Active smoking is a major preventable public health problem and an established critical factor for epigenetic modification. In this systematic review, we identified 17 studies addressing the association of active smoking exposure with methylation modifications in blood DNA, including 14 recent epigenome-wide association studies (EWASs) and 3 gene-specific methylation studies (GSMSs) on the gene regions identified by EWASs. Overall, 1460 smoking-associated CpG sites were identified in the EWASs, of which 62 sites were detected in multiple (≥3) studies. The three most frequently reported CpG sites (genes) in whole blood samples were cg05575921 (AHRR), cg03636183 (F2RL3), and cg19859270 (GPR15), followed by other loci within intergenic regions 2q37.1 and 6p21.33. These significant smoking-related genes were further assessed by specific methylation assays in three GSMSs and reflected not only current but also lifetime or long-term exposure to active smoking. In conclusion, this review summarizes the evidences for the use of blood DNA methylation patterns as biomarkers of smoking exposure for research and clinical practice. In particular, it provides a reservoir for constructing a smoking exposure index score which could be used to more precisely quantify long-term smoking exposure and evaluate the risks of smoking-induced diseases.

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DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies

Rationale and objectives Self-reported smoking underestimates disease risk. Smoking affects DNA methylation, in particular the cg05575921 site in the aryl hydrocarbon receptor repressor (AHRR ) gene. We tested the hypothesis that AHRR cg05575921 hypomethylation is associated with risk of smoking-related morbidity and mortality. Methods From the Copenhagen City Heart Study representing the Danish general population, we studied 9234 individuals. Using bisulphite treated leucocyte DNA, AHRR (cg05575921) methylation was measured. Rs1051730 ( CHRN3A ) genotype was used to evaluate smoking heaviness. Participants were followed for up to 22 years for exacerbations of COPD, event of lung cancer and all-cause mortality. Six-year lung cancer risk was calculated according to the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO M2012 ). Measurements and main results AHRR (cg05575921) hypomethylation was associated with former and current smoking status, high daily and cumulative smoking, short time since smoking cessation (all p values –31 ), and the smoking-related CHRN3A genotype (−0.48% per T-allele, p=0.002). The multifactorially adjusted HRs for the lowest versus highest methylation quintiles were 4.58 (95% CI 2.83 to 7.42) for COPD exacerbations, 4.87 (2.31 to 10.3) for lung cancer and 1.67 (1.48 to 1.88) for all-cause mortality. Finally, among 2576 high-risk smokers eligible for lung cancer screening by CT, observed cumulative incidences of lung cancer after 6 years for individuals in the lowest and highest methylation quintiles were 3.7% and 0.0% (p=2×10 –7 ), whereas predicted PLCO M2012 6-year risks were similar (4.3% and 4.4%, p=0.77). Conclusion AHRR (cg05575921) hypomethylation, a marker of smoking behaviour, provides potentially clinical relevant predictions of future smoking-related morbidity and mortality.

https://thorax.bmj.com/content/thoraxjnl/72/7/646.full.pdf

AHRR (cg05575921) hypomethylation marks smoking behaviour, morbidity and mortality

https://pure.rug.nl/ws/files/40253177/eFORGE_A_Tool_for_Identifying_Cell_Type_Specific_Signal_in_Epigenomic_Data.pdf

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

Understanding mediation is useful for identifying intermediates lying between an exposure and an outcome which, when intervened upon, will block (some or all of) the causal pathway between the exposure and outcome. Mediation approaches used in conventional epidemiology have been adapted to understanding the role of molecular intermediates in situations of high-dimensional omics data with varying degrees of success. In particular, the limitations of observational epidemiological study including confounding, reverse causation and measurement error can afflict conventional mediation approaches and may lead to incorrect conclusions regarding causal effects. Solutions to analysing mediation which overcome these problems include the use of instrumental variable methods such as Mendelian randomization, which may be applied to evaluate causality in increasingly complex networks of omics data.

/pdf/challenges-and-novel-approaches-for-investigating-molecular-5fhigu9oz5.pdf

Challenges and novel approaches for investigating molecular mediation.

Background:Maternal smoking during pregnancy, especially when sustained, leads to numerous adverse health outcomes in offspring. Pregnant women disproportionately underreport smoking and smokers te...

DNA Methylation Score as a Biomarker in Newborns for Sustained Maternal Smoking during Pregnancy

Smoking is the largest preventable cause of morbidity and mortality in the world. Although there are effective pharmacologic and behavioral treatments for smoking cessation, our inability to objectively quantify smokers’ progress in decreasing smoking has been a barrier to both clinical and research efforts. In prior work, we and others have shown that DNA methylation at cg05575921, a CpG residue in the aryl hydrocarbon receptor repressor (AHRR), can be used to determine smoking status and infer cigarette consumption history. In this study, we serially assessed self-report and existing objective markers of cigarette consumption in 35 subjects undergoing smoking cessation therapy, then quantified DNA methylation at cg05575921 at study entry and three subsequent time points. Five subjects who reported serum cotinine and exhaled carbon monoxide verified smoking abstinence for the three months prior to study exit averaged a 5.9% increase in DNA methylation at cg05575921 (p<0.004) over the six month study. Although the other 30 subjects did not achieve smoking cessation at the six-month time point, their self-reported reduction of cigarette consumption (mean = 6 cigarettes per day) was associated with a 2.8% increase DNA methylation at cg05575921 (p<0.05). Finally, a survey of subjects as they exited the study demonstrated strong support for the clinical use of epigenetic biomarkers. We conclude that AHRR methylation status is a quantifiable biomarker for progress in smoking cessation that could have substantial impact on both smoking cessation treatment and research.

/pdf/reversion-of-ahrr-demethylation-is-a-quantitative-biomarker-cuv7u9am0z.pdf

Reversion of AHRR Demethylation Is a Quantitative Biomarker of Smoking Cessation

Smoking is the largest preventable cause of morbidity and mortality in the world Despite the development of numerous preventive and treatment interventions, the rate of daily smoking in the United States is still approximately 22% Effective psychosocial interventions and pharmacologic agents exist for the prevention and treatment of smoking Unfortunately, both approaches are hindered by our inability to accurately quantify amount of cigarette consumption from the point of initial experimentation to the point of total dependency  Recently, we and others have demonstrated that smoking is associated with genome-wide changes in DNA methylation However, whether this advance in basic science can be employed as a reliable assay that is useful for clinical diagnosis and treatment has not been shown In this communication, we determine the sensitivity and specificity of five of the most consistently replicated CpG loci with respect to smoking status using data from a publically available dataset We show that methylation status at a CpG locus in the aryl hydrocarbon receptor repressor, cg05575921, is both sensitive and specific for smoking status in adults with a receiver operated curve characteristic (ROC) area under the curve of 099 Given recent demonstrations that methylation at this locus reflects both intensity of smoking and the degree of smoking cessation, we conclude that a methylation-based diagnostic at this locus could have a prominent role in understanding the impact of new products, such as e-cigarettes on initiation of cigarette smoking among adolescents, while improving the prevention and treatment of smoking and smoking related disorders

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Eleanor Andersen

Papers

Reversion of AHRR Demethylation Is a Quantitative Biomarker of Smoking Cessation

A quantitative epigenetic approach for the assessment of cigarette consumption.

CEC05-04 Invertebrate models of genetic diversity and case studies of their use in toxicology