Newborn DNA Methylation Signatures Related to Prenatal Smoking Exposures in the PACE Consortium

AbstractMaternal smoking during pregnancy is associated with adverse offspring health outcomes across their life course. We hypothesize that DNA methylation is a potential mediator of this relationship. To test this, we examined the association of prenatal maternal smoking with DNA methylation in 2,821 individuals (age 16 to 48 years) from five prospective birth cohort studies and perform Mendelian randomization and mediation analyses to assess, whether methylation markers have causal effects on disease outcomes in the offspring. We identify 69 differentially methylated CpGs in 36 genomic regions (P < 1×10−7), and show that DNA methylation may represent a biological mechanism through which maternal smoking is associated with increased risk of psychiatric morbidity in the exposed offspring.

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Nicotine and Its Downstream Metabolites in Maternal and Cord Sera: Biomarkers of Prenatal Smoking Exposure Associated with Offspring DNA Methylation

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17249552 ◽

2020 ◽

Vol 17 (24) ◽

pp. 9552

Author(s):

Parnian Kheirkhah Rahimabad ◽

Thilani M. Anthony ◽

A. Daniel Jones ◽

Shakiba Eslamimehr ◽

Nandini Mukherjee ◽

...

Keyword(s):

Dna Methylation ◽

Self Report ◽

Major Constituent ◽

Prenatal Smoking ◽

Nicotine Exposure ◽

Primary Metabolite ◽

Prenatal Nicotine Exposure ◽

Smoking Exposure ◽

Prenatal Nicotine ◽

In Pregnancy

Nicotine is a major constituent of cigarette smoke. Its primary metabolite in maternal and cord sera, cotinine, is considered a biomarker of prenatal smoking. Nicotine and cotinine half-lives are decreased in pregnancy due to their increased rate of metabolism and conversion to downstream metabolites such as norcotinine and 3-hydroxycotinine. Hence, downstream metabolites of nicotine may provide informative biomarkers of prenatal smoking. In this study of three generations (F0-mothers, F1-offspring who became mothers, and F2-offspring), we present a biochemical assessment of prenatal smoking exposure based on maternal and cord sera levels of nicotine, cotinine, norcotinine, and 3-hydroxycotinine. As potential markers of early effects of prenatal smoking, associations with differential DNA methylation (DNAm) in the F1- and F2-offspring were assessed. All metabolites in maternal and cord sera were associated with self-reported prenatal smoking, except for nicotine. We compared maternal self-report of smoking in pregnancy to biochemical evidence of prenatal smoking exposure. Self-report of F0-mothers of F1 in 1989–1990 had more accuracy identifying prenatal smoking related to maternal metabolites in maternal serum (sensitivity = 94.6%, specificity = 86.9%) compared to self-reports of F1-mothers of F2 (2010–2016) associated with cord serum markers (sensitivity = 66.7%, specificity = 78.8%). Nicotine levels in sera showed no significant association with any DNAm site previously linked to maternal smoking. Its downstream metabolites, however, were associated with DNAm sites located on the MYO1G, AHRR, and GFI1 genes. In conclusion, cotinine, norcotinine, and 3-hydroxycotinine in maternal and cord sera provide informative biomarkers and should be considered when assessing prenatal smoking. The observed association of offspring DNAm with metabolites, except for nicotine, may imply that the toxic effects of prenatal nicotine exposure are exerted by downstream metabolites, rather than nicotine. If differential DNA methylation on the MYO1G, AHRR, and GFI1 genes transmit adverse effects of prenatal nicotine exposure to the child, there is a need to investigate whether preventing changes in DNA methylation by reducing the metabolic rate of nicotine and conversion to harmful metabolites may protect exposed children.

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DNA methylation links prenatal smoking exposure to later life health outcomes in offspring

Clinical Epigenetics ◽

10.1186/s13148-019-0683-4 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 12

Author(s):

Petri Wiklund ◽

Ville Karhunen ◽

Rebecca C. Richmond ◽

Priyanka Parmar ◽

Alina Rodriguez ◽

...

Keyword(s):

Dna Methylation ◽

Health Outcomes ◽

Later Life ◽

Prenatal Smoking ◽

Smoking Exposure

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Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies

10.1101/2021.04.23.441014 ◽

2021 ◽

Author(s):

Alexandre A. Lussier ◽

Yiwen Zhu ◽

Brooke J. Smith ◽

Andrew J. Simpkin ◽

Andrew D.A.C. Smith ◽

...

Keyword(s):

Dna Methylation ◽

Association Studies ◽

Childhood Adversity ◽

Reference Points ◽

Time Dependent ◽

P Value ◽

Prenatal Smoking ◽

Parents And Children ◽

Successful Replication ◽

The Impact

ABSTRACTIntroductionBiomedical research has grown increasingly cooperative, with several large consortia compiling and sharing epigenomic data. Since data are typically preprocessed by consortia prior to distribution, the implementation of new pipelines can lead to different versions of the same dataset. Analytic frameworks also constantly evolve to incorporate cutting-edge methods and shifting best practices. However, it remains unknown how differences in data and analytic versions alter the results of epigenome-wide analyses, which has broad implications for the replicability of epigenetic associations. Thus, we assessed the impact of these changes using a subsample of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort.MethodsWe analyzed two versions of DNA methylation data, processed using separate preprocessing and analytic pipelines, to examine associations between childhood adversity and prenatal smoking exposure on DNA methylation at age 7. We performed two sets of analyses: (1) epigenome-wide association studies (EWAS); (2) Structured Life Course Modeling Approach (SLCMA), a two-stage method that models time-dependent effects. We also compared results from the SLCMA using more recent methodological recommendations.ResultsDifferences between ALSPAC data versions impacted both EWAS and SLCMA analyses, yielding different sets of associations at conventional p-value thresholds. However, the magnitude and direction of associations was generally consistent between data versions, regardless of significance thresholds. Updating the SLCMA analytic version similarly altered top associations, but time-dependent effects remained concordant.ConclusionsChanges to data and analytic versions influenced the results of epigenome-wide studies, particularly when using p-value thresholds as reference points for successful replication and stability.

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Invited Commentary: Is DNA Methylation an Actionable Mediator of Prenatal Exposure Effects on Child Health?

American Journal of Epidemiology ◽

10.1093/aje/kwz182 ◽

2019 ◽

Vol 188 (11) ◽

pp. 1887-1889 ◽

Cited By ~ 3

Author(s):

Christine Ladd-Acosta ◽

M Daniele Fallin

Keyword(s):

Dna Methylation ◽

Birth Weight ◽

Repeated Measures ◽

Ethnically Diverse ◽

Molecular Signature ◽

Prenatal Smoking ◽

Mediation Analyses ◽

Adverse Health Outcomes ◽

Smoking Exposure ◽

The Impact

Abstract A substantial body of literature has shown robust associations between prenatal smoking exposure and DNA methylation levels. The pattern of DNA methylation can be used as a molecular signature of past prenatal smoking exposure and might also provide mechanistic insights into associations between prenatal smoking exposure and adverse health outcomes. In this issue of the Journal, Cardenas et al. (Am J Epidemiol. 2019;188(11):1878–1886) evaluated whether DNA methylation mediates the association between prenatal smoking and low birth weight in a tissue that is mechanistically relevant to birth weight—the placenta—using formal mediation analyses. They found that methylation levels, at 5 loci, mediated smoking exposure effects on birth weight but only among children whose mothers smoked during pregnancy. Given the use of formal mediation methods and measurement in a mechanistically relevant tissue, this work has the potential to inform novel directions for intervention. Replication of these findings in larger and more racially and ethnically diverse samples, repeated measures to better tease apart the timing of DNA methylation changes with respect to exposure and birth weight, and continued use of intervention-focused mediation methods are needed before the impact of these findings will be fully realized.

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Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2018.0120 ◽

2019 ◽

Vol 374 (1770) ◽

pp. 20180120 ◽

Cited By ~ 7

Author(s):

Eilis Hannon ◽

Diana Schendel ◽

Christine Ladd-Acosta ◽

Jakob Grove ◽

Christine Søholm Hansen ◽

...

Keyword(s):

Dna Methylation ◽

Birth Weight ◽

Gestational Age ◽

Maternal Smoking ◽

Evolutionary Medicine ◽

Prenatal Smoking ◽

Smoking During Pregnancy ◽

Significance Threshold ◽

Birth Factors ◽

Obstetric Factors

There is great interest in the role epigenetic variation induced by non-genetic exposures may play in the context of health and disease. In particular, DNA methylation has previously been shown to be highly dynamic during the earliest stages of development and is influenced by in utero exposures such as maternal smoking and medication. In this study we sought to identify the specific DNA methylation differences in blood associated with prenatal and birth factors, including birth weight, gestational age and maternal smoking. We quantified neonatal methylomic variation in 1263 infants using DNA isolated from a unique collection of archived blood spots taken shortly after birth (mean = 6.08 days; s.d. = 3.24 days). An epigenome-wide association study (EWAS) of gestational age and birth weight identified 4299 and 18 differentially methylated positions (DMPs) respectively, at an experiment-wide significance threshold of p < 1 × 10 −7 . Our EWAS of maternal smoking during pregnancy identified 110 DMPs in neonatal blood, replicating previously reported genomic loci, including AHRR . Finally, we tested the hypothesis that DNA methylation mediates the relationship between maternal smoking and lower birth weight, finding evidence that methylomic variation at three DMPs may link exposure to outcome. These findings complement an expanding literature on the epigenomic consequences of prenatal exposures and obstetric factors, confirming a link between the maternal environment and gene regulation in neonates. This article is part of the theme issue ‘Developing differences: early-life effects and evolutionary medicine’.

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An integrative approach to detect epigenetic mechanisms that putatively mediate the influence of lifestyle exposures on disease susceptibility

International Journal of Epidemiology ◽

10.1093/ije/dyz119 ◽

2019 ◽

Vol 48 (3) ◽

pp. 887-898 ◽

Cited By ~ 6

Author(s):

Tom G Richardson ◽

Rebecca C Richmond ◽

Teri-Louise North ◽

Gibran Hemani ◽

George Davey Smith ◽

...

Keyword(s):

Gene Expression ◽

Risk Factors ◽

Dna Methylation ◽

Complex Traits ◽

Disease Susceptibility ◽

Association Studies ◽

Integrative Approach ◽

Prenatal Smoking ◽

Genome Wide Association Studies ◽

Cpg Sites

Abstract Background There is mounting evidence that our environment and lifestyle has an impact on epigenetic regulatory mechanisms, such as DNA methylation. It has been suggested that these molecular processes may mediate the effect of risk factors on disease susceptibility, although evidence in this regard has been challenging to uncover. Using genetic variants as surrogate variables, we have used two-sample Mendelian randomization (2SMR) to investigate the potential implications of putative changes to DNA methylation levels on disease susceptibility. Methods To illustrate our approach, we identified 412 CpG sites where DNA methylation was associated with prenatal smoking. We then applied 2SMR to investigate potential downstream effects of these putative changes on 643 complex traits using findings from large-scale genome-wide association studies. To strengthen evidence of mediatory mechanisms, we used multiple-trait colocalization to assess whether DNA methylation, nearby gene expression and complex trait variation were all influenced by the same causal genetic variant. Results We identified 22 associations that survived multiple testing (P < 1.89 × 10–7). In-depth follow-up analyses of particular note suggested that the associations between DNA methylation at the ASPSCR1 and REST/POL2RB gene regions, both linked with reduced lung function, may be mediated by changes in gene expression. We validated associations between DNA methylation and traits using independent samples from different stages across the life course. Conclusion Our approach should prove valuable in prioritizing CpG sites that may mediate the effect of causal risk factors on disease. In-depth evaluations of findings are necessary to robustly disentangle causality from alternative explanations such as horizontal pleiotropy.

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DNA methylation of GFI1 as a mediator of the association between prenatal smoking exposure and ADHD symptoms at 6 years: the Hokkaido Study on Environment and Children’s Health

Clinical Epigenetics ◽

10.1186/s13148-021-01063-z ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Kunio Miyake ◽

Chihiro Miyashita ◽

Atsuko Ikeda-Araki ◽

Ryu Miura ◽

Sachiko Itoh ◽

...

Keyword(s):

Dna Methylation ◽

Rating Scale ◽

Children's Health ◽

Children’S Health ◽

Prenatal Smoking ◽

Active Smoking ◽

Adhd Symptoms ◽

Smoking During Pregnancy ◽

Smoking Exposure ◽

Increased Risk

Abstract Background Prenatal smoking exposure has been associated with childhood attention-deficit/hyperactivity disorder (ADHD). However, the mechanism underlying this relationship remains unclear. We assessed whether DNA methylation differences may mediate the association between prenatal smoking exposure and ADHD symptoms at the age of 6 years. Results We selected 1150 mother–infant pairs from the Hokkaido Study on the Environment and Children’s Health. Mothers were categorized into three groups according to plasma cotinine levels at the third trimester: non-smokers (≤ 0.21 ng/mL), passive smokers (0.21–11.48 ng/mL), and active smokers (≥ 11.49 ng/mL). The children’s ADHD symptoms were determined by the ADHD-Rating Scale at the age of 6 years. Maternal active smoking during pregnancy was significantly associated with an increased risk of ADHD symptoms (odds ratio, 1.89; 95% confidence interval, 1.14–3.15) compared to non-smoking after adjusting for covariates. DNA methylation of the growth factor-independent 1 transcriptional repressor (GFI1) region, as determined by bisulfite next-generation sequencing of cord blood samples, mediated 48.4% of the total effect of the association between maternal active smoking during pregnancy and ADHD symptoms. DNA methylation patterns of other genes (aryl-hydrocarbon receptor repressor [AHRR], cytochrome P450 family 1 subfamily A member 1 [CYP1A1], estrogen receptor 1 [ESR1], and myosin IG [MYO1G]) regions did not exert a statistically significant mediation effect. Conclusions Our findings demonstrated that DNA methylation of GFI1 mediated the association between maternal active smoking during pregnancy and ADHD symptoms at the age of 6 years.

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DNA methylation as a marker for prenatal smoke exposure in adults

10.1101/121558 ◽

2017 ◽

Cited By ~ 3

Author(s):

R.C. Richmond ◽

M. Suderman ◽

R. Langdon ◽

C.L. Relton ◽

Smith G. Davey

Keyword(s):

Dna Methylation ◽

Peripheral Blood ◽

Smoke Exposure ◽

P Value ◽

Prenatal Smoking ◽

Cpg Sites ◽

Smoking In Pregnancy ◽

Parents And Children ◽

Avon Longitudinal Study ◽

Methylation Signal

AbstractPrenatal cigarette smoke is an environmental stressor that has a profound effect on DNA methylation in the exposed offspring. We have previously shown that some of these effects persist throughout childhood and into adolescence. Of interest is whether these signals persist into adulthood.We conducted an analysis to investigate associations between reported maternal smoking in pregnancy and DNA methylation in peripheral blood of women in the Avon Longitudinal Study of Parents and Children (ALSPAC) (n=754; mean age 30 years). We observed associations at 15 CpG sites in 11 gene regions, MYO1G, FRMD4A, CYP1A1, CNTNAP2, ARL4C, AHRR, TIFAB, MDM4, AX748264, DRD1, FTO (FDR < 5%). All but two of these CpG sites have previously been identified in relation to prenatal smoke exposure in the offspring at birth and the majority showed persistent hypermethylation among the offspring of smokers.We confirmed that most of these associations were not driven by own smoking and that they were still present 18 years later (N = 656; mean age 48 years). In addition, we replicated findings of a persistent methylation signal related to prenatal smoke exposure in peripheral blood among men in the ALSPAC cohort (N = 230; mean age 53 years). For both participant groups, there was a strong signal of association above that expected by chance at CpG sites previously associated with prenatal smoke exposure in newborns (Wilcoxon rank sum p-value < 2.2 × 10−4). Furthermore, we found that a prenatal smoking score, derived by combining methylation values at these CpG sites, could predict whether the mothers of the ALSPAC women smoked during pregnancy with an AUC 0.69 (95% 0.67, 0.73).

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Mediation by Placental DNA Methylation of the Association of Prenatal Maternal Smoking and Birth Weight

American Journal of Epidemiology ◽

10.1093/aje/kwz184 ◽

2019 ◽

Vol 188 (11) ◽

pp. 1878-1886 ◽

Cited By ~ 11

Author(s):

Andres Cardenas ◽

Sharon M Lutz ◽

Todd M Everson ◽

Patrice Perron ◽

Luigi Bouchard ◽

...

Keyword(s):

Dna Methylation ◽

Birth Weight ◽

Maternal Smoking ◽

Cell Types ◽

Prenatal Smoking ◽

Association Analyses ◽

Lower Birth Weight ◽

Cpg Sites ◽

Prenatal Maternal Smoking ◽

Infant Birth

Abstract Prenatal maternal smoking is a risk factor for lower birth weight. We performed epigenome-wide association analyses of placental DNA methylation (DNAm) at 720,077 cytosine-phosphate-guanine (CpG) sites and prenatal maternal smoking among 441 mother-infant pairs (2010–2014) and evaluated whether DNAm mediates the association between smoking and birth weight using mediation analysis. Mean birth weight was 3,443 (standard deviation, 423) g, and 38 mothers (8.6%) reported smoking at a mean of 9.4 weeks of gestation. Prenatal maternal smoking was associated with a 175-g lower birth weight (95% confidence interval (CI): −305.5, −44.8) and with differential DNAm of 71 CpGs in placenta, robust to latent-factor adjustment reflecting cell types (Bonferroni-adjusted P < 6.94 × 10−8). Of the 71 CpG sites, 7 mediated the association between prenatal smoking and birth weight (on MDS2, PBX1, CYP1A2, VPRBP, WBP1L, CD28, and CDK6 genes), and prenatal smoking × DNAm interactions on birth weight were observed for 5 CpG sites. The strongest mediator, cg22638236, was annotated to the PBX1 gene body involved in skeletal patterning and programming, with a mediated effect of 301-g lower birth weight (95% CI: −543, −86) among smokers but no mediated effect for nonsmokers (β = −38 g; 95% CI: −88, 9). Prenatal maternal smoking might interact with placental DNAm at specific loci, mediating the association with lower infant birth weight.

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