1
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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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2
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Fang F, Andersen AM, Philibert R, Hancock DB. Epigenetic biomarkers for smoking cessation. ADDICTION NEUROSCIENCE 2023; 6:100079. [PMID: 37123087 PMCID: PMC10136056 DOI: 10.1016/j.addicn.2023.100079] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cigarette smoking has been associated with epigenetic alterations that may be reversible upon cessation. As the most-studied epigenetic modification, DNA methylation is strongly associated with smoking exposure, providing a potential mechanism that links smoking to adverse health outcomes. Here, we reviewed the reversibility of DNA methylation in accessible peripheral tissues, mainly blood, in relation to cigarette smoking cessation and the utility of DNA methylation as a biomarker signature to differentiate current, former, and never smokers and to quantify time since cessation. We summarized thousands of differentially methylated Cytosine-Guanine (CpG) dinucleotides and regions associated with smoking cessation from candidate gene and epigenome-wide association studies, as well as the prediction accuracy of the multi-CpG predictors for smoking status. Overall, there is robust evidence for DNA methylation signature of cigarette smoking cessation. However, there are still gaps to fill, including (1) cell-type heterogeneity in measuring blood DNA methylation; (2) underrepresentation of non-European ancestry populations; (3) limited longitudinal data to quantitatively measure DNA methylation after smoking cessation over time; and (4) limited data to study the impact of smoking cessation on other epigenetic features, noncoding RNAs, and histone modifications. Epigenetic machinery provides promising biomarkers that can improve success in smoking cessation in the clinical setting. To achieve this goal, larger and more-diverse samples with longitudinal measures of a broader spectrum of epigenetic marks will be essential to developing a robust DNA methylation biomarker assay, followed by meeting validation requirements for the assay before being implemented as a clinically useful tool.
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Affiliation(s)
- Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
| | - Allan M. Andersen
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
- Behavioral Diagnostics LLC, 2500 Crosspark Rd, Coralville, IA 52241, USA
- Department of Biomedical Engineering, 5601 Seamans Center for the Engineering Arts and Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Dana B. Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
- Corresponding author. (D.B. Hancock)
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3
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Long JD, Gehlsen MP, Moody J, Weeks G, Philibert R. Predictors of Smoking in Older Adults and an Epigenetic Validation of Self-Report. Genes (Basel) 2022; 14:genes14010025. [PMID: 36672765 PMCID: PMC9912258 DOI: 10.3390/genes14010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
There are several established predictors of smoking, but it is unknown if these predictors operate similarly for young and old smokers. We examined clinical data from the National Lung Screening Trial (NLST) to determine the predictive ability of gender, body mass index (BMI), marital status, and race on smoking behavior, with emphasis on gender interactions. In addition, we validated the self-report of smoking behaviors for a subgroup that had available epigenetic data in the form of cg05575921 methylation. Participants were N=9572 current or former smokers from the NLST biofluids database, age 55-74, minimum of 30 pack years, and mostly White. A subgroup of N=3084 who had DNA were used for the self-report validation analysis. The predictor analysis was based on the larger group and used penalized logistic regression to predict the self-report of being a former or current smoker at baseline. Cg05575921 methylation showed a moderate ability to discriminate among former and current smokers, AUC = 0.85 (95% confidence interval = [0.83, 0.86]). The final selected variables for the prediction model were BMI, gender, BMI by gender, age, divorced (vs. married), education, and race. The gender by BMI interaction was such that males had a higher probability of current smoking for lower BMI, but this switched to females having higher current smoking for overweight to obese. There is evidence that the self-reported smoking behavior in NLST is moderately accurate. The results of the primary analysis are consistent with the general smoking literature, and our results provide additional specificity regarding the gender by BMI interaction. Body weight issues might play a role in smoking cessation for older established smokers in a similar manner as younger smokers. It could be that women have less success with cessation when their BMI increases.
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Affiliation(s)
- Jeffrey D. Long
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA; (J.D.L.); (J.M.); (G.W.)
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa, IA 52242, USA
| | - Michael P. Gehlsen
- South Saint Paul Public Schools, 104 5th Ave. S, South Saint Paul, MN 55075, USA;
| | - Joanna Moody
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA; (J.D.L.); (J.M.); (G.W.)
| | - Gracie Weeks
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA; (J.D.L.); (J.M.); (G.W.)
| | - Robert Philibert
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa, IA 52242, USA; (J.D.L.); (J.M.); (G.W.)
- Behavioral Diagnostics LLC, 2500 Crosspark Rd., Suite W245, Coralville, IA 53341, USA
- Department of Biomedical Engineering, University of Iowa, Iowa, IA 52242, USA
- Correspondence:
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4
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Beach SRH, Ong ML, Gibbons FX, Gerrard M, Lei MK, Dawes K, Philibert RA. Epigenetic and Proteomic Biomarkers of Elevated Alcohol Use Predict Epigenetic Aging and Cell-Type variation Better Than Self-Report. Genes (Basel) 2022; 13:1888. [PMID: 36292773 PMCID: PMC9601579 DOI: 10.3390/genes13101888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022] Open
Abstract
Excessive alcohol consumption (EAC) has a generally accepted effect on morbidity and mortality, outcomes thought to be reflected in measures of epigenetic aging (EA). As the association of self-reported EAC with EA has not been consistent with these expectations, underscoring the need for readily employable non-self-report tools for accurately assessing and monitoring the contribution of EAC to accelerated EA, newly developed alcohol consumption DNA methylation indices, such as the Alcohol T Score (ATS) and Methyl DetectR (MDR), may be helpful. To test that hypothesis, we used these new indices along with the carbohydrate deficient transferrin (CDT), concurrent as well as past self-reports of EAC, and well-established measures of cigarette smoking to examine the relationship of EAC to both accelerated EA and immune cell counts in a cohort of 437 young Black American adults. We found that MDR, CDT, and ATS were intercorrelated, even after controlling for gender and cotinine effects. Correlations between EA and self-reported EAC were low or non-significant, replicating prior research, whereas correlations with non-self-report indices were significant and more substantial. Comparing non-self-report indices showed that the ATS predicted more than four times as much variance in EA, CDT4 cells and B-cells as for both the MDR and CDT, and better predicted indices of accelerated EA. We conclude that each of the non-self-report indices have differing predictive capacities with respect to key alcohol-related health outcomes, and that the ATS may be particularly useful for clinicians seeking to understand and prevent accelerated EA. The results also underscore the likelihood of substantial underestimates of problematic use when self-report is used and a reduction in correlations with EA and variance in cell-types.
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Affiliation(s)
- Steven R. H. Beach
- Department of Psychology, University of Georgia, Athens, GA 30602, USA
- Center for Family Research, University of Georgia, Athens, GA 30602, USA
| | - Mei Ling Ong
- Department of Psychology, University of Georgia, Athens, GA 30602, USA
- Center for Family Research, University of Georgia, Athens, GA 30602, USA
| | - Frederick X. Gibbons
- Department of Psychological Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Meg Gerrard
- Department of Psychological Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Man-Kit Lei
- Center for Family Research, University of Georgia, Athens, GA 30602, USA
- Department of Sociology, University of Georgia, Athens, GA 30602, USA
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA 52246, USA
| | - Robert A. Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA 52246, USA
- Behavioral Diagnostics LLC, Coralville, IA 52241, USA
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5
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El-Haddad NW, El Kawak M, El Asmar K, Jabbour ME, Moussa MA, Habib RR, Dhaini HR. AhRR methylation contributes to disease progression in urothelial bladder cancer. Cancer Biomark 2022; 35:167-177. [PMID: 36093686 DOI: 10.3233/cbm-220002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Bladder Cancer (BCa) is the tenth most incidental malignancy worldwide. BCa is mostly attributed to environmental exposure and lifestyle, particularly tobacco smoking. The Aryl Hydrocarbon Receptor Repressor (AhRR) participates in the induction of many enzymes involved in metabolizing carcinogens, including tobacco smoke components. Additionally, studies have shown that smoking demethylates the (AhRR) gene in blood, suggesting AhRR demethylation as a specific serum smoking biomarker. OBJECTIVE This study aimed to validate AhRR demethylation as a smoking biomarker in the target tissue and investigate its contribution to bladder carcinogenesis. METHODS AhRR percent methylation was tested for its association with patient smoking status and oncogenic outcome indicators, particularly p53, RB1, and FGFR3 activating mutations, muscle-invasiveness, and tumor grade, in 180 BCa tissue-based DNA. RESULTS Results showed significantly higher AhRR percent methylation in muscle-invasive compared to non-muscle invasive tumors (42.86% vs. 33.98%; p= 0.011), while lower AhRR methylation was significantly associated with FGFR3 Codon 248 mutant genotype compared to wild-type (28.11% ± 9.44 vs. 37.87% ± 22.53; p= 0.036). All other tested associations were non-statistically significant. CONCLUSIONS Although AhRR methylation did not predict smoking status in BCa tumors, it seems to play a role in carcinogenesis and disease progression. Our findings make a basis for further research.
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Affiliation(s)
- Nataly W El-Haddad
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| | - Michelle El Kawak
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| | - Khalil El Asmar
- Department of Epidemiology and Population Health, American University of Beirut, Beirut, Lebanon
| | - Michel E Jabbour
- Department of Urology, St George Hospital University Medical Center, Beirut, Lebanon.,Faculty of Medicine, University of Balamand, Beirut, Lebanon
| | - Mohamad A Moussa
- Department of Urology, Lebanese University, Beirut, Lebanon.,Department of Surgery, Division of Urology, Al-Zahraa University Hospital, Beirut, Lebanon
| | - Rima R Habib
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| | - Hassan R Dhaini
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
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6
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Abstract
DNA methylation is an epigenetic modification that has consistently been shown to be linked with a variety of human traits and diseases. Because DNA methylation is dynamic and potentially reversible in nature and can reflect environmental exposures and predict the onset of diseases, it has piqued interest as a potential disease biomarker. DNA methylation patterns are more stable than transcriptomic or proteomic patterns, and they are relatively easy to measure to track exposure to different environments and risk factors. Importantly, technologies for DNA methylation quantification have become increasingly cost effective-accelerating new research in the field-and have enabled the development of novel DNA methylation biomarkers. Quite a few DNA methylation-based predictors for a number of traits and diseases already exist. Such predictors show potential for being more accurate than self-reported or measured phenotypes (such as smoking behavior and body mass index) and may even hold potential for applications in clinics. In this review, we will first discuss the advantages and challenges of DNA methylation biomarkers in general. We will then review the current state and future potential of DNA methylation biomarkers in two human traits that show rather consistent alterations in methylome-obesity and smoking. Lastly, we will briefly speculate about the future prospects of DNA methylation biomarkers, and possible ways to achieve them.
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Affiliation(s)
- Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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7
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Holloway JW, DeMeo DL. Omics and Lung Function: A Need for Integration. Am J Respir Crit Care Med 2022; 206:242-244. [PMID: 35608542 PMCID: PMC9890266 DOI: 10.1164/rccm.202205-0928ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
| | - Dawn L. DeMeo
- Department of Medicine,Division of Pulmonary and Critical Care MedicineBrigham and Women’s HospitalBoston, Massachusetts
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8
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Huo B, Manos D, Xu Z, Matheson K, Chun S, Fris J, Wallace AMR, French DG. Screening Criteria Evaluation for Expansion in Pulmonary Neoplasias (SCREEN). Semin Thorac Cardiovasc Surg 2022; 35:769-780. [PMID: 35878739 DOI: 10.1053/j.semtcvs.2022.06.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/06/2022] [Indexed: 12/14/2022]
Abstract
The SCREEN study investigated screening eligibility and survival outcomes between heavy smokers and light-or-never-smokers with lung cancer to determine whether expanded risk factor analysis is needed to refine screening criteria. SCREEN is a retrospective study of 917 lung cancer patients diagnosed between 2005 and 2018 in Nova Scotia, Canada. Screening eligibility was determined using the National Lung Screening Trial (NSLT) criteria. Mortality risk between heavy smokers and light-or-never-smokers was compared using proportional-hazards models. The median follow-up was 2.9 years. The cohort was comprised of 179 (46.1%) female heavy smokers and 306 (57.8%) female light-or-never-smokers. Light-or-never-smokers were more likely to have a diagnosis of adenocarcinoma [n=378 (71.6%)] compared to heavy smokers [n=234 (60.5%); P< 0.001]. Heavy smokers were more frequently diagnosed with squamous cell carcinoma [n=111 (28.7%)] compared to light-or-never-smokers, [n=100 (18.9%); P< 0.001]. Overall, 36.9% (338) of patients met NLST screening criteria. There was no difference in 5-year survival between light-or-never-smokers and heavy smokers [55.2% (338) vs 58.5% (529); P = 0.408; HR 1.06, 95% CI 0.80-1.40; P = 0.704]. Multivariate analysis showed that males had an increased mortality risk [HR 2.00 (95% CI 1.57-2.54); P< 0.001]. Half of lung cancer patients were missed with the conventional screening criteria. There were more curable, stage 1 tumors among light-or-never-smokers. Smoking status and age alone may be insufficient predictors of lung cancer risk and prognosis. Expanded risk factor analysis is needed to refine lung cancer screening criteria.
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Affiliation(s)
- Bright Huo
- Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Daria Manos
- Department of Diagnostic Radiology, Dalhousie University, Halifax, NS, Canada
| | - Zhaolin Xu
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Kara Matheson
- Research Methods Unit, Nova Scotia Health Authority, Halifax, NS, Canada
| | - Samuel Chun
- Department of Urology, Dalhousie University, Halifax, NS, Canada
| | - John Fris
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Alison M R Wallace
- Department of Pathology, Dalhousie University, Halifax, NS, Canada; Division of Thoracic Surgery, Department of Surgery, Dalhousie University, Halifax, NS, Canada
| | - Daniel G French
- Division of Thoracic Surgery, Department of Surgery, Dalhousie University, Halifax, NS, Canada.
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9
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Lei MK, Gibbons FX, Gerrard M, Beach SRH, Dawes K, Philibert R. Digital methylation assessments of alcohol and cigarette consumption account for common variance in accelerated epigenetic ageing. Epigenetics 2022; 17:1991-2005. [PMID: 35866695 PMCID: PMC9665121 DOI: 10.1080/15592294.2022.2100684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Smoking and Heavy Alcohol Consumption (HAC) are established risk factors for myriad complex disorders of ageing. Yet many prior studies of Epigenetic Ageing (EA) have shown only modest effects of smoking and drinking on accelerated ageing. One potential reason for this conundrum might be the reliance of some prior EA studies on self-reported substance use, which may be unreliable in many samples. To test whether novel, non-self-reported indices would show a stronger association of smoking and HAC to EA, we used methylation sensitive digital PCR (MSdPCR) and data from 437 African American subjects from Wave 7 of the Family and Community Health Study Offspring Cohort to examine the effects of subjective and objective measures of smoking and HAC on 7 indices of EA. Because of limited overall correlations between the various EA indices, we examined patterns of association separately for each index. Consistent with expectations, MSdPCR assessments of smoking and HAC, but not self-reported alcohol consumption, were strongly correlated with accelerated EA. MSdPCR assessments of smoking and HAC accounted for 57% of GrimAge acceleration and the shared variance in GrimAge and DunedinPOAM accelerated EA. We conclude that MSdPCR assessments of smoking and HAC are valuable tools for understanding EA, represent directly targetable conditions for the prevention of premature ageing, and substantially improve upon self-reported assessment of smoking and HAC.
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Affiliation(s)
- Man-Kit Lei
- Department of Sociology, University of Georgia, Athens, GA, USA.,Center for Family Research, University of Georgia, Athens, GA, USA
| | - Frederick X Gibbons
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, USA
| | - Meg Gerrard
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, USA
| | - Steven R H Beach
- Center for Family Research, University of Georgia, Athens, GA, USA.,Department of Psychology, University of Georgia, Athens, GA, USA
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.,Behavioral Diagnostics LLC, Coralville, IA, USA
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10
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Allen JP, Danoff JS, Costello MA, Hunt GL, Hellwig AF, Krol KM, Gregory SG, Giamberardino SN, Sugden K, Connelly JJ. Lifetime marijuana use and epigenetic age acceleration: A 17-year prospective examination. Drug Alcohol Depend 2022; 233:109363. [PMID: 35231715 PMCID: PMC8982677 DOI: 10.1016/j.drugalcdep.2022.109363] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/19/2022] [Accepted: 02/15/2022] [Indexed: 12/12/2022]
Abstract
AIMS This study was designed to assess links between lifetime levels of marijuana use and accelerated epigenetic aging. DESIGN Prospective longitudinal study, following participants annually from age 13 to age 30. SETTING AND PARTICIPANTS A community sample of 154 participants recruited from a small city in the Southeastern United States. MEASUREMENTS Participants completed annual assessments of marijuana use from age 13 to age 29 and provided blood samples that yielded two indices of epigenetic aging (DNAmGrimAge and DunedinPoAm) at age 30. Additional covariates examined included history of cigarette smoking, anxiety and depressive symptoms, childhood illness, gender, adolescent-era family income, and racial/ethnic minority status. FINDINGS Lifetime marijuana use predicted accelerated epigenetic aging, with effects remaining even after covarying cell counts, demographic factors and chronological age (β's = 0.32 & 0.27, p's < 0.001, 95% CI's = 0.21-0.43 & 0.16-0.39 for DNAmGrimAge and DunedinPoAm, respectively). Predictions remained after accounting for cigarette smoking (β's = 0.25 & 0.21, respectively, p's < 0.001, 95% CI's = 0.14-0.37 & 0.09-0.32 for DNAmGrimAge and DunedinPoAm, respectively). A dose-response effect was observed and there was also evidence that effects were dependent upon recency of use. Effects of marijuana use appeared to be fully mediated by hypomethylation of a site linked to effects of hydrocarbon inhalation (cg05575921). CONCLUSIONS Marijuana use predicted epigenetic changes linked to accelerated aging, with evidence suggesting that effects may be primarily due to hydrocarbon inhalation among marijuana smokers. Further research is warranted to explore mechanisms underlying this linkage.
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11
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Andersen A, Reimer R, Dawes K, Becker A, Hutchens N, Miller S, Dogan M, Hundley B, A Mills J, D Long J, Philibert R. DNA methylation differentiates smoking from vaping and non-combustible tobacco use. Epigenetics 2022; 17:178-190. [PMID: 33588690 PMCID: PMC8865289 DOI: 10.1080/15592294.2021.1890875] [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: 10/21/2020] [Revised: 01/08/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Increasing use of non-combusted forms of nicotine such as e-cigarettes poses important public health questions regarding their specific risks relative to combusted tobacco products such as cigarettes. To fully delineate these risks, improved biomarkers that can distinguish between these forms of nicotine use are needed. Prior work has suggested that methylation status at cg05575921 may serve as a specific biomarker of combusted tobacco smoke exposure. We hypothesized combining this epigenetic biomarker with conventional metabolite assays could classify the type of nicotine product consumption. Therefore, we determined DNA methylation and serum cotinine values in samples from 112 smokers, 35 e-cigarette users, 19 smokeless tobacco users, and 269 controls, and performed mass spectroscopy analyses of urine samples from all nicotine users and 22 verified controls to determine urinary levels of putatively nicotine product-specific substances; propylene glycol, 2-cyanoethylmercapturic acid (CEMA), and anabasine. 1) Cigarette smoking was associated with a dose dependent demethylation of cg05575921 and increased urinary CEMA and anabasine levels, 2) e-cigarette use did not demethylate cg05575921, 3) smokeless tobacco use also did not demethylate cg05575921 but was positively associated with anabasine levels 4) CEMA and cg05575921 levels were highly correlated and 5) propylene glycol levels did not reliably distinguish use groups. Cg05575921 assessments distinguish exposure to tobacco smoke from smokeless sources of nicotine including e-cigarettes and smokeless tobacco, neither of which are associated with cg05575921 demethylation. A combination of methylomic and metabolite profiling may allow for accurate classification use status of a variety of nicotine containing products.
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Affiliation(s)
- Allan Andersen
- Department of Psychiatry, University of Iowa, Iowa City, USA
| | - Rachel Reimer
- College of Public Health, Des Moines University, Des Moines, USA
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, USA
| | - Ashley Becker
- Department of Psychiatry, University of Iowa, Iowa City, USA
| | | | | | - Meesha Dogan
- Department of Psychiatry, University of Iowa, Iowa City, USA
- Behavioral Diagnostics LLC, Coralville, USA
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, United States
| | - Brandon Hundley
- Department of Psychiatry, University of Iowa, Iowa City, USA
| | - James A Mills
- Department of Psychiatry, University of Iowa, Iowa City, USA
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, USA
- Department of Biostatistics, University of Iowa, Iowa City, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, USA
- Behavioral Diagnostics LLC, Coralville, USA
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, United States
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12
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Langdon RJ, Yousefi P, Relton CL, Suderman MJ. Epigenetic modelling of former, current and never smokers. Clin Epigenetics 2021; 13:206. [PMID: 34789321 PMCID: PMC8597260 DOI: 10.1186/s13148-021-01191-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation (DNAm) performs excellently in the discrimination of current and former smokers from never smokers, where AUCs > 0.9 are regularly reported using a single CpG site (cg05575921; AHRR). However, there is a paucity of DNAm models which attempt to distinguish current, former and never smokers as individual classes. Derivation of a robust DNAm model that accurately distinguishes between current, former and never smokers would be particularly valuable to epidemiological research (as a more accurate smoking definition vs. self-report) and could potentially translate to clinical settings. Therefore, we appraise 4 DNAm models of ternary smoking status (that is, current, former and never smokers): methylation at cg05575921 (AHRR model), weighted scores from 13 CpGs created by Maas et al. (Maas model), weighted scores from a LASSO model of candidate smoking CpGs from the literature (candidate CpG LASSO model), and weighted scores from a LASSO model supplied with genome-wide 450K data (agnostic LASSO model). Discrimination is assessed by AUC, whilst classification accuracy is assessed by accuracy and kappa, derived from confusion matrices. RESULTS We find that DNAm can classify ternary smoking status with reasonable accuracy, including when applied to external data. Ternary classification using only DNAm far exceeds the classification accuracy of simply assigning all classes as the most prevalent class (63.7% vs. 36.4%). Further, we develop a DNAm classifier which performs well in discriminating current from former smokers (agnostic LASSO model AUC in external validation data: 0.744). Finally, across our DNAm models, we show evidence of enrichment for biological pathways and human phenotype ontologies relevant to smoking, such as haemostasis, molybdenum cofactor synthesis, body fatness and social behaviours, providing evidence of the generalisability of our classifiers. CONCLUSIONS Our findings suggest that DNAm can classify ternary smoking status with close to 65% accuracy. Both the ternary smoking status classifiers and current versus former smoking status classifiers address the present lack of former smoker classification in epigenetic literature; essential if DNAm classifiers are to adequately relate to real-world populations. To improve performance further, additional focus on improving discrimination of current from former smokers is necessary.
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Affiliation(s)
- Ryan J Langdon
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Paul Yousefi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew J Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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13
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Dawes K, Andersen A, Reimer R, Mills JA, Hoffman E, Long JD, Miller S, Philibert R. The relationship of smoking to cg05575921 methylation in blood and saliva DNA samples from several studies. Sci Rep 2021; 11:21627. [PMID: 34732805 PMCID: PMC8566492 DOI: 10.1038/s41598-021-01088-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
Numerous studies have shown that cg05575921 methylation decreases in response to smoking. However, secondary to methodological issues, the magnitude and dose dependency of that response is as of yet unclear. This lack of certainty is a barrier to the use of DNA methylation clinically to assess and monitor smoking status. To better define this relationship, we conducted a joint analysis of methylation sensitive PCR digital (MSdPCR) assessments of cg05575921 methylation in whole blood and/or saliva DNA to smoking using samples from 421 smokers and 423 biochemically confirmed non-smokers from 4 previously published studies. We found that cg05575921 methylation manifested a curvilinear dose dependent decrease in response to increasing cigarette consumption. In whole blood DNA, the Receiver Operating Characteristic (ROC) Area Under the Curve (AUC) of cg05575921 methylation for predicting daily smoking status was 0.98. In saliva DNA, the gross AUC was 0.91 with correction for cellular heterogeneity improving the AUC to 0.94. Methylation status was significantly associated with the Fagerstrom Test for Nicotine Dependence score, but with significant sampling heterogeneity. We conclude that MSdPCR assessments of cg05575921 methylation are a potentially powerful, clinically implementable tool for the assessment and management of smoking.
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Affiliation(s)
- Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
- Molecular Medicine Program, University of Iowa, Iowa City, IA, 52242, USA
| | - Allan Andersen
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
| | - Rachel Reimer
- Department of Public Health, Des Moines University, Des Moines, IA, 50312, USA
| | - James A Mills
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
| | - Eric Hoffman
- Department of Radiology, University of Iowa, Iowa City, IA, 52242, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Biostatistics, University of Iowa, Iowa City, IA, 52242, USA
| | - Shelly Miller
- Behavioral Diagnostics LLC, Coralville, IA, 52241, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA.
- Behavioral Diagnostics LLC, Coralville, IA, 52241, USA.
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14
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Dawes K, Sampson L, Reimer R, Miller S, Philibert R, Andersen A. Epigenetic Analyses of Alcohol Consumption in Combustible and Non-Combustible Nicotine Product Users. EPIGENOMES 2021; 5:epigenomes5030018. [PMID: 34968367 PMCID: PMC8594674 DOI: 10.3390/epigenomes5030018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Alcohol and tobacco use are highly comorbid and exacerbate the associated morbidity and mortality of either substance alone. However, the relationship of alcohol consumption to the various forms of nicotine-containing products is not well understood. To improve this understanding, we examined the relationship of alcohol consumption to nicotine product use using self-report, cotinine, and two epigenetic biomarkers specific for smoking (cg05575921) and drinking (Alcohol T Scores (ATS)) in n = 424 subjects. Cigarette users had significantly higher ATS values than the other groups (p < 2.2 × 10−16). Using the objective biomarkers, the intensity of nicotine and alcohol consumption was correlated in both the cigarette and smokeless users (R = −0.66, p = 3.1 × 10−14; R2 = 0.61, p = 1.97 × 10−4). Building upon this idea, we used the objective nicotine biomarkers and age to build and test a Balanced Random Forest classification model for heavy alcohol consumption (ATS > 2.35). The model performed well with an AUC of 0.962, 89.3% sensitivity, and 85% specificity. We conclude that those who use non-combustible nicotine products drink significantly less than smokers, and cigarette and smokeless users drink more with heavier nicotine use. These findings further highlight the lack of informativeness of self-reported alcohol consumption and suggest given the public and private health burden of alcoholism, further research into whether using non-combustible nicotine products as a mode of treatment for dual users should be considered.
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Affiliation(s)
- Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (L.S.); (R.P.); (A.A.)
- Behavioral Diagnostics LLC, Coralville, IA 52241, USA;
- Correspondence: ; Tel.: +1-319-361-2081
| | - Luke Sampson
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (L.S.); (R.P.); (A.A.)
| | - Rachel Reimer
- College of Public Health, Des Moines University, Des Moines, IA 50312, USA;
| | - Shelly Miller
- Behavioral Diagnostics LLC, Coralville, IA 52241, USA;
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (L.S.); (R.P.); (A.A.)
- Behavioral Diagnostics LLC, Coralville, IA 52241, USA;
| | - Allan Andersen
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (L.S.); (R.P.); (A.A.)
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15
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Hypomethylation of AHRR (cg05575921) Is Related to Smoking Status in the Mexican Mestizo Population. Genes (Basel) 2021; 12:genes12081276. [PMID: 34440450 PMCID: PMC8391630 DOI: 10.3390/genes12081276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022] Open
Abstract
Tobacco smoking results in a multifactorial disease involving environmental and genetic factors; epigenome-wide association studies (EWAS) show changes in DNA methylation levels due to cigarette consumption, partially reversible upon tobacco smoking cessation. Therefore, methylation levels could predict smoking status. This study aimed to evaluate the DNA methylation level of cg05575921 (AHRR) and cg23771366 (PRSS23) and their correlation with lung function variables, cigarette consumption, and nicotine addiction in the Mexican smoking population. We included 114 non-smokers (NS) and 102 current tobacco smokers (TS); we then further subclassified them as heavy smokers (HS) (n = 53) and light smokers (LS) (n = 49). We used restriction enzymes (MspI/HpaII) and qPCR to determine the DNA methylation level. We observed significant hypomethylation of cg05575921 in smokers compared to NS (p = 0.003); further analysis found a difference between HS and NS (p = 0.02). We did not observe differences between other groups or a positive correlation between methylation levels and age, BMI, cigarette consumption, nicotine addiction, or lung function. In conclusion, the cg05575921 site of AHRR is significantly hypomethylated in Mexican smokers, especially in HS (≥20 cigarettes per day).
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16
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Lee GM, Yoon JH, Lee WR, Kim LH, Yoo KB. Factors Associated With the Differences Between Self-Report Smoking and Urinary Cotinine Criteria. Asia Pac J Public Health 2021; 33:357-368. [PMID: 33511851 DOI: 10.1177/1010539520986248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
During self-reporting, respondents underreport their smoking status for various reasons. We aimed to evaluate the difference between smoking status self-reporting and urinary cotinine tests in Korea respondents. Logistic regression analyses were performed to identify factors associated with the differences between self-reporting and urinary cotinine criteria. The dependent variable was the underreporting of smoking status; independent variables were sociodemographic, health status, and secondhand smoke (SHS) exposure. Total underreporting was 3.6% when Cot ≥164 and 4.0% when Cot-variable (classified) criteria underreported. Positive associations were found between smoking and age, education, drinking, and SHS. Underreporting in the nonsmoker group (odds ratio [OR] = 2.336; confidence interval [CI] = 1.717-3.179) was significantly associated with SHS, but this difference was nonsignificant in the ex-smoker group (OR = 1.184; CI = 0.879-1.638). Underreporting was 3.6% to 4.0%, and C-statistics was about 0.7, indicating that outcomes could be classified. SHS in nonsmokers was positively associated with underreporting; however, only the nonsmoker group had positive associations, demonstrating unintentional underreporting due to SHS.
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Affiliation(s)
- Gyeong-Min Lee
- Department of Health Administration, Yonsei University, Wonju-si, Gangwon-do, Republic of Korea
| | - Jang-Ho Yoon
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Corvallis, OR, USA
| | - Woo-Ri Lee
- Department of Health Administration, Yonsei University, Wonju-si, Gangwon-do, Republic of Korea
| | - Li-Hyun Kim
- Department of Health Administration, Yonsei University, Wonju-si, Gangwon-do, Republic of Korea
| | - Ki-Bong Yoo
- Department of Health Administration, Yonsei University, Wonju-si, Gangwon-do, Republic of Korea.,Department of Information & Statistics, Yonsei University, Wonju-si, Gangwon-do, Republic of Korea
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17
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Philibert R, Mills JA, Long JD, Salisbury SE, Comellas A, Gerke A, Dawes K, Vander Weg M, Hoffman EA. The Reversion of cg05575921 Methylation in Smoking Cessation: A Potential Tool for Incentivizing Healthy Aging. Genes (Basel) 2020; 11:E1415. [PMID: 33260961 PMCID: PMC7760261 DOI: 10.3390/genes11121415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Smoking is the largest preventable cause of mortality and the largest environmental driver of epigenetic aging. Contingency management-based strategies can be used to treat smoking but require objective methods of verifying quitting status. Prior studies have suggested that cg05575921 methylation reverts as a function of smoking cessation, but that it can be used to verify the success of smoking cessation has not been unequivocally demonstrated. To test whether methylation can be used to verify cessation, we determined monthly cg05575921 levels in a group of 67 self-reported smokers undergoing biochemically monitored contingency management-based smoking cessation therapy, as part of a lung imaging protocol. A total of 20 subjects in this protocol completed three months of cotinine verified smoking cessation. In these 20 quitters, the reversion of cg05575921 methylation was dependent on their initial smoking intensity, with methylation levels in the heaviest smokers reverting to an average of 0.12% per day over the 3-month treatment period. In addition, we found suggestive evidence that some individuals may have embellished their smoking history to gain entry to the study. Given the prominent effect of smoking on longevity, we conclude that DNA methylation may be a useful tool for guiding and incentivizing contingency management-based approaches for smoking cessation.
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Affiliation(s)
- Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.A.M.); (J.D.L.); (K.D.)
- Behavioral Diagnostics LLC, Coralville, IA 52241, USA
| | - James A. Mills
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.A.M.); (J.D.L.); (K.D.)
| | - Jeffrey D. Long
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.A.M.); (J.D.L.); (K.D.)
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Sue Ellen Salisbury
- Department of Radiology, University of Iowa, Iowa City, IA 52242, USA; (S.E.S.); (E.A.H.)
| | - Alejandro Comellas
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.C.); (A.G.); (M.V.W.)
| | - Alicia Gerke
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.C.); (A.G.); (M.V.W.)
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.A.M.); (J.D.L.); (K.D.)
- Molecular Medicine Program, University of Iowa, Iowa City, IA 52242, USA
| | - Mark Vander Weg
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.C.); (A.G.); (M.V.W.)
- Center for Access & Delivery Research and Evaluation, Iowa City VA Health Care System, Iowa City, IA 52242, USA
| | - Eric A. Hoffman
- Department of Radiology, University of Iowa, Iowa City, IA 52242, USA; (S.E.S.); (E.A.H.)
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18
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Cigarette and Cannabis Smoking Effects on GPR15+ Helper T Cell Levels in Peripheral Blood: Relationships with Epigenetic Biomarkers. Genes (Basel) 2020; 11:genes11020149. [PMID: 32019074 PMCID: PMC7074551 DOI: 10.3390/genes11020149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Smoking causes widespread epigenetic changes that have been linked with an increased risk of smoking-associated diseases and elevated mortality. Of particular interest are changes in the level of T cells expressing G-protein-coupled receptor 15 (GPR15), a chemokine receptor linked with multiple autoimmune diseases, including inflammatory bowel disease, multiple sclerosis and psoriasis. Accordingly, a better understanding of the mechanisms by which smoking influences variation in the GPR15+ helper T cell subpopulation is of potential interest. Methods: In the current study, we used flow cytometry and digital PCR assays to measure the GPR15+CD3+CD4+ populations in peripheral blood from a cohort of n = 62 primarily African American young adults (aged 27–35 years) with a high rate of tobacco and cannabis use. Results: We demonstrated that self-reported tobacco and cannabis smoking predict GPR15+CD3+CD4+ helper T cell levels using linear regression models. Further, we demonstrated that methylation of two candidate CpGs, cg19859270, located in GPR15, and cg05575921, located in the gene Aryl Hydrocarbon Receptor Repressor (AHRR), were both significant predictors of GPR15+CD3+CD4+ cell levels, mediating the relationship between smoking habits and increases in GPR15+CD3+CD4+ cells. As hypothesized, the interaction between cg05575921 and cg19859270 was also significant, indicating that low cg05575921 methylation was more strongly predictive of GPR15+CD3+CD4+ cell levels for those who also had lower cg19859270 methylation. Conclusions: Smoking leads changes in two CpGs, cg05575921 and cg19859270, that mediate 38.5% of the relationship between tobacco and cannabis smoking and increased GPR15+ Th levels in this sample. The impact of cg19859270 in amplifying the association between cg05575921 and increased GPR15+ Th levels is of potential theoretical interest given the possibility that it reflects a permissive interaction between different parts of the adaptive immune system.
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19
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Philibert R, Dogan M, Beach SRH, Mills JA, Long JD. AHRR methylation predicts smoking status and smoking intensity in both saliva and blood DNA. Am J Med Genet B Neuropsychiatr Genet 2020; 183:51-60. [PMID: 31456352 DOI: 10.1002/ajmg.b.32760] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/15/2019] [Accepted: 08/12/2019] [Indexed: 01/21/2023]
Abstract
Many existing DNA repositories do not have robust characterizations of smoking, while for many currently ongoing studies, the advent of vaping has rendered traditional cotinine-based methods of determining smoking status unreliable. Previously, we have shown that methylation status at cg05575921 in whole blood DNA can reliably predict cigarette consumption. However, whether methylation status in saliva can be used similarly has yet to be established. Herein, we use DNA from 418 biochemically confirmed smokers or nonsmokers to compare and contrast the utility of cg05575921 in classifying and quantifying cigarette smoking. Using whole blood DNA, a model incorporating age, gender, and methylation status had a receiver operating characteristic (ROC) area under the curve (AUC) for predicting smoking status of 0.995 with a nonlinear demethylation response to smoking. Using saliva DNA, the ROC AUC for predicting smoking was 0.971 with the plot of the relationship of DNA methylation to daily cigarette consumption being very similar to that seen for whole blood DNA. The addition of information from another methylation marker designed to correct for cellular heterogeneity improved the AUC for saliva DNA to 0.981. Finally, in 31 subjects who reported quitting smoking 10 or more years previously, cg05575921 methylation was nonsignificantly different from controls. We conclude that DNA methylation status at cg05575921 in DNA from whole blood or saliva predicts smoking status and daily cigarette consumption. We suggest these epigenetic assessments for objectively ascertaining smoking status will find utility in research, clinical, and civil applications.
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Affiliation(s)
- Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, Iowa.,Behavioral Diagnostics LLC, Coralville, Iowa
| | - Meeshanthini Dogan
- Department of Psychiatry, University of Iowa, Iowa City, Iowa.,Cardio Diagnostics LLC, Coralville, Iowa
| | - Steven R H Beach
- Center for Family Studies, University of Georgia, Athens, Georgia
| | - James A Mills
- Department of Psychiatry, University of Iowa, Iowa City, Iowa
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, Iowa.,Department of Biostatistics, University of Iowa, Iowa City, Iowa
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20
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Philibert RA, Dogan MV, Mills JA, Long JD. AHRR Methylation is a Significant Predictor of Mortality Risk in Framingham Heart Study. J Insur Med 2019; 48:79-89. [PMID: 31618096 DOI: 10.17849/insm-48-1-1-11.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background.-The ability to predict mortality is useful to clinicians, policy makers and insurers. At the current time, prediction of future mortality is still an inexact process with some proposing that epigenetic assessments could play a role in improving prognostics. In past work, we and others have shown that DNA methylation status at cg05575921, a well-studied measure of smoking intensity, is also a predictor of mortality. However, the exact extent of that predictive capacity and its independence of other commonly measured mortality risk factors are unknown. Objective.-To determine the capacity of methylation to predict mortality. Method.-We analyzed the relationship of methylation at cg05575921 and cg04987734, a recently described quantitative marker of heavy alcohol consumption, to mortality in the Offspring Cohort of the Framingham Heart Study using proportional hazards survival analysis. Results.-In this group of participants (n = 2278) whose average age was 66 ± 9 years, we found that the inclusion of both cg05575921 and cg04987734 methylation to a base model consisting of age and sex only, or to a model containing 11 commonly used mortality risk factors, improved risk prediction. What is more, prediction accuracy for the base model plus methylation data was increased compared to the base model plus known predictors of mortality (CHD, COPD, or stroke). Conclusion.-Cg05575921, and to a smaller extent cg04987734, are strong predictors of mortality risk in older Americans and that incorporation of DNA methylation assessments to these and other loci may be useful to population scientists, actuaries and policymakers to better understand the relationship of environmental risk factors, such as smoking and drinking, to mortality.
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Affiliation(s)
- Robert A Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA 52242.,Behavioral Diagnostics LLC, Coralville, IA, USA
| | - Meeshanthini V Dogan
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA 52242.,CardioDiagnostics LLC, Coralville, IA, USA
| | - James A Mills
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA 52242
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA 52242.,Department of Biostatistics, University of Iowa, Iowa City, IA, USA
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21
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McGinnis KA, Justice AC, Tate JP, Kranzler HR, Tindle HA, Becker WC, Concato J, Gelernter J, Li B, Zhang X, Zhao H, Crothers K, Xu K. Using DNA methylation to validate an electronic medical record phenotype for smoking. Addict Biol 2019; 24:1056-1065. [PMID: 30284751 DOI: 10.1111/adb.12670] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/22/2018] [Accepted: 07/22/2018] [Indexed: 12/14/2022]
Abstract
A validated, scalable approach to characterizing (phenotyping) smoking status is needed to facilitate genetic discovery. Using established DNA methylation sites from blood samples as a criterion standard for smoking behavior, we compare three candidate electronic medical record (EMR) smoking metrics based on longitudinal EMR text notes. With data from the Veterans Aging Cohort Study (VACS), we employed a validated algorithm to translate each smoking-related text note into current, past or never categories. We compared three alternative summary characterizations of smoking: most recent, modal and trajectories using descriptive statistics and Spearman's correlation coefficients. Logistic regression and area under the curve analyses were used to compare the associations of these phenotypes with the DNA methylation sites, cg05575921 and cg03636183, which are known to have strong associations with current smoking. DNA methylation data were available from the VACS Biomarker Cohort (VACS-BC), a sub-study of VACS. We also considered whether the associations differed by the certainty of trajectory group assignment (<0.80/≥0.80). Among 140 152 VACS participants, EMR summary smoking phenotypes varied in frequency by the metric chosen: current from 33 to 53 percent; past from 16 to 24 percent and never from 24 to 33 percent. The association between the EMR smoking pairs was highest for modal and trajectories (rho = 0.89). Among 728 individuals in the VACS-BC, both DNA methylation sites were associated with all three EMR summary metrics (p < 0.001), but the strongest association with both methylation sites was observed for trajectories (p < 0.001). Longitudinal EMR smoking data support using a summary phenotype, the validity of which is enhanced when data are integrated into statistical trajectories.
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Affiliation(s)
| | - Amy C. Justice
- Veterans Affairs Connecticut Healthcare System; West Haven CT USA
- Yale School of Medicine; New Haven CT USA
- Yale School of Public Health; New Haven CT USA
| | - Janet P. Tate
- Veterans Affairs Connecticut Healthcare System; West Haven CT USA
- Yale School of Medicine; New Haven CT USA
| | - Henry R. Kranzler
- VISN 4 MIRECC; Crescenz VAMC; Philadelphia PA USA
- University of Pennsylvania Perelman School of Medicine; Philadelphia PA USA
| | - Hilary A. Tindle
- Vanderbilt University Medical Center; Nashville TN USA
- Geriatric Research Education and Clinical Centers (GRECC), Veterans Affairs Tennessee Valley Healthcare System; Nashville TN USA
| | - William C. Becker
- Veterans Affairs Connecticut Healthcare System; West Haven CT USA
- Yale School of Medicine; New Haven CT USA
| | - John Concato
- Veterans Affairs Connecticut Healthcare System; West Haven CT USA
- Yale School of Medicine; New Haven CT USA
| | - Joel Gelernter
- Veterans Affairs Connecticut Healthcare System; West Haven CT USA
- Yale School of Medicine; New Haven CT USA
| | - Boyang Li
- Yale School of Medicine; New Haven CT USA
| | | | - Hongyu Zhao
- Yale School of Medicine; New Haven CT USA
- Yale School of Public Health; New Haven CT USA
| | | | - Ke Xu
- Veterans Affairs Connecticut Healthcare System; West Haven CT USA
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22
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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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23
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London SJ. Methylation, smoking, and reduced lung function. Eur Respir J 2019; 54:54/1/1900920. [PMID: 31273037 DOI: 10.1183/13993003.00920-2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
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24
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de Vocht F, Suderman M, Ruano-Ravina A, Thomas R, Wakeford R, Relton C, Tilling K, Boyd A. Residential exposure to radon and DNA methylation across the lifecourse: an exploratory study in the ALSPAC birth cohort. Wellcome Open Res 2019; 4:3. [PMID: 30906879 PMCID: PMC6426102 DOI: 10.12688/wellcomeopenres.14991.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
Background: Radon (and its decay products) is a known human carcinogen and the leading cause of lung cancer in never-smokers and the second in ever-smokers. The carcinogenic mechanism from radiation is a combination of genetic and epigenetic processes, but compared to the genetic mechanisms, epigenetic processes remain understudied in humans. This study aimed to explore associations between residential radon exposure and DNA methylation in the general population. Methods: Potential residential radon exposure for 75-metre area buffers was linked to genome-wide DNA methylation measured in peripheral blood from children and mothers of the Accessible Resource for Integrated Epigenomic Studies subsample of the ALSPAC birth cohort. Associations with DNA methylation were tested at over 450,000 CpG sites at ages 0, 7 and 17 years (children) and antenatally and during middle-age (mothers). Analyses were adjusted for potential residential and lifestyle confounding factors and were determined for participants with complete data (n = 786 to 980). Results: Average potential exposure to radon was associated in an exposure-dependent manner with methylation at cg25422346 in mothers during pregnancy, with no associations at middle age. For children, radon potential exposure was associated in an exposure-dependent manner with methylation of cg16451995 at birth, cg01864468 at age 7, and cg04912984, cg16105117, cg23988964, cg04945076, cg08601898, cg16260355 and cg26056703 in adolescence. Conclusions: Residential radon exposure was associated with DNA methylation in an exposure-dependent manner. Although chance and residual confounding cannot be excluded, the identified associations may show biological mechanisms involved in early biological effects from radon exposure.
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Affiliation(s)
- Frank de Vocht
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Richard Thomas
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, UK
| | - Richard Wakeford
- Centre for Occupational and Environmental Health, University of Manchester, Manchester, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kate Tilling
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Andy Boyd
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, UK
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25
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Sugden K, Hannon EJ, Arseneault L, Belsky DW, Broadbent JM, Corcoran DL, Hancox RJ, Houts RM, Moffitt TE, Poulton R, Prinz JA, Thomson WM, Williams BS, Wong CCY, Mill J, Caspi A. Establishing a generalized polyepigenetic biomarker for tobacco smoking. Transl Psychiatry 2019; 9:92. [PMID: 30770782 PMCID: PMC6377665 DOI: 10.1038/s41398-019-0430-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/17/2019] [Accepted: 01/24/2019] [Indexed: 12/27/2022] Open
Abstract
Large-scale epigenome-wide association meta-analyses have identified multiple 'signatures'' of smoking. Drawing on these findings, we describe the construction of a polyepigenetic DNA methylation score that indexes smoking behavior and that can be utilized for multiple purposes in population health research. To validate the score, we use data from two birth cohort studies: The Dunedin Longitudinal Study, followed to age-38 years, and the Environmental Risk Study, followed to age-18 years. Longitudinal data show that changes in DNA methylation accumulate with increased exposure to tobacco smoking and attenuate with quitting. Data from twins discordant for smoking behavior show that smoking influences DNA methylation independently of genetic and environmental risk factors. Physiological data show that changes in DNA methylation track smoking-related changes in lung function and gum health over time. Moreover, DNA methylation changes predict corresponding changes in gene expression in pathways related to inflammation, immune response, and cellular trafficking. Finally, we present prospective data about the link between adverse childhood experiences (ACEs) and epigenetic modifications; these findings document the importance of controlling for smoking-related DNA methylation changes when studying biological embedding of stress in life-course research. We introduce the polyepigenetic DNA methylation score as a tool both for discovery and theory-guided research in epigenetic epidemiology.
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Affiliation(s)
- Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
| | - Eilis J Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Louise Arseneault
- Social, Genetic, and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Daniel W Belsky
- Department of Epidemiology & Butler Aging Center, Columbia University Mailman School of Public Health, New York, NY, USA
| | | | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Robert J Hancox
- Department of Preventive and Social Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Renate M Houts
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Social, Genetic, and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, University of Otago, Dunedin, New Zealand
| | - Joseph A Prinz
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - W Murray Thomson
- Department of Oral Sciences, University of Otago, Dunedin, New Zealand
| | - Benjamin S Williams
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Chloe C Y Wong
- Social, Genetic, and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Avshalom Caspi
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Social, Genetic, and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
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26
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Andersen AM, Ryan PT, Gibbons FX, Simons RL, Long JD, Philibert RA. A Droplet Digital PCR Assay for Smoking Predicts All-Cause Mortality. J Insur Med 2019; 47:220-229. [PMID: 30702368 PMCID: PMC7518325 DOI: 10.17849/insm-47-4-1-10.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVES -Determine whether an epigenetic assay for smoking predicts all-cause mortality in adults participating in a longitudinal study of Iowa adoptees. BACKGROUND -Improved biomarkers for smoking are needed given its large public health impact and significant limitations of both self-report and current biomarkers, such as cotinine in detecting smoking. In the past 5 years, multiple epigenome-wide association studies of smoking have identified loci suitable for translation as epigenetic biomarkers for smoking, in particular the CpG cg05575921. Digital polymerase chain reaction methods hold promise for the development of this and other epigenetic biomarkers. METHODS -Participants in the Iowa Adoption Studies were interviewed regarding their smoking habits. DNA was prepared from whole blood and bisulfite-converted for methylation analysis and digital droplet polymerase chain reaction assay of methylation at cg05575921 was performed. National Death Index records were requested for 584 study participants, resulting in 24 complete matches, 210 partial matches and 350 non-matching records. Complete matches were coded as deceased while the remainder were coded as alive (ie, censored). In total, methylation data and vital status information were available for a total of N = 193 subjects, including 15 deceased and 178 non-deceased. Cox regression was used to examine the ability of cg05575921 methylation as a continuous value to predict the timing of mortality with and without the inclusion of age, sex, race, BMI, marital status, educational status, socioeconomic status, cardiovascular risk factors, and a history of cancer as covariates. RESULTS -Methylation at cg05575921 predicted the hazard of mortality as the sole predictor and after accounting for major demographic and clinical risk factors. The fitted model showed the hazard ratio increased by 3.5% for every 1% decrease in methylation. CONCLUSIONS -Decreased methylation at cg05575921, an emerging epigenetic biomarker for smoking, was associated with early mortality in a longitudinal study of adults after accounting for the impact of major demographic and clinical risk factors for all-cause mortality. This approach may be useful in clinical research or actuarial assessments.
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Affiliation(s)
- Allan M. Andersen
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA 52242
| | - Philip T. Ryan
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA 52242
| | - Fredrick X. Gibbons
- Department of Psychological Sciences, University of Connecticut, Storrs, CT 06269
| | - Ronald L. Simons
- Department of Sociology, University of Georgia, Athens, GA 30602
| | - Jeffrey D. Long
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA 52242
- Department of Biostatistics, University of Iowa, Iowa City, IA USA 52242
| | - Robert A. Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA 52242
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA 52242
- Behavioral Diagnostics, Coralville IA 52241
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27
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de Vocht F, Suderman M, Ruano-Ravina A, Thomas R, Wakeford R, Relton C, Tilling K, Boyd A. Residential exposure to radon and DNA methylation across the lifecourse: an exploratory study in the ALSPAC birth cohort. Wellcome Open Res 2019; 4:3. [PMID: 30906879 PMCID: PMC6426102 DOI: 10.12688/wellcomeopenres.14991.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2018] [Indexed: 10/12/2023] Open
Abstract
Background: Radon (and its decay products) is a known human carcinogen and the leading cause of lung cancer in never-smokers and the second in ever-smokers. The carcinogenic mechanism from radiation is a combination of genetic and epigenetic processes, but compared to the genetic mechanisms, epigenetic processes remain understudied in humans. This study aimed to explore associations between residential radon exposure and DNA methylation in the general population. Methods: Potential residential radon exposure for 75-metre area buffers was linked to genome-wide DNA methylation measured in peripheral blood from children and mothers of the Accessible Resource for Integrated Epigenomic Studies subsample of the ALSPAC birth cohort. Associations with DNA methylation were tested at over 450,000 CpG sites at ages 0, 7 and 17 years (children) and antenatally and during middle-age (mothers). Analyses were adjusted for potential residential and lifestyle confounding factors and were determined for participants with complete data (n = 786-980). Results: Average potential exposure to radon was associated in an exposure-dependent manner with methylation at cg25422346 in mothers during pregnancy, with no associations at middle age. For children, radon potential exposure was associated in an exposure-dependent manner with methylation of cg16451995 at birth, cg01864468 at age 7, and cg04912984, cg16105117, cg23988964, cg04945076, cg08601898, cg16260355 and cg26056703 in adolescence. Conclusions: Residential radon exposure was associated with DNA methylation in an exposure-dependent manner. Although residual confounding cannot be excluded, the identified associations may show biological mechanisms involved in early biological effects from radon exposure.
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Affiliation(s)
- Frank de Vocht
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Richard Thomas
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, UK
| | - Richard Wakeford
- Centre for Occupational and Environmental Health, University of Manchester, Manchester, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kate Tilling
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Andy Boyd
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, UK
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28
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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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29
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Rosen AD, Robertson KD, Hlady RA, Muench C, Lee J, Philibert R, Horvath S, Kaminsky ZA, Lohoff FW. DNA methylation age is accelerated in alcohol dependence. Transl Psychiatry 2018; 8:182. [PMID: 30185790 PMCID: PMC6125381 DOI: 10.1038/s41398-018-0233-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/25/2018] [Accepted: 07/14/2018] [Indexed: 12/12/2022] Open
Abstract
Alcohol dependence (ALC) is a chronic, relapsing disorder that increases the burden of chronic disease and significantly contributes to numerous premature deaths each year. Previous research suggests that chronic, heavy alcohol consumption is associated with differential DNA methylation patterns. In addition, DNA methylation levels at certain CpG sites have been correlated with age. We used an epigenetic clock to investigate the potential role of excessive alcohol consumption in epigenetic aging. We explored this question in five independent cohorts, including DNA methylation data derived from datasets from blood (n = 129, n = 329), liver (n = 92, n = 49), and postmortem prefrontal cortex (n = 46). One blood dataset and one liver tissue dataset of individuals with ALC exhibited positive age acceleration (p < 0.0001 and p = 0.0069, respectively), whereas the other blood and liver tissue datasets both exhibited trends of positive age acceleration that were not significant (p = 0.83 and p = 0.57, respectively). Prefrontal cortex tissue exhibited a trend of negative age acceleration (p = 0.19). These results suggest that excessive alcohol consumption may be associated with epigenetic aging in a tissue-specific manner and warrants further investigation using multiple tissue samples from the same individuals.
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Affiliation(s)
- Allison D. Rosen
- 0000 0004 0481 4802grid.420085.bSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Keith D. Robertson
- 0000 0004 0459 167Xgrid.66875.3aDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Ryan A. Hlady
- 0000 0004 0459 167Xgrid.66875.3aDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Christine Muench
- 0000 0004 0481 4802grid.420085.bSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Jisoo Lee
- 0000 0004 0481 4802grid.420085.bSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Robert Philibert
- 0000 0004 1936 8294grid.214572.7Department of Psychiatry, University of Iowa, Iowa City, IA USA
| | - Steve Horvath
- 0000 0000 9632 6718grid.19006.3eDepartment of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA ,0000 0000 9632 6718grid.19006.3eDepartment of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA USA
| | - Zachary A. Kaminsky
- 0000 0001 2171 9311grid.21107.35Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA ,0000 0001 2171 9311grid.21107.35Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Falk W. Lohoff
- 0000 0004 0481 4802grid.420085.bSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
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Philibert R, Dogan M, Noel A, Miller S, Krukow B, Papworth E, Cowley J, Knudsen A, Beach SR, Black D. Genome-wide and digital polymerase chain reaction epigenetic assessments of alcohol consumption. Am J Med Genet B Neuropsychiatr Genet 2018; 177:479-488. [PMID: 29704316 PMCID: PMC9518929 DOI: 10.1002/ajmg.b.32636] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/13/2018] [Accepted: 03/27/2018] [Indexed: 01/19/2023]
Abstract
The lack of readily employable biomarkers of alcohol consumption is a problem for clinicians and researchers. In 2014, we published a preliminary DNA methylation signature of heavy alcohol consumption that remits as a function of abstinence. Herein, we present new genome-wide methylation findings from a cohort of additional subjects and a meta-analysis of the data. Using DNA from 47 consecutive heavy drinkers admitted for alcohol detoxification in the context of alcohol treatment and 47 abstinent controls, we replicate the 2014 results and show that 21,221 CpG residues are differentially methylated in active heavy drinkers. Meta-analysis of all data from the 448,058 probes common to the two methylation platforms shows a similarly profound signature with confirmation of findings from other groups. Principal components analyses show that genome-wide methylation changes in response to alcohol consumption load on two major factors with one component accounting at least 50% of the total variance in both smokers and nonsmoking alcoholics. Using data from the arrays, we derive a panel of five methylation probes that classifies use status with a receiver operator characteristic area under the curve (AUC) of 0.97. Finally, using droplet digital polymerase chain reaction (PCR), we convert these array-based findings to two marker assays with an AUC of 0.95 and a four marker set AUC of 0.98. We conclude that DNA methylation assessments are capable of quantifying alcohol use status and suggest that readily employable digital PCR approaches for substance consumption may find widespread use in alcohol-related research and patient care.
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Affiliation(s)
- Robert Philibert
- Behavioral Diagnostics, Coralville, Iowa 52241,Department of Psychiatry, University of Iowa, Iowa City, IA 52242,to whom correspondence should be addressed at: 2500 Crosspark Road, Suite W245, Coralville, IA 52241,
| | - Meesha Dogan
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242,Cardio Diagnostics, Coralville, Iowa 52241
| | - Amanda Noel
- Behavioral Diagnostics, Coralville, Iowa 52241
| | | | | | | | - Joseph Cowley
- Center for Alcohol and Drug Services, Davenport, IA 52804
| | | | | | - Donald Black
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242
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Beach SR, Lei MK, Simons RL, Dogan MV, Gibbons FX, Philibert RA. MTHFR regulatory effects on methylation of CG05575921 in response to smoking: Effects are also discernable using MTHFR expression. Am J Med Genet B Neuropsychiatr Genet 2018; 177:529-534. [PMID: 29745998 PMCID: PMC6105525 DOI: 10.1002/ajmg.b.32624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 02/15/2018] [Accepted: 02/26/2018] [Indexed: 11/06/2022]
Affiliation(s)
| | | | | | - Meeshanthini V. Dogan
- Department of Psychiatry, The University of Iowa, Iowa City, IA
- Biomedical Engineering, The University of Iowa
| | | | - Robert A. Philibert
- Department of Psychiatry, The University of Iowa, Iowa City, IA
- Neuroscience and Genetics Programs, The University of Iowa, Iowa City, IA
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Philibert R, Dogan M, Noel A, Miller S, Krukow B, Papworth E, Cowley J, Long JD, Beach SRH, Black DW. Dose Response and Prediction Characteristics of a Methylation Sensitive Digital PCR Assay for Cigarette Consumption in Adults. Front Genet 2018; 9:137. [PMID: 29740475 PMCID: PMC5928210 DOI: 10.3389/fgene.2018.00137] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
The tobacco use disorders are the largest preventable cause of morbidity and mortality in the world. A substantial barrier to the development of better intervention and screening measures is the lack of clinically employable biomarkers to detect the existence and extent of tobacco consumption. In prior work, we and others have shown that array based assessment of DNA methylation status at cg05575921 is a sensitive and quantitative method for assessing cigarette consumption. Unfortunately, in general, arrays are not practical clinical tools. Herein, we detail the prediction performance metrics and dose dependency of a clinically implementable droplet digital PCR (ddPCR) assay for cigarette consumption in adults. First, we demonstrate that measurements of cg05575921 as determined by Illumina array and ddPCR are highly correlated (R2 = 0.98, n = 92). Second, using clinical data and biomaterial from 177 subjects ranging from 18 to 78 years of age, we show that the Receiver Operating Characteristic (ROC) area under the curve (AUC) for classifying smoking status using methylation status at cg05575921 is 0.99. Finally, we conduct modeling analyses of cigarette consumption over discrete time periods to show that methylation status is best correlated with mean cigarette consumption over the past year (R2 = 0.5) and that demethylation at cg05575921 is dose dependent with a demethylation (delta beta) of 1% being equivalent to 1.2 cigarettes per day. But we do not find a relationship between Fagerstrom score and DNA methylation. We conclude that ddPCR assessment of cg05575921 methylation is an accurate method for assessing the presence and extent of cigarette consumption in adult subjects. We suggest that skillful clinical implementation of this approach alone or in combination with other assessment methods could lead to substantial reduction of cigarette consumption related morbidity and mortality.
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Affiliation(s)
- Robert Philibert
- Behavioral Diagnostics LLC, Coralville, IA, United States
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
| | - Meesha Dogan
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
- Cardio Diagnostics, Coralville, IA, United States
| | - Amanda Noel
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Shelly Miller
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Brianna Krukow
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Emma Papworth
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Joseph Cowley
- Center for Alcohol and Drug Services, Davenport, IA, United States
| | | | - Steven R. H. Beach
- Center for Family Studies at the University of Georgia, Athens, GA, United States
| | - Donald W. Black
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
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Kular L, Kular S. Epigenetics applied to psychiatry: Clinical opportunities and future challenges. Psychiatry Clin Neurosci 2018; 72:195-211. [PMID: 29292553 DOI: 10.1111/pcn.12634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/12/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022]
Abstract
Psychiatric disorders are clinically heterogeneous and debilitating chronic diseases resulting from a complex interplay between gene variants and environmental factors. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, instruct the cell/tissue to correctly interpret external signals and adjust its functions accordingly. Given that epigenetic modifications are sensitive to environment, stable, and reversible, epigenetic studies in psychiatry could represent a promising approach to better understanding and treating disease. In the present review, we aim to discuss the clinical opportunities and challenges arising from the epigenetic research in psychiatry. Using selected examples, we first recapitulate key findings supporting the role of adverse life events, alone or in combination with genetic risk, in epigenetic programming of neuropsychiatric systems. Epigenetic studies further report encouraging findings about the use of methylation changes as diagnostic markers of disease phenotype and predictive tools of progression and response to treatment. Then we discuss the potential of using targeted epigenetic pharmacotherapy, combined with psychosocial interventions, for future personalized medicine for patients. Finally, we review the methodological limitations that could hinder interpretation of epigenetic data in psychiatry. They mainly arise from heterogeneity at the individual and tissue level and require future strategies in order to reinforce the biological relevance of epigenetic data and its translational use in psychiatry. Overall, we suggest that epigenetics could provide new insights into a more comprehensive interpretation of mental illness and might eventually improve the nosology, treatment, and prevention of psychiatric disorders.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sonia Kular
- Adult Psychiatry Unit of Laval Secteur Est, Laval, France
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Dogan MV, Grumbach IM, Michaelson JJ, Philibert RA. Integrated genetic and epigenetic prediction of coronary heart disease in the Framingham Heart Study. PLoS One 2018; 13:e0190549. [PMID: 29293675 PMCID: PMC5749823 DOI: 10.1371/journal.pone.0190549] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
An improved method for detecting coronary heart disease (CHD) could have substantial clinical impact. Building on the idea that systemic effects of CHD risk factors are a conglomeration of genetic and environmental factors, we use machine learning techniques and integrate genetic, epigenetic and phenotype data from the Framingham Heart Study to build and test a Random Forest classification model for symptomatic CHD. Our classifier was trained on n = 1,545 individuals and consisted of four DNA methylation sites, two SNPs, age and gender. The methylation sites and SNPs were selected during the training phase. The final trained model was then tested on n = 142 individuals. The test data comprised of individuals removed based on relatedness to those in the training dataset. This integrated classifier was capable of classifying symptomatic CHD status of those in the test set with an accuracy, sensitivity and specificity of 78%, 0.75 and 0.80, respectively. In contrast, a model using only conventional CHD risk factors as predictors had an accuracy and sensitivity of only 65% and 0.42, respectively, but with a specificity of 0.89 in the test set. Regression analyses of the methylation signatures illustrate our ability to map these signatures to known risk factors in CHD pathogenesis. These results demonstrate the capability of an integrated approach to effectively model symptomatic CHD status. These results also suggest that future studies of biomaterial collected from longitudinally informative cohorts that are specifically characterized for cardiac disease at follow-up could lead to the introduction of sensitive, readily employable integrated genetic-epigenetic algorithms for predicting onset of future symptomatic CHD.
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Affiliation(s)
- Meeshanthini V. Dogan
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
- Department of Psychiatry, University of Iowa, Iowa City, Iowa, United States of America
- Cardio Diagnostics LLC, Coralville, Iowa, United States of America
| | - Isabella M. Grumbach
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Iowa City Veterans Affairs Healthcare System, Iowa City, Iowa, United States of America
| | - Jacob J. Michaelson
- Department of Psychiatry, University of Iowa, Iowa City, Iowa, United States of America
| | - Robert A. Philibert
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States of America
- Department of Psychiatry, University of Iowa, Iowa City, Iowa, United States of America
- Behavioral Diagnostics LLC, Coralville, Iowa, United States of America
- * E-mail:
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Philibert R, Glatt SJ. Optimizing the chances of success in the search for epigenetic biomarkers: Embracing genetic variation. Am J Med Genet B Neuropsychiatr Genet 2017; 174:589-594. [PMID: 28696057 PMCID: PMC5562041 DOI: 10.1002/ajmg.b.32569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 06/16/2017] [Indexed: 01/21/2023]
Abstract
The emphasis on clinical translation in biomedical research continues to grow. This focus has been particularly notable in those investigators using epigenetic approaches to decipher the biology of complex behavioral disorders. As a result of these efforts, reproducible findings for several disorders, such as smoking, have been generated, giving rise to hopes that biomarkers for other behavioral illnesses would be forthcoming. Unfortunately, that biomedical cornucopia has not yet materialized. In this editorial, we review progress to date and discuss barriers to generating epigenetic biomarkers for complex behavioral disorders. We highlight the need to incorporate information on genetic variation and develop more powerful bioinformatics tools in order to optimize the likelihood of success. We emphasize that searches should focus on clearly defined, readily distinguishable behavioral constructs and suggest that some well-intentioned methods, such as correction for cellular heterogeneity, may actually impede the identification of clinically relevant biomarkers in peripheral blood. Finally, we describe how the understanding created by the development of these biomarkers may lead to more valid animal models of neuropsychiatric illness. We conclude that the prospects for epigenetic biomarkers for complex disorders are bright, but emphasize that the journey to the clinical implementation of these findings will be a slow, iterative process.
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Affiliation(s)
- Robert Philibert
- Behavioral Diagnostics, Coralville, Iowa
- Department of Psychiatry, University of Iowa, Iowa City, Iowa
| | - Stephen J Glatt
- Psychiatric Genetic Epidemiology and Neurobiology Laboratory (PsychGENe Lab), Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York
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