, Mason D, Quintela I, Robinson O, Sabidó E, Santorelli G, Schwarze PE, Siskos AP, Slama R, Vafeiadi M, Martí E, Vrijheid M, Bustamante M. In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in children. BMC Med 2020; 18:243. [PMID: 32811491 PMCID: PMC7437049 DOI: 10.1186/s12916-020-01686-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/29/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The adverse health effects of early life exposure to tobacco smoking have been widely reported. In spite of this, the underlying molecular mechanisms of in utero and postnatal exposure to tobacco smoke are only partially understood. Here, we aimed to identify multi-layer molecular signatures associated with exposure to tobacco smoke in these two exposure windows. METHODS We investigated the associations of maternal smoking during pregnancy and childhood secondhand smoke (SHS) exposure with molecular features measured in 1203 European children (mean age 8.1 years) from the Human Early Life Exposome (HELIX) project. Molecular features, covering 4 layers, included blood DNA methylation and gene and miRNA transcription, plasma proteins, and sera and urinary metabolites. RESULTS Maternal smoking during pregnancy was associated with DNA methylation changes at 18 loci in child blood. DNA methylation at 5 of these loci was related to expression of the nearby genes. However, the expression of these genes themselves was only weakly associated with maternal smoking. Conversely, childhood SHS was not associated with blood DNA methylation or transcription patterns, but with reduced levels of several serum metabolites and with increased plasma PAI1 (plasminogen activator inhibitor-1), a protein that inhibits fibrinolysis. Some of the in utero and childhood smoking-related molecular marks showed dose-response trends, with stronger effects with higher dose or longer duration of the exposure. CONCLUSION In this first study covering multi-layer molecular features, pregnancy and childhood exposure to tobacco smoke were associated with distinct molecular phenotypes in children. The persistent and dose-dependent changes in the methylome make CpGs good candidates to develop biomarkers of past exposure. Moreover, compared to methylation, the weak association of maternal smoking in pregnancy with gene expression suggests different reversal rates and a methylation-based memory to past exposures. Finally, certain metabolites and protein markers evidenced potential early biological effects of postnatal SHS, such as fibrinolysis.
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Affiliation(s)
- Marta Vives-Usano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Carles Hernandez-Ferrer
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Léa Maitre
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Carlos Ruiz-Arenas
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Sandra Andrusaityte
- Department of Environmental Sciences, Vytautas Magnus University, K. Donelaicio Street 58, 44248, Kaunas, Lithuania
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Fundación Pública Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), SERGAS, Rúa Choupana s/n, 15706, Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER) y Centro Nacional de Genotipado (CEGEN-PRB3-ISCIII), Universidade de Santiago de Compostela, Praza do Obradoiro s/n, 15782, Santiago de Compostela, Spain
| | - Maribel Casas
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1540 Alcazar Street, Los Angeles, 90033, USA
| | - Muireann Coen
- Oncology Safety, Clinical Pharmacology and Safety Sciences, R&D Biopharmaceuticals, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0RE, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Quantitative Genomics Medicine Laboratories (qGenomics), Esplugues del Llobregat, Barcelona, Catalonia, Spain
| | - Juan R González
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Regina Grazuleviciene
- Department of Environmental Sciences, Vytautas Magnus University, K. Donelaicio Street 58, 44248, Kaunas, Lithuania
| | - Kristine B Gutzkow
- Department af Environmental Health, Norwegian Institute of Public Health, Lovisenberggt 6, 0456, Oslo, Norway
| | - Hector C Keun
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
- Cancer Metabolism and Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Chung-Ho E Lau
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Solène Cadiou
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, 38000, Grenoble, France
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, 38000, Grenoble, France
| | - Dan Mason
- Bradford Institute for Health Research, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK
| | - Inés Quintela
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3-ISCIII), Universidade de Santiago de Compostela, Praza do Obradoiro s/n, 15782, Santiago de Compostela, Spain
| | - Oliver Robinson
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, St. Mary's Hospital Campus, London, W21PG, UK
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gillian Santorelli
- Bradford Institute for Health Research, Bradford Royal Infirmary, Bradford, BD9 6RJ, UK
| | - Per E Schwarze
- Department af Environmental Health, Norwegian Institute of Public Health, Lovisenberggt 6, 0456, Oslo, Norway
| | - Alexandros P Siskos
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
- Cancer Metabolism and Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Rémy Slama
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, 38000, Grenoble, France
| | - Marina Vafeiadi
- Department of Social Medicine, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Eulàlia Martí
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Departament de Biomedicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
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9
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Aberg KA, Dean B, Shabalin AA, Chan RF, Han LK, Zhao M, van Grootheest G, Xie LY, Milaneschi Y, Clark SL, Turecki G, Penninx BW, van den Oord EJ. Methylome-wide association findings for major depressive disorder overlap in blood and brain and replicate in independent brain samples. Mol Psychiatry 2020; 25:1344-1354. [PMID: 30242228 PMCID: PMC6428621 DOI: 10.1038/s41380-018-0247-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 06/26/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022]
Abstract
We present the first large-scale methylome-wide association studies (MWAS) for major depressive disorder (MDD) to identify sites of potential importance for MDD etiology. Using a sequencing-based approach that provides near-complete coverage of all 28 million common CpGs in the human genome, we assay methylation in MDD cases and controls from both blood (N = 1132) and postmortem brain tissues (N = 61 samples from Brodmann Area 10, BA10). The MWAS for blood identified several loci with P ranging from 1.91 × 10-8 to 4.39 × 10-8 and a resampling approach showed that the cumulative association was significant (P = 4.03 × 10-10) with the signal coming from the top 25,000 MWAS markers. Furthermore, a permutation-based analysis showed significant overlap (P = 5.4 × 10-3) between the MWAS findings in blood and brain (BA10). This overlap was significantly enriched for a number of features including being in eQTLs in blood and the frontal cortex, CpG islands and shores, and exons. The overlapping sites were also enriched for active chromatin states in brain including genic enhancers and active transcription start sites. Furthermore, three loci located in GABBR2, RUFY3, and in an intergenic region on chromosome 2 replicated with the same direction of effect in the second brain tissue (BA25, N = 60) from the same individuals and in two independent brain collections (BA10, N = 81 and 64). GABBR2 inhibits neuronal activity through G protein-coupled second-messenger systems and RUFY3 is implicated in the establishment of neuronal polarity and axon elongation. In conclusion, we identified and replicated methylated loci associated with MDD that are involved in biological functions of likely importance to MDD etiology.
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Affiliation(s)
- Karolina A. Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA,Correspondence should be addressed to: Karolina A. Aberg, P.O. Box 980533, Richmond, VA 23298, Phone: (804) 628-3023, Fax: (804) 628-3991,
| | - Brian Dean
- The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia,Centre for Mental Health, Swinburne University, Hawthorn, Victoria, Australia
| | - Andrey A. Shabalin
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Robin F. Chan
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Laura K.M. Han
- Department of Psychiatry, Amsterdam Neuroscience, VU University Medical Center, GGZ inGeest, Amsterdam, The Netherlands
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Gerard van Grootheest
- Department of Psychiatry, Amsterdam Neuroscience, VU University Medical Center, GGZ inGeest, Amsterdam, The Netherlands
| | - Lin Y. Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience, VU University Medical Center, GGZ inGeest, Amsterdam, The Netherlands
| | - Shaunna L. Clark
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Gustavo Turecki
- Douglas Mental Health University Institute and McGill University, Montréal, Québec, Canada
| | - Brenda W.J.H. Penninx
- Department of Psychiatry, Amsterdam Neuroscience, VU University Medical Center, GGZ inGeest, Amsterdam, The Netherlands
| | - Edwin J.C.G. van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA, USA
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10
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Mulder RH, Walton E, Neumann A, Houtepen LC, Felix JF, Bakermans-Kranenburg MJ, Suderman M, Tiemeier H, van IJzendoorn MH, Relton CL, Cecil CAM. Epigenomics of being bullied: changes in DNA methylation following bullying exposure. Epigenetics 2020; 15:750-764. [PMID: 31992121 PMCID: PMC7574379 DOI: 10.1080/15592294.2020.1719303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bullying among children is ubiquitous and associated with pervasive mental health problems. However, little is known about the biological pathways that change after exposure to bullying. Epigenome-wide changes in DNA methylation in peripheral blood were studied from pre- to post measurement of bullying exposure, in a longitudinal study of the population-based Generation R Study and Avon Longitudinal Study of Parents and Children (combined n = 1,352). Linear mixed-model results were meta-analysed to estimate how DNA methylation changed as a function of exposure to bullying. Sensitivity analyses including co-occurring child characteristics and risks were performed, as well as a Gene Ontology analysis. A candidate follow-up was employed for CpG (cytosine-phosphate-guanine) sites annotated to 5-HTT and NR3C1. One site, cg17312179, showed small changes in DNA methylation associated to bullying exposure (b = -2.67e-03, SE = 4.97e-04, p = 7.17e-08). This site is annotated to RAB14, an oncogene related to Golgi apparatus functioning, and its methylation levels decreased for exposed but increased for non-exposed. This result was consistent across sensitivity analyses. Enriched Gene Ontology pathways for differentially methylated sites included cardiac function and neurodevelopmental processes. Top CpG sites tended to have overall low levels of DNA methylation, decreasing in exposed, increasing in non-exposed individuals. There were no gene-wide corrected findings for 5-HTT and NR3C1. This is the first study to identify changes in DNA methylation associated with bullying exposure at the epigenome-wide significance level. Consistent with other population-based studies, we do not find evidence for strong associations between bullying exposure and DNA methylation.
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Affiliation(s)
- Rosa H Mulder
- Institute of Education and Child Studies, Leiden University , Leiden, The Netherlands.,Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands
| | - Esther Walton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK.,Department of Psychology, University of Bath , Bath, UK
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Lady Davis Institute for Medical Research, Jewish General Hospital , Montreal, Qc, Canada
| | - Lotte C Houtepen
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands
| | | | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Social and Behavioral Science, Harvard TH Chan School of Public Health , Boston, MA, USA
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam , Rotterdam, The Netherlands.,School of Clinical Medicine, University of Cambridge , Cambridge, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Psychology, Institute of Psychology, Psychiatry & Neuroscience, King's College London , London, UK
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11
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Carrasco-Rios M, Ortolá R, Rodríguez-Artalejo F, García-Esquinas E. Exposure to secondhand tobacco smoke is associated with reduced muscle strength in US adults. Aging (Albany NY) 2019; 11:12674-12684. [PMID: 31815682 PMCID: PMC6949081 DOI: 10.18632/aging.102594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/26/2019] [Indexed: 01/26/2023]
Abstract
Secondhand tobacco smoke (SHS) exposure is a well-established risk factor for several diseases in adults. Despite the evidence that active tobacco smoke is harmful for the muscles, the association between SHS and muscle strength is still uncertain.We analyzed data from 5390 nonsmoking U.S. adults aged >30 years who participated in the National Health and Nutrition Examination Survey (NHANES) 2011-2014. Exposure to SHS was assessed with serum cotinine concentrations. Grip strength was measured using a Takei digital handgrip dynamometer, and combined grip strength was calculated as the sum of the largest reading from each hand. Median (interquartile range) serum cotinine and grip strength were 0.015 ng/mL (IQR 0.011-0.36) and 65.5 kg (IQR 53.4-86.4), respectively. After adjusting for sociodemographic, anthropometric, health-related behavioral, and clinical risk factors, the highest (0.047-9.9 ng/mL) vs lowest (≤0.011 ng/mL) quartile of serum cotinine was associated with a reduction in combined grip strength of 1.41 kg (95%CI: -2.58, -0.24), p-trend=0.02. These results were consistent across socio-demographic and clinical subgroups. In the US nonsmoking adult population, even low levels of exposure to passive smoking were associated with decreased grip strength. Despite great achievements in tobacco control, extending public health interventions to reduce SHS exposure is still needed.
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Affiliation(s)
- Monica Carrasco-Rios
- Department of Preventive Medicine and Public Health, School of Medicine, Universidad Autónoma de Madrid/ IdiPAZ, Madrid, Spain
| | - Rosario Ortolá
- Department of Preventive Medicine and Public Health, School of Medicine, Universidad Autónoma de Madrid/ IdiPAZ, Madrid, Spain
| | - Fernando Rodríguez-Artalejo
- Department of Preventive Medicine and Public Health, School of Medicine, Universidad Autónoma de Madrid/ IdiPAZ, Madrid, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Esther García-Esquinas
- Department of Preventive Medicine and Public Health, School of Medicine, Universidad Autónoma de Madrid/ IdiPAZ, Madrid, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
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12
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Kalkbrenner AE, Meier SM, Madley-Dowd P, Ladd-Acosta C, Fallin MD, Parner E, Schendel D. Familial confounding of the association between maternal smoking in pregnancy and autism spectrum disorder in offspring. Autism Res 2019; 13:134-144. [PMID: 31464107 DOI: 10.1002/aur.2196] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 08/06/2019] [Indexed: 12/20/2022]
Abstract
Evidence supports no link between maternal smoking in pregnancy and autism spectrum disorder (autism) overall. To address remaining questions about the unexplained heterogeneity between study results and the possibility of risk for specific autism sub-phenotypes, we conducted a whole-population cohort study in Denmark. We followed births 1991-2011 (1,294,906 persons, including 993,301 siblings in 728,271 families), from 1 year of age until an autism diagnosis (13,547), death, emigration, or December 31, 2012. Autism, with and without attention deficit hyperactivity disorder (ADHD) and with and without intellectual disability (ID) were based on ICD-8 and ICD-10 codes from Danish national health registers, including 3,319 autism + ADHD, 10,228 autism - no ADHD, 2,205 autism + ID, and 11,342 autism - no ID. We estimated hazard ratios (HRs) and 95% confidence intervals (95% CIs) between any maternal smoking (from birth records) and autism (or sub-phenotypes) using survival models with robust standard errors, stratifying by birth year and adjusting for child sex, parity, and parental age, education, income, and psychiatric history. To additionally address confounding using family designs, we constructed a maternal cluster model (adjusting for the smoking proportion within the family), and a stratified sibling model. Associations with maternal smoking and autism were elevated in conventional adjusted analyses (HR of 1.17 [1.13-1.22]) but attenuated in the maternal cluster (0.98 [0.88-1.09]) and sibling (0.86 [0.64-1.15]) models. Similarly, risks of autism sub-phenotypes with maternal smoking were attenuated in the family-based models. Together these results support that smoking in pregnancy is not linked with autism or select autism comorbid sub-phenotypes after accounting for familial confounding. Autism Res 2020, 13: 134-144. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Smoking during pregnancy has many harmful impacts, which may include harming the baby's developing brain. However, in a study of thousands of families in Denmark, it does not appear that smoking in pregnancy leads to autism or autism in combination with intellectual problems or attention deficits, once you account for the way smoking patterns and developmental disabilities run in families.
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Affiliation(s)
- Amy E Kalkbrenner
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Sandra M Meier
- Child and Adolescent Mental Health Centre-Mental Health Services Capital Region, Copenhagen Region, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Paul Madley-Dowd
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Margaret Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Erik Parner
- Department of Public Health, Section for Biostatistics, Aarhus University, Aarhus, Denmark
| | - Diana Schendel
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Department of Economics and Business, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus, Denmark
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13
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Imboden M, Wielscher M, Rezwan FI, Amaral A, Schaffner E, Jeong A, Beckmeyer-Borowko A, Harris SE, Starr JM, Deary I, Flexeder C, Waldenberger M, Peters A, Schulz H, Chen S, Sunny SK, Karmaus WJ, Jiang Y, Erhart G, Kronenberg F, Arathimos R, Sharp GC, Henderson AJ, Fu Y, Piirilä P, Pietiläinen KH, Ollikainen M, Johansson A, Gyllensten U, de Vries M, van der Plaat DA, de Jong K, Boezen HM, Hall I, Tobin MD, Jarvelin MR, Holloway J, Jarvis D, Probst-Hensch NM. Epigenome-wide association study of lung function level and its change. Eur Respir J 2019; 54:13993003.00457-2019. [PMID: 31073081 PMCID: PMC6610463 DOI: 10.1183/13993003.00457-2019] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/27/2019] [Indexed: 12/19/2022]
Abstract
Previous reports link differential DNA methylation (DNAme) to environmental exposures that are associated with lung function. Direct evidence on lung function DNAme is, however, limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults.In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, 6-15 years apart, in the same participants of three adult population-based discovery cohorts (n=2043). Associated DNAme markers (p<5×10-7) were tested in seven replication cohorts (adult: n=3327; childhood: n=420). Technical bias-adjusted residuals of a regression of the normalised absolute β-values on control probe-derived principle components were regressed on level and change of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and their ratio (FEV1/FVC) in the covariate-adjusted discovery EWAS. Inverse-variance-weighted meta-analyses were performed on results from discovery and replication samples in all participants and never-smokers.EWAS signals were enriched for smoking-related DNAme. We replicated 57 lung function DNAme markers in adult, but not childhood samples, all previously associated with smoking. Markers not previously associated with smoking failed replication. cg05575921 (AHRR (aryl hydrocarbon receptor repressor)) showed the statistically most significant association with cross-sectional lung function (FEV1/FVC: pdiscovery=3.96×10-21 and pcombined=7.22×10-50). A score combining 10 DNAme markers previously reported to mediate the effect of smoking on lung function was associated with lung function (FEV1/FVC: p=2.65×10-20).Our results reveal that lung function-associated methylation signals in adults are predominantly smoking related, and possibly of clinical utility in identifying poor lung function and accelerated decline. Larger studies with more repeat time-points are needed to identify lung function DNAme in never-smokers and in children.
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Affiliation(s)
- Medea Imboden
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland,These authors contributed equally to this work
| | - Matthias Wielscher
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK,Dept of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK,These authors contributed equally to this work
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK,These authors contributed equally to this work
| | - André F.S. Amaral
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK,Population Health and Occupational Disease, NHLI, Imperial College London, London, UK,These authors contributed equally to this work
| | - Emmanuel Schaffner
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Anna Beckmeyer-Borowko
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Medical Genetics Section, University of Edinburgh Centre for Genomic and Experimental Medicine and MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK,Dept of Psychology, University of Edinburgh, Edinburgh, UK
| | - Claudia Flexeder
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Su Chen
- Dept of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | - Shadia Khan Sunny
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried J.J. Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Gertraud Erhart
- Division of Genetic Epidemiology, Dept of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Dept of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ryan Arathimos
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK,Dept of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gemma C. Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK,Dept of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK,Bristol Dental School, University of Bristol, Bristol, UK
| | | | - Yu Fu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Päivi Piirilä
- Unit of Clinical Physiology, HUS Medical Imaging Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Kirsi H. Pietiläinen
- Obesity Research Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland,Abdominal Center, Endocrinology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Asa Johansson
- Dept of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Dept of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Dept of Epidemiology, Groningen, The Netherlands,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Diana A. van der Plaat
- University of Groningen, University Medical Center Groningen, Dept of Epidemiology, Groningen, The Netherlands,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen, Dept of Epidemiology, Groningen, The Netherlands,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H. Marike Boezen
- University of Groningen, University Medical Center Groningen, Dept of Epidemiology, Groningen, The Netherlands,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Nottingham, UK,National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals, Nottingham, UK
| | - Martin D. Tobin
- Dept of Health Sciences, University of Leicester, Leicester, UK,National Institute of Health Research Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Marjo-Riitta Jarvelin
- Dept of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland,Biocenter Oulu, University of Oulu, Oulu, Finland,Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland,Dept of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK,These authors contributed equally to this work
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK,These authors contributed equally to this work
| | - Deborah Jarvis
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK,Population Health and Occupational Disease, NHLI, Imperial College London, London, UK,These authors contributed equally to this work
| | - Nicole M. Probst-Hensch
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland,University of Basel, Basel, Switzerland,These authors contributed equally to this work
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14
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Tantoh DM, Lee KJ, Nfor ON, Liaw YC, Lin C, Chu HW, Chen PH, Hsu SY, Liu WH, Ho CC, Lung CC, Wu MF, Liaw YC, Debnath T, Liaw YP. Methylation at cg05575921 of a smoking-related gene (AHRR) in non-smoking Taiwanese adults residing in areas with different PM 2.5 concentrations. Clin Epigenetics 2019; 11:69. [PMID: 31060609 PMCID: PMC6503351 DOI: 10.1186/s13148-019-0662-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/08/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND DNA methylation is associated with cancer, metabolic, neurological, and autoimmune disorders. Hypomethylation of aryl hydrocarbon receptor repressor (AHRR) especially at cg05575921 is associated with smoking and lung cancer. Studies on the association between AHRR methylation at cg05575921 and sources of polycyclic aromatic hydrocarbon (PAH) other than smoking are limited. The aim of our study was to assess the pattern of blood DNA methylation at cg05575921 in non-smoking Taiwanese adults living in areas with different PM2.5 levels. METHODS Data on blood DNA methylation, smoking, and residence were retrieved from the Taiwan Biobank dataset (2008-2015). Current and former smokers, as well as individuals with incomplete information were excluded from the current study. The final analysis included 708 participants (279 men and 429 women) aged 30-70 years. PM2.5 levels have been shown to increase as one moves from the northern through central towards southern Taiwan. Based on this trend, the study areas were categorized into northern, north-central, central, and southern regions. RESULTS Living in PM2.5 areas was associated with lower methylation levels: compared with the northern area (reference area), living in north-central, central, and southern areas was associated with lower methylation levels at cg05575921. However, only methylation levels in those living in central and southern areas were significant (β = - 0.01003, P = 0.009 and β = - 0.01480, P < 0.001, respectively. Even though methylation levels in those living in the north-central area were not statistically significant, the test for linear trend was significant (P < 0.001). When PM2.5 was included in the regression model, a unit increase in PM2.5 was associated with 0.00115 (P < 0.001) lower cg05575921 methylation levels. CONCLUSION Living in PM2.5 areas was inversely associated with blood AHRR methylation levels at cg05575921. The methylation levels were lowest in participants residing in southern followed by central and north-central areas. Moreover, when PM2.5 was included in the regression model, it was inversely associated with methylation levels at cg05575921. Blood methylation at cg05575921 (AHRR) in non-smokers might indicate different exposures to PM2.5 and lung cancer which is a PM2.5-related disease.
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Affiliation(s)
- Disline Manli Tantoh
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Kuan-Jung Lee
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Yi-Chia Liaw
- Department of Medical Education, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chin Lin
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pei-Hsin Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Shu-Yi Hsu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Wen-Hsiu Liu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Chen-Chang Ho
- Department of Physical Education, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Chia-Chi Lung
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Ming-Fang Wu
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung City, Taiwan
| | - Yi-Ching Liaw
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Tonmoy Debnath
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, No. 110 Sec. 1 Jianguo N. Road, Taichung City, 40201, Taiwan. .,Department of Family and Community Medicine, Chung Shan Medical University Hospital, Taichung City, Taiwan.
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15
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Kemp Jacobsen K, Johansen JS, Mellemgaard A, Bojesen SE. AHRR (cg05575921) methylation extent of leukocyte DNA and lung cancer survival. PLoS One 2019; 14:e0211745. [PMID: 30730943 PMCID: PMC6366765 DOI: 10.1371/journal.pone.0211745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/26/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Prior studies have shown that AHRR (cg05575921) hypomethylation may be a marker of smoking, lung cancer risk and potentially lung cancer survival (in some lung cancer subtypes). It is unknown if AHRR (cg05575921) hypomethylation is associated with reduced survival among lung cancer patients. METHODS In bisulfite treated leukocyte DNA from 465 lung cancer patients from the Copenhagen prospective lung cancer study, we measured AHRR (cg05575921) methylation. 380 died during max follow-up of 4.4 years. Cox proportional hazard models were used to analyze survival as a function of AHRR (cg05575921) methylation. RESULTS We observed the expected inverse correlation between cumulative smoking and AHRR methylation, as methylation (%) decreased (Coefficient -0.03; 95% confidence interval, -0.04- -0.02, p = 8.6x10-15) for every pack-year. Cumulative smoking > 60 pack-years was associated with reduced survival (hazard ratio and 95% confidence interval 1.48; 1.05-2.09), however, AHRR (cg05575921) methylation was not associated with survival when adjusted for sex, body mass index, smoking status, ethnicity, performance status, TNM Classification, and histology type of lung cancer. CONCLUSION AHRR (cg05575921) methylation is linked to smoking but does not provide independent prognostic information in lung cancer patients.
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Affiliation(s)
- Katja Kemp Jacobsen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Jakob Sidenius Johansen
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anders Mellemgaard
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Stig Egil Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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16
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Active and secondhand smoke exposure throughout life and DNA methylation in breast tumors. Cancer Causes Control 2019; 30:53-62. [PMID: 30617699 DOI: 10.1007/s10552-018-1102-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
Abstract
PURPOSE Tobacco smoke exposure has been associated with altered DNA methylation. However, there is a paucity of information regarding tobacco smoke exposure and DNA methylation of breast tumors. METHODS We conducted a case-only analysis using breast tumor tissue from 493 postmenopausal and 225 premenopausal cases in the Western New York Exposures and Breast Cancer (WEB) study. Methylation of nine genes (SFN, SCGB3A1, RARB, GSTP1, CDKN2A, CCND2, BRCA1, FHIT, and SYK) was measured with pyrosequencing. Participants reported their secondhand smoke (SHS) and active smoking exposure for seven time periods. Unconditional logistic regression was used to estimate odds ratios (OR) of having methylation higher than the median. RESULTS SHS exposure was associated with tumor DNA methylation among postmenopausal but not premenopausal women. Active smoking at certain ages was associated with increased methylation of GSTP1, FHIT, and CDKN2A and decreased methylation of SCGB3A1 and BRCA1 among both pre- and postmenopausal women. CONCLUSION Exposure to tobacco smoke may contribute to breast carcinogenesis via alterations in DNA methylation. Further studies in a larger panel of genes are warranted.
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17
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Epigenetic signatures of starting and stopping smoking. EBioMedicine 2018; 37:214-220. [PMID: 30389506 PMCID: PMC6286188 DOI: 10.1016/j.ebiom.2018.10.051] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 01/28/2023] Open
Abstract
Background Multiple studies have made robust associations between differential DNA methylation and exposure to cigarette smoke. But whether a DNA methylation phenotype is established immediately upon exposure, or only after prolonged exposure is less well–established. Here, we assess DNA methylation patterns from peripheral blood samples in current smokers in response to dose and duration of exposure, along with the effects of smoking cessation on DNA methylation in former smokers. Methods Dimensionality reduction was applied to DNA methylation data at 90 previously identified smoking–associated CpG sites for over 4900 individuals in the Generation Scotland cohort. K–means clustering was performed to identify clusters associated with current and never smoker status based on these methylation patterns. Cluster assignments were assessed with respect to duration of exposure in current smokers (years as a smoker), time since smoking cessation in former smokers (years), and dose (cigarettes per day). Findings Two clusters were specified, corresponding to never smokers (97·5% of whom were assigned to Cluster 1) and current smokers (81·1% of whom were assigned to Cluster 2). The exposure time point from which >50% of current smokers were assigned to the smoker–enriched cluster varied between 5 and 9 years in heavier smokers and between 15 and 19 years in lighter smokers. Low–dose former smokers were more likely to be assigned to the never smoker–enriched cluster in the first year following cessation. In contrast, a period of at least two years was required before the majority of former high–dose smokers were assigned to the never smoker–enriched cluster. Interpretation Our findings suggest that smoking–associated DNA methylation changes are a result of prolonged exposure to cigarette smoke, and can be reversed following cessation. The length of time in which these signatures are established and recovered is dose dependent. Should DNA methylation–based signatures of smoking status be predictive of smoking–related health outcomes, our findings may provide an additional criterion on which to stratify risk.
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18
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Commodore A, Mukherjee N, Chung D, Svendsen E, Vena J, Pearce J, Roberts J, Arshad SH, Karmaus W. Frequency of heavy vehicle traffic and association with DNA methylation at age 18 years in a subset of the Isle of Wight birth cohort. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy028. [PMID: 30697444 PMCID: PMC6343046 DOI: 10.1093/eep/dvy028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 05/08/2023]
Abstract
Assessment of changes in DNA methylation (DNA-m) has the potential to identify adverse environmental exposures. To examine DNA-m among a subset of participants (n = 369) in the Isle of Wight birth cohort who reported variable near resident traffic frequencies. We used self-reported frequencies of heavy vehicles passing by the homes of study subjects as a proxy measure for TRAP, which were: never, seldom, 10 per day, 1-9 per hour and >10 per hour. Methylation of cytosine-phosphate-guanine (CpG) dinucleotide sequences in the DNA was assessed from blood samples collected at age 18 years (n = 369) in the F1 generation. We conducted an epigenome wide association study to examine CpGs related to the frequency of heavy vehicles passing by subjects' homes, and employed multiple linear regression models to assess potential associations. We repeated some of these analysis in the F2 generation (n = 140). Thirty-five CpG sites were associated with heavy vehicular traffic. After adjusting for confounders, we found 23 CpGs that were more methylated, and 11 CpGs that were less methylated with increasing heavy vehicular traffic frequency among all subjects. In the F2 generation, 2 of 31 CpGs were associated with traffic frequencies and the direction of the effect was the same as in the F1 subset while differential methylation of 7 of 31 CpG sites correlated with gene expression. Our findings reveal differences in DNA-m in participants who reported higher heavy vehicular traffic frequencies when compared to participants who reported lower frequencies.
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Affiliation(s)
- A Commodore
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - N Mukherjee
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN 38152, USA
| | - D Chung
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - E Svendsen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - J Vena
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - J Pearce
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - J Roberts
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - S H Arshad
- Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - W Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN 38152, USA
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19
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Park SL, Patel YM, Loo LWM, Mullen DJ, Offringa IA, Maunakea A, Stram DO, Siegmund K, Murphy SE, Tiirikainen M, Le Marchand L. Association of internal smoking dose with blood DNA methylation in three racial/ethnic populations. Clin Epigenetics 2018; 10:110. [PMID: 30139389 PMCID: PMC6108111 DOI: 10.1186/s13148-018-0543-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related death. While cigarette smoking is the primary cause of this malignancy, risk differs across racial/ethnic groups. For the same number of cigarettes smoked, Native Hawaiians compared to whites are at greater risk and Japanese Americans are at lower risk of developing lung cancer. DNA methylation of specific CpG sites (e.g., in AHRR and F2RL3) is the most common blood epigenetic modification associated with smoking status. However, the influence of internal smoking dose, measured by urinary nicotine equivalents (NE), on DNA methylation in current smokers has not been investigated, nor has a study evaluated whether for the same smoking dose, circulating leukocyte DNA methylation patterns differ by race. METHODS We conducted an epigenome-wide association study (EWAS) of NE in 612 smokers from three racial/ethnic groups: whites (n = 204), Native Hawaiians (n = 205), and Japanese Americans (n = 203). Genome-wide DNA methylation profiling of blood leukocyte DNA was measured using the Illumina 450K BeadChip array. Average β value, the ratio of signal from a methylated probe relative to the sum of the methylated and unmethylated probes at that CpG, was the dependent variables in linear regression models adjusting for age, sex, race (for pan-ethnic analysis), and estimated cell-type distribution. RESULTS We found that NE was significantly associated with six differentially methylated CpG sites (Bonferroni corrected p < 1.48 × 10-7): four in or near the FOXK2, PBX1, FNDC7, and FUBP3 genes and two in non-annotated genetic regions. Higher levels of NE were associated with increasing methylation beta-valuesin all six sites. For all six CpG sites, the association was only observed in Native Hawaiians, suggesting that the influence of smoking dose on DNA methylation patterns is heterogeneous across race/ethnicity (p interactions < 8.8 × 10-8). We found two additional CpG sites associated with NE in only Native Hawaiians. CONCLUSIONS In conclusion, internal smoking dose was associated with increased DNA methylation in circulating leukocytes at specific sites in Native Hawaiian smokers but not in white or Japanese American smokers.
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Affiliation(s)
- Sungshim L Park
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 1509G, Los Angeles, CA, 90033, USA.
| | - Yesha M Patel
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 1509G, Los Angeles, CA, 90033, USA
| | - Lenora W M Loo
- Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Daniel J Mullen
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90032, USA
| | - Ite A Offringa
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90032, USA
| | - Alika Maunakea
- University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 1509G, Los Angeles, CA, 90033, USA
| | - Kimberly Siegmund
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 1509G, Los Angeles, CA, 90033, USA
| | - Sharon E Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Maarit Tiirikainen
- Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA.
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20
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García-Esquinas E, Jiménez A, Pastor-Barriuso R, Jones MR, Perez-Gomez B, Navas-Acien A, Tellez-Plaza M. Impact of declining exposure to secondhand tobacco smoke in public places to decreasing smoking-related cancer mortality in the US population. ENVIRONMENT INTERNATIONAL 2018; 117:260-267. [PMID: 29775915 PMCID: PMC6136453 DOI: 10.1016/j.envint.2018.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/03/2018] [Accepted: 05/03/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND The major decrease in exposure to secondhand smoke (SHS) in public places in recent decades could have contributed to the decline in smoking-related cancer mortality observed in the US population. METHODS Prospective study among 11,856 non-smoking adults aged ≥40 years who participated in NHANES 1988-1994 or 1999-2004 and were followed for mortality through 2006. We estimated the amount of change in cancer mortality over time attributed to the intermediate pathway of changes in SHS exposure in public places, after adjustment for risk factors and SHS exposure at home. RESULTS The adjusted smoking-related cancer mortality rate ratios (95% CI) for a two-fold increase in serum cotinine and a 1-hour increase in occupational SHS exposure time were 1.10 (1.03, 1.17) and 1.14 (1.06, 1.24) for all-cancer, and 1.13 (1.03, 1.24) and 1.14 (1.02, 1.26) for smoking-related cancer, respectively. The absolute reduction in mortality comparing 1999-2004 to 1988-1994 was 75.8 (-25.5, 177.0) and 77.0 (2.6, 151.4) deaths/100,000 person-years, for all-cancer and smoking-related cancer, respectively. Among these avoided all-cancer deaths, 45.8 (2.8, 89.5) and 18.1 (-1.2, 39.6)/100,000 person-year were attributable to changes in serum cotinine concentrations and occupational SHS exposure time, respectively. The corresponding numbers of smoking-related cancer avoided deaths were 36.4 (0.7, 72.8) and 9.9 (-3.8, 24.9)/100,000 person-year. CONCLUSIONS Declines in SHS exposure were associated with reductions in all-cancer and smoking-related cancer mortality, supporting that smoking bans in public places may have reduced cancer mortality among non-smoking adults.
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Affiliation(s)
- Esther García-Esquinas
- Department of Preventive Medicine and Public Health, Universidad Autónoma de Madrid/IdiPaz and CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Angélica Jiménez
- Institute for Biomedical Research Hospital Clinic of Valencia (INCLIVA), Valencia, Spain
| | - Roberto Pastor-Barriuso
- National Center of Epidemiology, Carlos III Institutes of Health and CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Miranda R Jones
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Beatriz Perez-Gomez
- National Center of Epidemiology, Carlos III Institutes of Health and CIBER of Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University, New York, NY, USA.
| | - Maria Tellez-Plaza
- Institute for Biomedical Research Hospital Clinic of Valencia (INCLIVA), Valencia, Spain; Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
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