DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis

The potential role of environmentally associated DNA methylation in childhood acute lymphoblastic leukaemia subtypes

Various genetic aberrations are suggested to initiate the development of acute lymphoblastic leukaemia (ALL) but alone are insufficient for disease onset. Epigenetic alteration, such as DNA methylation changes, plays a key role in human health. Evidence suggests DNA methylation may be an intermediate mechanism through which the environment contributes to ALL manifestation. ALL is categorized into subtypes based on leukaemia-associated genetic events, and it is plausible that different exposures pose differing risks for given subtypes. Using our previously established meet-in-the-middle approach, we performed CpG-level analysis to investigate DNA methylation as an intermediate mechanism between risk exposures and ALL. Differentially methylated CpGs (DMCs) were integrated, identifying overlapping methylation, with hypergeometric tests used to assess the probability of concurring methylation considering directionality. DMC analysis reinforced previous gene-level findings suggesting altered DNA methylation associated with maternal radiation exposure, alcohol intake, and plasma folate during pregnancy is also present in the disease. Whilst maternal folate-associated and leukaemia-associated methylation appear consistent across most subtypes, the effect of other exposures appears subtype-specific. We suggest environmentally associated methylation includes driver and/or 'navigator' changes, the latter influencing biological pathways contributing to ALL. This analysis aids understanding of which risk factors may contribute to specific subtypes or which influence ALL risk more generally.

Genetic and environmental factors contributing to anophthalmia and microphthalmia: Current understanding and future directions

Anophthalmia is defined as a complete absence of one eye or both the eyes, while microphthalmia represents the presence of a small eye within the orbit. The estimated birth prevalence for anophthalmia is approximately 3 per 100000 live births, and for microphthalmia, it is around 14 per 100000 live births. However, combined evidence suggests that the prevalence of these malformations could be as high as 30 per 100000 individuals. Microphthalmia is reported to occur in 3.2% to 11.2% of blind children. Anophthalmia and microphthalmia (A/M) are part of a phenotypic spectrum alongside ocular coloboma, hypothesized to share a common genetic basis. Both A/M can occur in isolation or as part of a syndrome. Their complex etiology involves chromosomal aberrations, monogenic inheritance pattern, and the contribution of environmental factors such as gestational-acquired infections, maternal vitamin A deficiency (VAD), exposure to X-rays, solvent misuse, and thalidomide exposure. A/M exhibit significant clinical and genetic heterogeneity with over 90 genes identified so far. Familial cases of A/M have a complex genetic basis, including all Mendelian modes of inheritance, i.e., autosomal dominant, recessive, and X-linked. Most cases arise sporadically due to de novo mutations. Examining gene expression during eye development and the effects of various environmental variables will help us better understand the phenotypic heterogeneity found in A/M, leading to more effective diagnosis and management strategies. The present review focuses on key genetic factors, developmental abnormalities, and environmental modifiers linked with A/M. It also emphasizes at potential research areas including multiomic methods and disease modeling with induced pluripotent stem cell technologies, which aim to create innovative treatment options.

Associations of parental air pollution and greenness exposures with offspring asthma outcomes

BACKGROUND

Air pollution and greenness impact respiratory health, but intergenerational effects remain unclear.We investigated whether pre-conception parental residential exposure to air pollution and greenness at age 20-44 years is associated with offspring asthma outcomes in the Lifespan and inter-generational respiratory effects of exposures to greenness and air pollution (Life-GAP) project.

METHODS

We analyzed data on 3684 RHINESSA study participants born after the year 1990 (mean age 19, standard deviation 4), offspring of 2689 RHINE study participants. Modelled annual concentrations of particulate matter (PM2.5, PM10), nitrogen dioxide (NO2), elemental carbon (EC), and ozone (O3), and greenness (Normalized Difference Vegetation Index, NDVI) were assigned to parental residential addresses in 1990, corresponding to 1-18 years prior to birth (mean: 6 years, SD: 5). We analyzed associations using generalized structural equation modelling (GSEM), with cluster-robust standard errors allowing for intra-family correlation, while adjusting for potential confounders.

RESULTS

Among offspring participants, 18% reported lifetime asthma, 9% active asthma, 8% asthma medication, 5% asthma attacks, and 37% any asthma symptom. An interquartile range (IQR) increase in parental residential NDVI exposure was associated with less lifetime asthma (OR = 0.79, 95%CI: 0.64, 0.98 per 0.3 units). Similar associations were observed for active asthma and asthma medication use. Associations of air pollution with asthma outcomes were inconclusive.

CONCLUSION

Parental exposure to residential green spaces before conception was associated with lower asthma risk in offspring. Urban planning policies prioritizing green spaces may be a key public health intervention for future cities.

Maternal asthma and newborn DNA methylation

BACKGROUND

Prenatal exposure to maternal asthma may influence DNA methylation patterns in offspring, potentially affecting their susceptibility to later diseases including asthma.

OBJECTIVE

To investigate the relationship between parental asthma and newborn blood DNA methylation.

METHODS

Epigenome-wide association analyses were conducted in 13 cohorts on 7433 newborns with blood methylation data from the Illumina450K or EPIC array. We used fixed effects meta-analyses to identify differentially methylated CpGs (DMCs) and comb-p to identify differentially methylated regions (DMRs) associated with maternal asthma during pregnancy and maternal asthma ever. Paternal asthma was analyzed for comparison. Models were adjusted for covariates and cell-type composition. We examined whether implicated sites related to gene expression analyses in publicly available data for childhood blood and adult lung.

RESULTS

We identified 27 CpGs associated with maternal asthma during pregnancy at False Discovery Rate < 0.05 but none for maternal asthma ever. Two distinct CpGs were associated with paternal asthma. We observed 5 DMRs associated with maternal asthma during pregnancy 3 associated with maternal asthma ever and 13 DMRs associated with paternal asthma. Gene expression analysis using data in blood from 832 children and lung from 424 adults showed associations between identified DMCs using maternal asthma and expression of several genes, including HLA genes and HOXA5, previously implicated in asthma or lung function.

CONCLUSION

Parental asthma, especially maternal asthma during pregnancy, may be associated with alterations in newborn DNA methylation. These findings might shed light on underlying mechanisms for asthma susceptibility.

Methylation profile scores of environmental exposures and risk of relapse after a first episode of schizophrenia

Both genetic and environmental factors have been found to play a significant role in psychosis relapse, either independently or through their synergistic interaction. Recently, DNA methylation (DNAm) has been proposed through the calculation of methylation profile scores (MPS). The aim of the present study is to evaluate the association of MPS as a surrogate marker of the biological impact of early stressful life events (including stressful intrauterine conditions and obstetric complications, childhood adversity and toxic habits), with the risk of schizophrenia (SCZ) relapse. 91 participants from a cohort of first-episode schizophrenia (FES) patients with less than five years of evolution were classified as non-relapse (patients who had not experienced a relapse after 3 years of enrollment) or relapse (patients who relapsed during the 3-year follow-up). As inclusion criteria, patients fulfilled Andreasen's criteria of symptomatic remission. Genome-wide DNA methylation (DNAm) was profiled and fourteen MPS reflecting environmental exposure were constructed including both early stressful life events (including stressful intrauterine conditions and delivery issues, childhood adversity) and toxic habits. Increased levels of MPS reflecting gestational diabetes (p = 0.009), hypertensive disorders during pregnancy (p = 0.004), pre-eclampsia (p = 0.049), early preterm birth (p = 0.030), childhood adversity abuse (p = 0.021) and all childhood adversity (p = 0.030) were significantly associated with an increased risk of relapse. Our study suggests that changes in specific methylation patterns may represent one of the biological mechanisms linking early stressful life events to an increased risk of relapse.

Epigenetic timing effects on child developmental outcomes: a longitudinal meta-regression of findings from the Pregnancy And Childhood Epigenetics Consortium

BACKGROUND

DNA methylation (DNAm) is a developmentally dynamic epigenetic process; yet, most epigenome-wide association studies (EWAS) have examined DNAm at only one timepoint or without systematic comparisons between timepoints. Thus, it is unclear whether DNAm alterations during certain developmental periods are more informative than others for health outcomes, how persistent epigenetic signals are across time, and whether epigenetic timing effects differ by outcome.

METHODS

We applied longitudinal meta-regression models to published meta-analyses from the PACE consortium that examined DNAm at two timepoints-prospectively at birth and cross-sectionally in childhood-in relation to the same child outcome (ADHD symptoms, general psychopathology, sleep duration, BMI, asthma). These models allowed systematic comparisons of effect sizes and statistical significance between timepoints. Furthermore, we tested correlations between DNAm regression coefficients to assess the consistency of epigenetic signals across time and outcomes. Finally, we performed robustness checks, estimated between-study heterogeneity, and tested pathway enrichment.

RESULTS

Our findings reveal three new insights: (i) across outcomes, DNAm effect sizes are consistently larger in childhood cross-sectional analyses compared to prospective analyses at birth; (ii) higher effect sizes do not necessarily translate into more significant findings, as associations also become noisier in childhood for most outcomes (showing larger standard errors in cross-sectional vs prospective analyses); and (iii) DNAm signals are highly time-specific, while also showing evidence of shared associations across health outcomes (ADHD symptoms, general psychopathology, and asthma). Notably, these observations could not be explained by sample size differences and only partly to differential study-heterogeneity. DNAm sites changing associations were enriched for neural pathways.

CONCLUSIONS

Our results highlight developmentally-specific associations between DNAm and child health outcomes, when assessing DNAm at birth vs childhood. This implies that EWAS results from one timepoint are unlikely to generalize to another. Longitudinal studies with repeated epigenetic assessments are direly needed to shed light on the dynamic relationship between DNAm, development and health, as well as to enable the creation of more reliable and generalizable epigenetic biomarkers. More broadly, this study underscores the importance of considering the time-varying nature of DNAm in epigenetic research and supports the potential existence of epigenetic "timing effects" on child health.

Linking epidemiology and genomics of maternal smoking during pregnancy in utero and in ageing: a population-based study using human foetuses and the UK Biobank cohort

BACKGROUND

Maternal smoking and foetal exposure to nicotine and other harmful chemicals in utero remains a serious public health issue with little knowledge about the underlying genetics and consequences of maternal smoking in ageing individuals. Here, we investigated the epidemiology and genomic architecture of maternal smoking in a middle-aged population and compare the results to effects observed in the developing foetus.

METHODS

In the current project, we included 351,562 participants from the UK Biobank (UKB) and estimated exposure to maternal smoking status during pregnancy through self-reporting from the UKB participants about the mother's smoking status around their birth. In addition, we analysed 64 foetal liver transcriptomic expression datasets collected from women seeking elective pregnancy terminations. Foetal maternal smoking exposure was confirmed through measurement of foetal plasma cotinine levels.

FINDINGS

Foetal exposure to maternal smoking had a greater impact on males than females, with more differentially expressed genes in liver tissue (3313 vs. 1163) and higher liver pathway activation. In the UKB, maternal smoking exposure was linked to an unhealthy lifestyle, lower education, and liver damage. In a genome-wide analysis in the UKB, we leveraged the shared genetic basis between affected offspring and their mothers and identified five genome-wide significant regions. We found a low heritability of the trait (∼4%) and implicated several disease-related genes in a transcriptome-wide association study. Maternal smoking increased all-cause mortality risk (Hazard ratio and 95% CI: 1.10 [1.04; 1.16], P = 4.04 × 10-4), which was attenuated in non-smoking males.

INTERPRETATION

Although male foetuses are more affected than females by maternal smoking in pregnancy, this effect was largely reduced in middle-aged individuals. Importantly, our results highlight that the overall 10% increased mortality due to maternal smoking in pregnancy was greatly attenuated in non-smokers. This study demonstrates the importance of campaigns promoting offspring smoking prevention in families where the parent(s) smoke.

FUNDING

Funding for this project was provided by the University of Aberdeen, the Science Initiative Panel of the Institute of Medical Science, the UK Medical Research Council, the Seventh Framework Programme of the European Union under Grant Agreement 212885 (REEF), NHS Grampian Endowments grants and the European Commission Horizon Europe research grant Agreement 101094099 (INITIALISE).

Epigenetic Echoes: Bridging Nature, Nurture, and Healing Across Generations

Trauma can impact individuals within a generation (intragenerational) and future generations (transgenerational) through a complex interplay of biological and environmental factors. This review explores the epigenetic mechanisms that have been correlated with the effects of trauma across generations, including DNA methylation, histone modifications, and non-coding RNAs. These mechanisms can regulate the expression of stress-related genes (such as the glucocorticoid receptor (NR3C1) and FK506 binding protein 5 (FKBP5) gene), linking trauma to biological pathways that may affect long-term stress regulation and health outcomes. Although research using model organisms has elucidated potential epigenetic mechanisms underlying the intergenerational effects of trauma, applying these findings to human populations remains challenging due to confounding variables, methodological limitations, and ethical considerations. This complexity is compounded by difficulties in establishing causality and in disentangling epigenetic influences from shared environmental factors. Emerging therapies, such as psychedelic-assisted treatments and mind-body interventions, offer promising avenues to address both the psychological and potential epigenetic aspects of trauma. However, translating these findings into effective interventions will require interdisciplinary methods and culturally sensitive approaches. Enriched environments, cultural reconnection, and psychosocial interventions have shown the potential to mitigate trauma's impacts within and across generations. By integrating biological, social, and cultural perspectives, this review highlights the critical importance of interdisciplinary frameworks in breaking cycles of trauma, fostering resilience, and advancing comprehensive healing across generations.

Living in endemic area for infectious diseases is associated to differences in immunosenescence and inflammatory signatures

Research on aged individuals from developed countries show that lifestyle factors such as diet, physical activity, stress, smoking, and sleep quality impact aging. However, other relevant factors may influence aging in less-studied populations, such as Brazilian cohorts. This study aimed to analyze immunosenescence profile of individuals living in an endemic area for several infectious diseases in Brazil. We showed that these individuals exhibited accelerated epigenetic aging and increased production of IL-12p70, IL-17A, and IL-9. Production of inflammatory mediators IL-12p70, IL-6, IL-1β, IL-2, and IL-1ra in individuals with flu-like symptoms and those with COVID-19 was higher among residents in endemic areas than in residents from a control non-endemic area. Furthermore, residents of the endemic area had a more prominent inflammatory profile during viral infection and a different pattern of plasma mediators when compared to residents of a non-endemic area. Our data suggests that these two cohorts had specific immune signatures regardless of the presence or the type of infection at study. Therefore, we demonstrated that there were distinct patterns of immune responses and epigenetic aging depending on the environment the individuals live in. These observations add a layer of diversity to the studies of human aging by including individuals from less represented regions.

Maternal Smoking Intensity During Pregnancy and Early Adolescent Cardiovascular Health

BACKGROUND

The adverse cardiovascular effects of smoking are well established. We aimed to investigate the less well-understood effects of pregnancy smoke exposure on offspring cardiovascular health in early adolescence.

METHODS AND RESULTS

Data were drawn from the nationally representative Longitudinal Study of Australian Children's Child Health CheckPoint. Mothers reported mean daily cigarettes smoked in each trimester (≤10 versus >10/day), and smoking cessation during pregnancy. Blood pressure, pulse wave velocity, carotid intima-media thickness, and retinal microvascular parameters were measured in early adolescence (mean 11.5 years). Hypertension was defined as systolic blood pressure ≥120 or diastolic blood pressure ≥80 mm Hg. 187 (11.8%) of 1582 women (mean age 30.7±0.2 years), smoked during pregnancy, of whom 143 (76.5%) smoked throughout pregnancy, and 58 (31.0%) smoked >10 cigarettes/day. Compared with those born to nonsmoking mothers, the odds of hypertension in early adolescence were 1.44 (95% CI, 1.01-2.06) if mothers ever smoked, 1.99 (1.22-3.24) if mothers smoked >10 cigarettes/day, and 1.64 (1.11-2.42) if mothers smoked throughout pregnancy There was limited evidence of associations between smoking throughout pregnancy and other cardiovascular measures. Offspring of mothers who stopped smoking during pregnancy and nonsmokers had similar cardiovascular measures, apart from hypertension.

CONCLUSIONS

Offspring of mothers who smoked in pregnancy have increased risks of hypertension in adolescence, with increased risk with greater exposure intensity and duration. Mothers who stopped smoking during pregnancy had offspring with similar cardiovascular health to those born to nonsmokers. Our findings underscore the importance of specific strategies to stop maternal smoking before conception and during pregnancy.

DNA Salivary Methylation Levels of the ACE2 Promoter Are Not Related to ACE2 (rs2285666 and rs2074192), TMPRSS2 (rs12329760 and rs2070788) and ACE1 rs1799752 Polymorphisms in COVID-19 Survivors with Post-COVID-19 Condition

Genetics and epigenetics are mechanisms proposed for explaining post-COVID-19 condition. This secondary analysis aimed to investigate if DNA methylation levels of the ACE2 promoter are different depending on the genotype of five COVID-19-related polymorphisms in individuals who had been previously hospitalized due to SARS-CoV-2 infection. We collected non-stimulated saliva samples from 279 (48.7% female, age: 56.0 ± 12.5 years) previously hospitalized COVID-19 survivors. The participants self-reported for the presence of post-COVID symptomatology that started after the infection and persisted at the time of the appointment. Three potential genotypes of ACE2 rs2285666 and rs2074192, TMPRSS2 rs12329760 and rs2070788, and ACE1 rs1799752 polymorphisms were identified from saliva samples. Further, methylation levels at five different locations (CpG) of dinucleotides in the ACE2 promoter were quantified using bisulfited pyrosequencing. Differences in the methylation percentage (%) of each CpG according to the genotype of the five polymorphisms were analyzed. Participants were evaluated up to 17.8 (SD: 5.2) months after hospital discharge. Eighty-eight percent (88.1%) of patients reported at least one post-COVID symptom (mean number of post-COVID symptoms: 3.0; SD: 1.9). Overall, we did not observe significant differences in the methylation levels of the ACE2 promoter according to the genotype of ACE2 rs2285666 and rs2074192, TMPRSS2 rs12329760 and rs2070788, or ACE1 rs1799752 single nucleoid polymorphisms. This study did not find an association between genetics (genotypes of five COVID-19-associated polymorphisms) and epigenetics (methylation levels of the ACE2 promoter) in a cohort of COVID-19 survivors with post-COVID-19 condition who were hospitalized during the first wave of the pandemic.

DNA methylation biomarkers of intellectual/developmental disability across the lifespan

Epigenetic mechanisms, including DNA methylation, act at the interface of genes and environment by allowing a static genome to respond and adapt to a dynamic environment during the lifespan of an individual. Genome-wide DNA methylation analyses on a wide range of human biospecimens are beginning to identify epigenetic biomarkers that can predict risk of intellectual/developmental disabilities (IDD). DNA methylation-based epigenetic signatures are becoming clinically useful in categorizing benign from pathogenic genetic variants following exome sequencing. While DNA methylation marks differ by tissue source, recent studies have shown that accessible perinatal tissues, such as placenta, cord blood, newborn blood spots, and cell free DNA may serve as accessible surrogate tissues for testing epigenetic biomarkers relevant to understanding genetic, environmental, and gene by environment interactions on the developing brain. These DNA methylation signatures may also provide important information about the biological pathways that become dysregulated prior to disease progression that could be used to develop early pharmacological interventions. Future applications could involve preventative screenings using DNA methylation biomarkers during pregnancy or the newborn period for IDDs and other neurodevelopmental disorders. DNA methylation biomarkers in adolescence and adulthood are also likely to be clinically useful for tracking biological aging or co-occurring health conditions that develop across the lifespan. In conclusion, DNA methylation biomarkers are expected to become more common in clinical diagnoses of IDD, to improve understanding of complex IDD etiologies, to improve endpoints for clinical trials, and to monitor potential health concerns for individuals with IDD as they age.

DNA methylation differences between cord and adult white blood cells reflect postnatal immune cell maturation

Epigenetic modifications such as DNA methylation are both cell type and developmental age specific. Here, we show that the immunological maturation of blood cell types influences DNA methylation changes from naive cord blood to fully functional adult blood. Lymphoid cells in adult blood showed more variability than in cord blood suggesting an antigen-dependent maturation of DNA methylation in lymphoid cells throughout the lifespan. Fewer DNA methylation changes between cord and adult blood were observed in myeloid cells, particularly in monocytes, which demonstrated the least number of DNA methylation changes between cord and adult blood. We also noted differences in epigenetic ages by immune cell types within the same individuals, specifically in cord blood where monocytes were epigenetically oldest compared to the other cell types. In addition, we provide a publicly available resource to the community as an R Shiny web application to interactively explore epigenetic patterns between naive cord white blood cells and fully functional adult white blood cells for six immune cell types.

Genetic-epigenetic interactions (meQTLs) in orofacial clefts etiology

Objectives

Nonsyndromic orofacial clefts (OFCs) etiology involves multiple genetic and environmental factors with over 60 identified risk loci; however, they account for only a minority of the estimated risk. Epigenetic factors such as differential DNA methylation (DNAm) are also associated with OFCs risk and can alter risk for different cleft types and modify OFCs penetrance. DNAm is a covalent addition of a methyl (CH3) group to the nucleotide cytosine that can lead to changes in expression of the targeted gene. DNAm can be affected by environmental influences and genetic variation via methylation quantitative loci (meQTLs). We hypothesize that aberrant DNAm and the resulting alterations in gene expression play a key role in the etiology of OFCs, and that certain common genetic variants that affect OFCs risk do so by influencing DNAm.

Methods

We used genotype from 10 cleft-associated SNPs and genome-wide DNA methylation data (Illumina 450K array) for 409 cases with OFCs and 456 controls and identified 23 cleft-associated meQTLs. We then used an independent cohort of 362 cleft-discordant sib pairs for replication. We used methylation-specific qPCR to measure methylation levels of each CpG site and combined genotypic and methylation data for an interaction analysis of each SNP-CpG pair using the R package MatrixeQTL in a linear model. We also performed a Paired T-test to analyze differences in DNA methylation between each member of the sibling pairs.

Results

We replicated 9 meQTLs, showing interactions between rs13041247 (MAFB) - cg18347630 (PLCG1) (P=0.04); rs227731 (NOG) - cg08592707 (PPM1E) (P=0.01); rs227731 (NOG) - cg10303698 (CUEDC1) (P=0.001); rs3758249 (FOXE1) - cg20308679 (FRZB) (P=0.04); rs8001641 (SPRY2) - cg19191560 (LGR4) (P=0.04); rs987525(8q24) - cg16561172(MYC) (P=0.00000963); rs7590268(THADA) - cg06873343 (TTYH3) (P=0.04); rs7078160 (VAX1) - cg09487139 (P=0.05); rs560426 (ABCA4/ARHGAP29) - cg25196715 (ABCA4/ARHGAP29) (P=0,03). Paired T-test showed significant differences for cg06873343 (TTYH3) (P=0.04); cg17103269 (LPIN3) (P=0.002), and cg19191560 (LGR4) (P=0.05).

Conclusions

Our results confirm previous evidence that some of the common non-coding variants detected through GWAS studies can influence the risk of OFCs via epigenetic mechanisms, such as DNAm, which can ultimately affect and regulate gene expression. Given the large prevalence of non-coding SNPs in most OFCs genome wide association studies, our findings can potentially address major knowledge gaps, like missing heritability, reduced penetrance, and variable expressivity associated with OFCs phenotypes.

Role of Epigenetics in Chronic Lung Disease

Epigenetics regulates gene expression and thus cellular processes that underlie the pathogenesis of chronic lung diseases such as chronic obstructive pulmonary disease (COPD), asthma, and idiopathic pulmonary fibrosis (IPF). Environmental factors (e.g., air pollution, smoking, infections, poverty), but also conditions such as gastroesophageal reflux, induce epigenetic changes long before lung disease is diagnosed. Therefore, epigenetic signatures have the potential to serve as biomarkers that can be used to identify younger patients who are at risk for premature loss of lung function or diseases such as IPF. Epigenetic analyses also contribute to a better understanding of chronic lung disease. This can be used directly to improve therapies, as well as for the development of innovative drugs. Here, we highlight the role of epigenetics in the development and progression of chronic lung disease, with a focus on DNA methylation.

Association between maternal smoking during pregnancy and developmental disabilities in US children and adolescents: A cross-sectional study from NHANES

INTRODUCTION

Maternal smoking during pregnancy is associated with placental DNA methylation and RNA expression, offspring DNA methylation, and affects the decline of mature neurons and the prenatal human brain development trajectory.

METHODS

This study is a secondary analysis of data from the National Health and Nutrition Examination Survey (NHANES) spanning 2003 to 2008, comprising 10111 children and adolescents. Inclusion criteria required participants to have complete questionnaire responses regarding maternal smoking during pregnancy and receipt of special education or early intervention services. The risk of developmental disabilities was assessed using a multifactor logistic regression model.

RESULTS

In the cohort of 10111 children and adolescents, 727 (7.2%) received special education or early intervention services. Of these participants, 1504 (14.9%) were exposed to maternal smoking during pregnancy. The prevalence of maternal smoking was higher (12.3%) in the group receiving special education or early intervention compared to those who did not (6.3%). After adjusting for other relevant factors in a multifactorial logistic regression model, maternal smoking during pregnancy was significantly associated with an increased likelihood of requiring special education or early intervention services (adjusted odds ratio, AOR=1.51; 95% CI: 1.24-1.83, p<0.001).

CONCLUSIONS

This cross-sectional analysis found an association between maternal smoking during pregnancy and the need for special education or early intervention services among US children and adolescents, after adjusting for confounding variables. Our findings suggest that maternal smoking during pregnancy may increase the odds of developmental disabilities.

Molecular Regulation of Palatogenesis and Clefting: An Integrative Analysis of Genetic, Epigenetic Networks, and Environmental Interactions

Palatogenesis is a complex developmental process requiring temporospatially coordinated cellular and molecular events. The following review focuses on genetic, epigenetic, and environmental aspects directing palatal formation and their implication in orofacial clefting genesis. Essential for palatal shelf development and elevation (TGF-β, BMP, FGF, and WNT), the subsequent processes of fusion (SHH) and proliferation, migration, differentiation, and apoptosis of neural crest-derived cells are controlled through signaling pathways. Interruptions to these processes may result in the birth defect cleft lip and/or palate (CL/P), which happens in approximately 1 in every 700 live births worldwide. Recent progress has emphasized epigenetic regulations via the class of non-coding RNAs with microRNAs based on critically important biological processes, such as proliferation, apoptosis, and epithelial-mesenchymal transition. These environmental risks (maternal smoking, alcohol, retinoic acid, and folate deficiency) interact with genetic and epigenetic factors during palatogenesis, while teratogens like dexamethasone and TCDD inhibit palatal fusion. In orofacial cleft, genetic, epigenetic, and environmental impact on the complex epidemiology. This is an extensive review, offering current perspectives on gene-environment interactions, as well as non-coding RNAs, in palatogenesis and emphasizing open questions regarding these interactions in palatal development.

Smoke's Enduring Legacy: Bridging Early-Life Smoking Exposures and Later-Life Epigenetic Age Acceleration

Current literature states that early-life exposure to smoking produces adverse health outcomes in later life, primarily as a result of subsequent engagements with firsthand smoking. The implications of prior research are that smoking cessation can reduce health risk in later life to levels comparable to the risk of those who have never smoked. However, recent evidence suggests that smoking exposure during childhood can have independent and permanent negative effects on health-in particular, on epigenetic aging. This investigation examines whether the effect of early-life firsthand smoking on epigenetic aging is more consistent with (1) a sensitive periods model, which is characterized by independent effects due to early firsthand exposures; or (2) a cumulative risks model, which is typified by persistent smoking. The findings support both models. Smoking during childhood can have long-lasting effects on epigenetic aging, regardless of subsequent engagements. Our evidence suggests that adult cessation can be effective but that the epigenetic age acceleration in later life is largely due to early firsthand smoking itself.

Associations of maternal night shift work during pregnancy with DNA methylation in offspring: a meta-analysis in the PACE consortium

BACKGROUND

Night shift work during pregnancy has been associated with differential DNA methylation in placental tissue, but no studies have explored this association in cord blood. We aimed to examine associations of maternal night shift work with cord blood DNA methylation.

METHODS

A total of 4487 mother-newborn pairs from 7 studies were included. Maternal night shift work during pregnancy was ascertained via questionnaires and harmonized into "any" versus "no". DNA methylation was measured in cord blood using the Illumina Infinium Methylation arrays. Robust linear regression models adjusted for relevant confounders were run in the individual cohorts, and results were meta-analyzed.

RESULTS

Maternal night shift work during pregnancy ranged from 3.4% to 26.3%. Three CpGs were differentially methylated in relation to maternal night shift work during pregnancy at a false discovery rate adjusted P < 0.05: cg10945885 (estimate (β) 0.38%, standard error (SE) 0.07), cg00773359 (β 0.25%, SE 0.05), and cg21836426 (β - 0.29%, SE 0.05). Associations of the identified CpGs were found in previous literature for gestational age and childhood and adolescent BMI. In a mouse model of prenatal jet lag exposure, information on offspring DNA methylation of ten homologous genes annotated to the 16 CpGs with P < 1 × 10-5 in our analysis was available, of which eight were associated (enrichment P: 1.62 × 10-11).

CONCLUSION

Maternal night shift work during pregnancy was associated with newborn DNA methylation at 3 CpGs. Top findings overlapped with those in a mouse model of gestational jet lag. This work strengthens evidence that DNA methylation could be a marker or mediator of impacts of circadian rhythm disturbances.

A meta-analysis of epigenome-wide association studies of ultra-processed food consumption with DNA methylation in European children

BACKGROUND/OBJECTIVE

There is limited knowledge on how diet affects the epigenome of children. Ultra-processed food (UPF) consumption is emerging as an important factor impacting health, but mechanisms need to be uncovered. We therefore aimed to assess the association between UPF consumption and DNA methylation in children.

METHODS

We conducted a meta-analysis of epigenome-wide association studies (EWAS) from a total of 3152 children aged 5-11 years from four European studies (HELIX, Generation XXI, ALSPAC, and Generation R). UPF consumption was defined applying the Nova food classification system (group 4), and DNA methylation was measured in blood with Illumina Infinium Methylation arrays. Associations were estimated within each cohort using robust linear regression models, adjusting for relevant covariates, followed by a meta-analysis of the resulting EWAS estimates.

RESULTS

Although no CpG was significant at FDR level, we found suggestive associations (p-value < 10-5) between UPF consumption and methylation at seven CpG sites. Three of them, cg00339913 (PHYHIP), cg03041696 (intergenic), and cg03999434 (intergenic), were negatively associated, whereas the other four, cg14665028 (NHEJ1), cg18968409 (intergenic), cg24730307 (intergenic), and cg09709951 (ATF7), were positively associated with UPF intake. These CpGs have been previously associated with health outcomes such as carcinomas, and the related genes are mainly involved in pathways related to thyroid hormones and liver function.

CONCLUSION

We only found suggestive changes in methylation at 7 CpGs associated with UPF intake in a large EWAS among children: although this shows a potential impact of UPF intake on DNAm, this might not be a key mechanism underlying the health effects of UPFs in children. There is a need for more detailed dietary assessment in children studies and of intervention studies to assess potential epigenetic changes linked to a reduction in UPF in the diet.

Association of exposure to second-hand smoke during childhood with blood DNA methylation

INTRODUCTION

By recent estimates, 40% of children worldwide are exposed to second-hand smoke (SHS), which has been associated with adverse health outcomes. While numerous studies have linked maternal smoking during pregnancy (MSDP) to widespread differences in child blood DNA methylation (DNAm), research specifically examining postnatal SHS exposure remains sparse. To address this gap, we conducted epigenome-wide meta-analyses to identify associations of postnatal SHS and child blood DNAm.

METHODS

Six cohorts from the Pregnancy And Childhood Epigenetics (PACE) Consortium (total N = 2,695), with SHS data and child blood DNAm (aged 7-9 years) measured with the Illumina 450K array were included in the meta-analysis. Linear regression models adjusted for covariates were fitted to examine the association between the number of household smokers in postnatal life (0, 1, 2+) and child blood DNAm. Sensitivity models without adjusting for MSDP and restricted to mothers who did not smoke during pregnancy were evaluated.

RESULTS

Our analysis revealed significant associations (False Discovery Rate < 0.05) between household postnatal SHS exposure and DNAm at 11 CpGs in exposed children. Nine CpGs were mapped to genes (MYO1G, FAM184B, CTDSPL2, LTBP3, PDE10A, and FIBCD1), while 2 CpGs were located in open sea regions. Notably, all except 2 CpGs (mapped to FIBCD1 and CTDSPL2) have previously been linked to either personal smoking habits or in utero exposure to smoking. The models restricted to non-smoking mothers provided similar results. Importantly, several of these CpGs and their associated genes are implicated in conditions exacerbated by or directly linked to SHS.

CONCLUSIONS

Our findings highlight the potential biological effects of SHS on blood DNAm. These findings support further research on epigenetic factors mediating deleterious effects of SHS on child health and call for public health policies aimed at reducing exposure, particularly in environments where children are present.

Influence of exposure to endocrine disruptors and other environmental chemicals on breast development in girls: A systematic review of human studies

BACKGROUND

Age at thelarche has decreased over recent decades. This change in female puberty timing may be influenced by exposure to endocrine disrupting chemicals (EDCs) during critical periods of development.

OBJECTIVE

To review the scientific literature for evidence on the association of exposure to EDCs and other environmental chemicals with the timing of thelarche in girls.

METHODS

A systematic search for original peer-reviewed articles published up to July 2023 was conducted in three databases (Medline/PubMed, Scopus, and Web of Science), following the PECO strategy and PRISMA guidelines. The quality of evidence and reporting and the risk of bias were evaluated using GRADE, STROBE, and ROBINS-E tools.

RESULTS

Out of 3094 articles retrieved in the search, 67 met the review inclusion criteria. Data from 10 out of the 14 studies offering high-quality suggest that in utero and/or childhood exposure to certain synthetic and natural chemicals is associated with earlier breast development in girls; 8 of these 10 studies described a relationship with exposure to organohalogenated compounds in utero and to phthalates in childhood.

CONCLUSIONS

This systematic review provides the first overview of available human data on the association of EDCs/environmental chemicals with the timing of thelarche. Further high-quality research is urgently needed to fully elucidate the influence of this exposure on breast development timing in girls.

DNA methylation in mammalian development and disease

The DNA methylation field has matured from a phase of discovery and genomic characterization to one seeking deeper functional understanding of how this modification contributes to development, ageing and disease. In particular, the past decade has seen many exciting mechanistic discoveries that have substantially expanded our appreciation for how this generic, evolutionarily ancient modification can be incorporated into robust epigenetic codes. Here, we summarize the current understanding of the distinct DNA methylation landscapes that emerge over the mammalian lifespan and discuss how they interact with other regulatory layers to support diverse genomic functions. We then review the rising interest in alternative patterns found during senescence and the somatic transition to cancer. Alongside advancements in single-cell and long-read sequencing technologies, the collective insights made across these fields offer new opportunities to connect the biochemical and genetic features of DNA methylation to cell physiology, developmental potential and phenotype.

Impact of COVID-19, lockdowns and vaccination on immune responses in a HIV cohort in the Netherlands

INTRODUCTION

During the COVID-19 pandemic, major events with immune-modulating effects at population-level included COVID-19 infection, lockdowns, and mass vaccinations campaigns. As immune responses influence many immune-mediated diseases, population scale immunological changes may have broad consequences.

METHODS

We investigated the impact of lockdowns, COVID-19 infection and vaccinations on immune responses in the 2000HIV study including 1895 asymptomatic virally-suppressed people living with HIV recruited between October 2019 and October 2021. Their inflammatory profile was assessed by targeted plasma proteomics, immune responsiveness by cytokine production capacity of circulating immune cells, and epigenetic profile by genome-wide DNA methylation of immune cells.

RESULTS

Past mild COVID-19 infection had limited long-term immune effects. In contrast, COVID-19 vaccines and especially lockdowns significantly altered both the epigenetic profile in immune cells at DNA methylation level and immune responses. Lockdowns resulted in a strong overall exaggerated immune responsiveness, while COVID-19 vaccines moderately dampened immune responses. Lockdown-associated immune responsiveness alterations were confirmed in 30 healthy volunteers from the 200FG cohort that, like the 2000HIV study, is part of the Human Functional Genomics Project.

DISCUSSION

Our data suggest that lockdowns have unforeseen immunological effects. Furthermore, COVID-19 vaccines have immunological effects beyond anti-SARS-CoV-2 activity, and studies of their impact on non-COVID-19 immune-mediated pathology are warranted.

Artificial intelligence and deep learning algorithms for epigenetic sequence analysis: A review for epigeneticists and AI experts

Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA methylation, histone modifications, chromatin conformation, and non-coding RNA. The changes in gene regulation and expression can manifest in the form of various diseases and disorders such as cancer and congenital deformities. Over the last few decades, high-throughput experimental approaches have been used to identify and understand epigenetic changes, but these laboratory experimental approaches and biochemical processes are time-consuming and expensive. To overcome these challenges, machine learning and artificial intelligence (AI) approaches have been extensively used for mapping epigenetic modifications to their phenotypic manifestations. In this paper we provide a narrative review of published research on AI models trained on epigenomic data to address a variety of problems such as prediction of disease markers, gene expression, enhancer-promoter interaction, and chromatin states. The purpose of this review is twofold as it is addressed to both AI experts and epigeneticists. For AI researchers, we provided a taxonomy of epigenetics research problems that can benefit from an AI-based approach. For epigeneticists, given each of the above problems we provide a list of candidate AI solutions in the literature. We have also identified several gaps in the literature, research challenges, and recommendations to address these challenges.

Novel DNA methylation changes in mouse lungs associated with chronic smoking

Smoking is a potent cause of asthma exacerbations, chronic obstructive pulmonary disease (COPD) and many other health defects, and changes in DNA methylation (DNAm) have been identified as a potential link between smoking and these health outcomes. However, most studies of smoking and DNAm have been done using blood and other easily accessible tissues in humans, while evidence from more directly affected tissues such as the lungs is lacking. Here, we identified DNAm patterns in the lungs that are altered by smoking. We used an established mouse model to measure the effects of chronic smoke exposure first on lung phenotype immediately after smoking and then after a period of smoking cessation. Next, we determined whether our mouse model recapitulates previous DNAm patterns observed in smoking humans, specifically measuring DNAm at a candidate gene responsive to cigarette smoke, Cyp1a1. Finally, we carried out epigenome-wide DNAm analyses using the newly released Illumina mouse methylation microarrays. Our results recapitulate some of the phenotypes and DNAm patterns observed in human studies but reveal 32 differentially methylated genes specific to the lungs which have not been previously associated with smoking. The affected genes are associated with nicotine dependency, tumorigenesis and metastasis, immune cell dysfunction, lung function decline, and COPD. This research emphasizes the need to study CS-mediated DNAm signatures in directly affected tissues like the lungs, to fully understand mechanisms underlying CS-mediated health outcomes.

Animal and plant protein intake during infancy and childhood DNA methylation: a meta-analysis in the NutriPROGRAM consortium

BACKGROUND

Higher early-life animal protein intake is associated with a higher childhood obesity risk compared to plant protein intake. Differential DNA methylation may represent an underlying mechanism.

METHODS

We analysed associations of infant animal and plant protein intakes with DNA methylation in early (2-6 years, N = 579) and late (7̄-12 years, N = 604) childhood in two studies. Study-specific robust linear regression models adjusted for relevant confounders were run, and then meta-analysed using a fixed-effects model. We also performed sex-stratified meta-analyses. Follow-up analyses included pathway analysis and eQTM look-up.

RESULTS

Infant animal protein intake was not associated with DNA methylation in early childhood, but was associated with late-childhood DNA methylation at cg21300373 (P = 4.27 × 10¯8, MARCHF1) and cg10633363 (P = 1.09 × 10¯7, HOXB9) after FDR correction. Infant plant protein intake was associated with early-childhood DNA methylation at cg25973293 (P = 2.26 × 10-7, C1orf159) and cg15407373 (P = 2.13 × 10-7, MBP) after FDR correction. There was no overlap between the findings from the animal and plant protein analyses. We did not find enriched functional pathways at either time point using CpGs associated with animal and plant protein. These CpGs were not previously associated with childhood gene expression. Sex-stratified meta-analyses showed sex-specific DNA methylation associations for both animal and plant protein intake.

CONCLUSION

Infant animal protein intake was associated with DNA methylation at two CpGs in late childhood. Infant plant protein intake was associated with DNA methylation in early childhood at two CpGs. A potential mediating role of DNA methylation at these CpGs between infant protein intake and health outcomes requires further investigation.

Maternal adverse childhood experiences (ACEs) and offspring imprinted gene DMR methylation at birth

Adverse childhood experiences (ACEs) contribute to numerous negative health outcomes across the life course and across generations. Here, we extend prior work by examining the association of maternal ACEs, and their interaction with financial stress and discrimination, with methylation status within eight differentially methylated regions (DMRs) in imprinted domains in newborns. ACEs, financial stress during pregnancy, and experience of discrimination were self-reported among 232 pregnant women. DNA methylation was assessed at PEG10/SGCE, NNAT, IGF2, H19, PLAGL1, PEG3, MEG3-IG, and DLK1/MEG3 regulatory sequences using pyrosequencing. Using multivariable linear regression models, we found evidence to suggest that financial stress was associated with hypermethylation of MEG3-IG in non-Hispanic White newborns; discrimination was associated with hypermethylation of IGF2 and NNAT in Hispanic newborns, and with hypomethylation of PEG3 in non-Hispanic Black newborns. We also found evidence that maternal ACEs interacted with discrimination to predict offspring PLAGL1 altered DMR methylation, in addition to interactions between maternal ACEs score and discrimination predicting H19 and SGCE/PEG10 altered methylation in non-Hispanic White newborns. However, these interactions were not statistically significant after multiple testing corrections. Findings from this study suggest that maternal ACEs, discrimination, and financial stress are associated with newborn aberrant methylation in imprinted gene regions.

Prenatal chemical exposures and the methylome: current evidence and opportunities for environmental epigenetics

Exposure to pollutants and chemicals during critical developmental periods in early life can impact health and disease risk across the life course. Research in environmental epigenetics has provided increasing evidence that prenatal exposures affect epigenetic markers, particularly DNA methylation. In this article, we discuss the role of DNA methylation in early life programming and review evidence linking the intrauterine environment to epigenetic modifications, with a focus on exposure to tobacco smoke, metals, and endocrine-disrupting chemicals. We also discuss challenges and novel approaches in environmental epigenetic research and explore the potential of epigenetic biomarkers in studies of pediatric populations as indicators of exposure and disease risk. Overall, we aim to highlight how advancements in environmental epigenetics may transform our understanding of early-life exposures and inform new approaches for supporting long-term health.

Intercontinental insights into autism spectrum disorder: a synthesis of environmental influences and DNA methylation

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterized by a broad range of symptoms. The etiology of ASD is thought to involve complex gene-environment interactions, which are crucial to understanding its various causes and symptoms. DNA methylation is an epigenetic mechanism that potentially links genetic predispositions to environmental factors in the development of ASD. This review provides a global perspective on ASD, focusing on how DNA methylation studies may reveal gene-environment interactions characteristic of specific geographical regions. It delves into the role of DNA methylation in influencing the causes and prevalence of ASD in regions where environmental influences vary significantly. We also address potential explanations for the high ASD prevalence in North America, considering lifestyle factors, environmental toxins, and diagnostic considerations. Asian and European studies offer insights into endocrine-disrupting compounds, persistent organic pollutants, maternal smoking, and their associations with DNA methylation alterations in ASD. In areas with limited data on DNA methylation and ASD, such as Africa, Oceania, and South America, we discuss prevalent environmental factors based on epidemiological studies. Additionally, the review integrates global and country-specific prevalence data from various studies, providing a comprehensive picture of the variables influencing ASD diagnoses over region and year of assessment. This prevalence data, coupled with regional environmental variables and DNA methylation studies, provides a perspective on the complexities of ASD research. Integrating global prevalence data, we underscore the need for a comprehensive global understanding of ASD's complex etiology. Expanded research into epigenetic mechanisms of ASD is needed, particularly in underrepresented populations and locations, to enhance biomarker development for diagnosis and intervention strategies for ASD that reflect the varied environmental and genetic landscapes worldwide.

Alcohol Use Disorder-Associated DNA Methylation in the Nucleus Accumbens and Dorsolateral Prefrontal Cortex

Background

Alcohol use disorder (AUD) has a profound public health impact. However, understanding of the molecular mechanisms that underlie the development and progression of AUD remains limited. Here, we investigated AUD-associated DNA methylation changes within and across 2 addiction-relevant brain regions, the nucleus accumbens and dorsolateral prefrontal cortex.

Methods

Illumina HumanMethylation EPIC array data from 119 decedents (61 cases, 58 controls) were analyzed using robust linear regression with adjustment for technical and biological variables. Associations were characterized using integrative analyses of public annotation data and published genetic and epigenetic studies. We also tested for brain region-shared and brain region-specific associations using mixed-effects modeling and assessed implications of these results using public gene expression data from human brain.

Results

At a false discovery rate of ≤.05, we identified 105 unique AUD-associated CpGs (annotated to 120 genes) within and across brain regions. AUD-associated CpGs were enriched in histone marks that tag active promoters, and our strongest signals were specific to a single brain region. Some concordance was found between our results and those of earlier published alcohol use or dependence methylation studies. Of the 120 genes, 23 overlapped with previous genetic associations for substance use behaviors, some of which also overlapped with previous addiction-related methylation studies.

Conclusions

Our findings identify AUD-associated methylation signals and provide evidence of overlap with previous genetic and methylation studies. These signals may constitute predisposing genetic differences or robust methylation changes associated with AUD, although more work is needed to further disentangle the mechanisms that underlie these associations and their implications for AUD.

Characterising developmental dynamics of adult epigenetic clock sites

BACKGROUND

DNA methylation (DNAm), an epigenetic mechanism that regulates gene activity in response to genetic and environmental influences, changes as we age. DNAm at specific sites on the genome can be used to calculate 'epigenetic clocks', which are powerful biomarkers of age, as well as of ageing. However, little is known about how these clock sites 'behave' during development and what factors influence their variability in early life. This knowledge could be used to optimise healthy ageing well before the onset of age-related conditions.

METHODS

We leveraged results from two longitudinal population-based cohorts (N = 5019 samples from 2348 individuals) to characterise trajectories of adult clock sites from birth to early adulthood. To explore what factors may drive early individual differences at these clock sites, we also tested for enrichment of genetic factors and prenatal exposures based on existing epigenome-wide association meta-analyses.

FINDINGS

We find that clock sites (i) diverge widely in their developmental trajectories, often showing non-linear change over time; (ii) are substantially more likely than non-clock sites to vary between individuals already from birth, differences that are predictive of DNAm variation at later ages; and (iii) show enrichment for genetic influences and prenatal environmental exposures, including prenatal smoking, diet and maternal physical health conditions.

INTERPRETATION

These results suggests that age(ing)-related epigenetic processes might originate-and differ between individuals-already very early in development. Understanding what drives these differences may in future help us to devise better strategies to promote healthy ageing.

FUNDING

This research was conducted while C.A.M.C. was a Hevolution/AFAR New Investigator Awardee in Aging Biology and Geroscience Research. Full personal funding details, as well as cohort funding details, can be found in the Acknowledgements.

Tobacco Exposures are Associated With Healthcare Utilization and Healthcare Costs in Pregnant Persons and Their Newborn Babies

INTRODUCTION

Identifying healthcare utilization and costs associated with active and passive smoking during pregnancy could help improve health management strategies.

AIMS AND METHODS

Data are from the Newborn Epigenetics STudy (NEST), a birth cohort enrolled from 2005 to 2011 in Durham and adjacent counties in North Carolina, United States. Participants included those for whom prenatal serum samples were assayed and for whom administrative data were obtainable (N = 1045). Zero-inflated poisson regression models were used to assess associations between cotinine, adjusted for covariates (eg, race and ethnicity, age at delivery, cohabitation status, and education), and health care utilization outcomes. Generalized linear regression models were used to estimate average total charges. Simulation models were conducted to determine the economic benefits of reducing secondhand smoke and smoking during pregnancy.

RESULTS

Increasing levels of cotinine were positively associated with parent's number of emergency department (ED) visits (coefficient[b] = 0.0012, standard error [SE] = 0.0002; p < .001), the number of ICU hours (b = 0.0079, SE = 0.0025; p = .002), time spent in the ICU (b = 0.0238, SE = 0.0020, p < .001), and the number of OP visits (b = 0.0003, SE = 0.0001; p < .001). For infants, higher cotinine levels were associated with higher number of ED (b = 0.0012, SE = 0.0004; p = .005), ICU (b = 0.0050, SE = 0.001; p < .001), and OP (b = 0.0006, SE = 0.0002; p < .001) visits and longer time spent in the ED (b = 0.0025, SE = 0.0003; p < .001), ICU (b = 0.0005, SE = 0.0001; p < .001), and IP (b = 0.0020, SE = 0.0002; p < .001). Simulation results showed that a 5% reduction in smoking would correspond to a potential median cost savings of $150 533 from ED visits of parents and infants.

CONCLUSIONS

Our findings highlight the importance of smoke exposure cessation during pregnancy to reduce health care utilization and costs for both parents and infants.

IMPLICATIONS

This study reinforces the importance of reducing smoking and secondhand smoke exposure during pregnancy. Focusing on expanding cessation services to this group could help reduce morbidities observed within this population. Furthermore, there is the potential for healthcare cost savings to healthcare systems, especially for those with high delivery numbers. These cost savings are represented by potential reductions in ED, OP, and ICU hours and visits.

Epigenome-wide association study of fluoride exposure during early adolescence and DNA methylation among U.S. children

Exposure to fluoride in early childhood has been associated with altered cognition, intelligence, attention, and neurobehavior. Fluoride-related neurodevelopment effects have been shown to vary by sex and very little is known about the mechanistic processes involved. There is limited research on how fluoride exposure impacts the epigenome, potentially leading to changes in DNA methylation of specific genes regulating key developmental processes. In the Cincinnati Childhood Allergy and Air Pollution Study (CCAAPS), urine samples were analyzed using a microdiffusion method to determine childhood urinary fluoride adjusted for specific gravity (CUFsg) concentrations. Whole blood DNA methylation was assessed using the Infinium MethylationEPIC BeadChip 850 k Array. In a cross-sectional analysis, we interrogated epigenome-wide DNA methylation at 775,141 CpG loci across the methylome in relation to CUFsg concentrations in 272 early adolescents at age 12 years. Among all participants, higher concentrations of CUF were associated with differential methylation of one CpG (p < 6 × 10-8) located in the gene body of GBF1 (cg25435255). Among females, higher concentrations of CUFsg were associated with differential methylation of 7 CpGs; only three CpGs were differentially methylated among males with no overlap of significant CpGs observed among females. Secondary analyses revealed several differentially methylated regions (DMRs) and CpG loci mapping to genes with key roles in psychiatric outcomes, social interaction, and cognition, as well as immunologic and metabolic phenotypes. While fluoride exposure may impact the epigenome during early adolescence, the functional consequences of these changes are unclear warranting further investigation.

Environmental exposures influence multigenerational epigenetic transmission

Epigenetic modifications control gene expression and are essential for turning genes on and off to regulate and maintain differentiated cell types. Epigenetics are also modified by a multitude of environmental exposures, including diet and pollutants, allowing an individual's environment to influence gene expression and resultant phenotypes and clinical outcomes. These epigenetic modifications due to gene-environment interactions can also be transmitted across generations, raising the possibility that environmental influences that occurred in one generation may be transmitted beyond the second generation, exerting a long-lasting effect. In this review, we cover the known mechanisms of epigenetic modification acquisition, reprogramming and persistence, animal models and human studies used to understand multigenerational epigenetic transmission, and examples of environmentally induced epigenetic change and its transmission across generations. We highlight the importance of environmental health not only on the current population but also on future generations that will experience health outcomes transmitted through epigenetic inheritance.

Maternal e-cigarette exposure alters DNA methylome, site-specific CpG and CH methylation, and transcriptomic signatures in the neonatal brain

Maternal use of e-cigarette (e-cig) aerosols poses significant risks to fetal brain development, potentially increasing susceptibility to neurodevelopmental disorders in later life. However, the underlying mechanisms remain incompletely understood. This study aimed to understand the effects of fetal e-cig exposure on DNA methylome and transcriptomic changes in the neonatal brain. Pregnant rats were exposed to e-cig aerosols, and neonatal brains (5 males and 5 females/group) from both control and e-cig-exposed groups were used for experimental analysis. Results indicated that prenatal e-cig exposure altered site-specific DNA methylation patterns at both CpG and CH (non-CpG) sites, predominantly in intergenic and intronic regions, with sex dimorphism in methylation and gene expression changes. Gene ontology analysis revealed that e-cig exposure not only affected neuron projection development and axonogenesis but also altered pathways related to neurodegeneration and long-term depression. These findings provide novel insights into the dynamic changes of CpG and CH methylation induced by e-cig exposure, underscoring the susceptibility of the developing brain to maternal e-cig exposure and its potential implications for developmental disorders and neurodegenerative diseases later in life.

A comprehensive lifestyle index and its associations with DNA methylation and type 2 diabetes among Ghanaian adults: the rodam study

BACKGROUND

A series of modifiable lifestyle factors, such as diet quality, physical activity, alcohol intake, and smoking, may drive the rising burden of type 2 diabetes (T2DM) among sub-Saharan Africans globally. It is unclear whether epigenetic changes play a mediatory role in the associations between these lifestyle factors and T2DM. We assessed the associations between a comprehensive lifestyle index, DNA methylation and T2DM among Ghanaian adults.

METHODS

We used whole-blood Illumina 450 k DNA methylation data from 713 Ghanaians from the Research on Obesity and Diabetes among African Migrants (RODAM) study. We constructed a comprehensive lifestyle index based on established cut-offs for diet quality, physical activity, alcohol intake, and smoking status. In the T2DM-free discovery cohort (n = 457), linear models were fitted to identify differentially methylated positions (DMPs) and differentially methylated regions (DMRs) associated with the lifestyle index after adjustment for age, sex, body mass index (BMI), and technical covariates. Associations between the identified DMPs and the primary outcome (T2DM), as well as secondary outcomes (fasting blood glucose (FBG) and HbA1c), were determined via logistic and linear regression models, respectively.

RESULTS

In the present study population (mean age: 52 ± 10 years; male: 42.6%), the comprehensive lifestyle index showed a significant association with one DMP annotated to an intergenic region on chromosome 7 (false discovery rate (FDR) = 0.024). Others were annotated to ADCY7, SMARCE1, AHRR, LOXL2, and PTBP1 genes. One DMR was identified and annotated to the GFPT2 gene (familywise error rate (FWER) from bumphunter bootstrap = 0.036). None of the DMPs showed significant associations with T2DM; directions of effect were positive for the DMP in the AHRR and inverse for all the other DMPs. Higher methylation of the ADCY7 DMP was associated with higher FBG (p = 0.024); LOXL2 DMP was associated with lower FBG (p = 0.023) and HbA1c (p = 0.049); and PTBP1 DMP was associated with lower HbA1c (p = 0.002).

CONCLUSIONS

In this explorative epigenome-wide association study among Ghanaians, we identified one DMP and DMR associated with a comprehensive lifestyle index not previously associated with individual lifestyle factors. Based on our findings, we infer that lifestyle factors in combination, affect DNA methylation, thereby influencing the risk of T2DM among Ghanaian adults living in different contexts.

Sex differences in DNA methylation variations according to ART conception-evidence from the Norwegian mother, father, and child cohort study

Previous studies have shown cord-blood DNA methylation differences in newborns conceived using assisted reproductive technologies (ART) compared to those conceived naturally. However, whether these ART-related DNA methylation differences vary with children's sex is unknown. We hypothesize that the DNA methylation differences in cord blood between ART-conceived and naturally conceived newborns also varies by the sex of the child, with distinct patterns of differential methylation present in males and females. We investigated sex differences in cord-blood DNA methylation variation according to conception by ART using the Illumina MethylationEPIC platform, comparing 456 ART-conceived versus 507 naturally-conceived girls, and 503 ART-conceived and 473 naturally-conceived boys. We identified 37 differentially methylated CpGs according to ART-conception among girls, and 70 differentially methylated CpGs according to ART-conception among boys, when we used a 1% false discovery rate to account for multiple testing. Ten CpGs were differentially methylated according to conception by ART in both sexes. Among the genes that were associated with these CpGs, we found the BRCA1; NBR2 gene (two CpGs) was hypermethylated in girls while the APC2 (two CpGs) and NECAB3;ACTL10, (four CpGs) related to cellular signaling were hypomethylated in boys. These findings confirm the presence of sex-specific epigenetic differences, illustrating the nuanced impact of ART on the fetal epigenome. There is a need for further explorations into the implications for sex-specific developmental trajectories and health outcomes in ART-conceived children.

Skin Rejuvenation by Modulation of DNA Methylation

Skin aging is driven by a complex set of cellular pathways. Among these, epigenetic mechanisms have garnered particular attention, because of their sensitivity to environmental and lifestyle factors. DNA methylation represents the longest known and best understood epigenetic mechanism. We explain how DNA methylation might function as an interface between the environment and the genome of human skin. Exposures to different environmental factors and lifestyles are known to modulate age-related methylation patterns, as illustrated by their effect on DNA methylation clocks. Human skin provides a particularly well-suited tissue for understanding age-related methylation changes and it has been shown recently that modulation of DNA methylation can induce skin rejuvenation. We explain how the use of mildly demethylating agents can be safeguarded to ensure the specific removal of age-related DNA methylation changes. We also identify important areas of future research, leading to a deeper understanding of the mechanisms that drive epigenetic aging and to the development of further refined intervention strategies.

Maternal tobacco exposure during pregnancy and atopic dermatitis in offspring: A systematic review and meta-analysis

The main purpose of this review was to examine the evidence of the relationship between active smoking or passive smoking during pregnancy and atopic dermatitis in offspring. The protocol was written following the PRISMA Checklist and was registered in the PROSPERO database (registration number CRD42022381136). We implemented a comprehensive search in PubMed, Embase and Web of Science databases to identify all potentially related articles from inception through 1 December 2022. We assessed cohort studies and case-control studies using the Newcastle-Ottawa Scale (NOS), and the Joanna Briggs Institute (JBI) critical appraisal tool to assess the quality of cross-sectional studies. Heterogeneity was investigated by using Cochrane Q tests and I2 statistics. In addition, according to the research design, population source and population size, the reasons for the heterogeneity were analysed. A total of 15 observational studies were included in this analysis. Our meta-analysis suggests that atopic dermatitis in offspring is not associated with active smoking during pregnancy (pooled OR, 0.96 [95% CI 0.86-1.07]); however, it is related to passive smoking (OR, 1.52 [95% CI 1.36-1.70]). Passive smoking during pregnancy is associated with an increased risk of eczema development in offspring. More research is needed to explore the risk of active smoking and eczema development in offspring, especially the association between measurements of pregnancy cotinine levels in maternal body fluids and AD in offspring.

Newborn adiposity is associated with cord blood DNA methylation at IGF1R and KLF7

OBJECTIVE

This study aimed to identify whether cord blood DNA methylation at specific loci is associated with neonatal adiposity, a key risk factor for childhood obesity.

METHODS

An epigenome-wide association study was conducted using the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) Study as a discovery sample. Linear regression models adjusted for maternal and offspring covariates and cell counts were used to analyze associations between neonatal adiposity as measured by sum of three skinfold thicknesses and cord blood DNA methylation. Assays were performed with Illumina EPIC arrays (791,359 CpG sites after quality control). Replication was performed in an independent cohort, Genetics of Glucose regulation in Gestation and Growth (Gen3G).

RESULTS

In 2740 HAPO samples, significant associations were identified at 89 CpG sites after accounting for multiple testing (Bonferroni-adjusted p < 0.05). Replication analyses conducted in 139 Gen3G participants confirmed associations for seven CpG sites. These included IGF1R, which encodes a transmembrane receptor involved in cell growth and survival that binds insulin-like growth factor I and insulin, and KLF7, which encodes a regulator of cell proliferation and inhibitor of adipogenesis; both are key regulators of growth during fetal life.

CONCLUSIONS

These findings support epigenetic mechanisms in the developmental origins of neonatal adiposity and as potential biomarkers of metabolic disease risk.

Alterations of senescence-associated markers in patients with non-syndromic cleft lip and palate

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common craniofacial anomalies. Abnormal Alu methylation in DNA of the pregnant mother may influence the abnormal development of the child. This study aimed to examine Alu methylation and cellular senescence in NSCL/P patients and their mothers as well as the correlation with the severity of NSCL/P. A total of 39 patients with NSCL/P and 33 mothers were enrolled. Of these patients, 6 were cleft lip only (CLO), 9 were cleft palate only (CPO), and 24 were cleft lip and palate (CLP). Alu methylation and senescence markers were determined in the white blood cells of NSCL/P patients, their mothers, and in the lip and palatal tissues of patients at the time of cheiloplasty and palatoplasty. Total Alu methylation was not significantly different between groups. However, a decrease in Alu hypermethylation, increased partial Alu methylation, RAGE, and p16 expression were shown in CLP, the most severe cleft type. Alu methylation in tissues did not differ between groups. In mothers, an increase in Alu methylation was observed only in the CLP. Therefore, the pathogenesis of NSCL/P may be related to Alu methylation of the mother promoting loss of Alu methylation and subsequently senescence in the children.

Prenatal exposure to maternal smoking and adult lung cancer risk: a nested case-control study using peripheral blood leukocyte DNA methylation prediction of exposure

A prior study reported no association between prenatal smoking methylation scores and adult lung cancer risk adjusting for methylation-predicted adult smoking, without considering maternal smoking trends by birth cohort. To address this gap, we examined the association between prenatal smoking methylation scores and adult lung cancer, independent of methylation-predicted adult packyears and by birth cohort, in a study nested in CLUE II. Included were 208 incident lung cancer cases ascertained by cancer registry linkage and 208 controls matched on age, sex, and smoking. DNA methylation was measured in prediagnostic blood. We calculated two prenatal smoking scores, using 19 (Score-19) and 15 (Score-15) previously identified CpGs and a methylation-predicted adult packyears score. Conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) adjusting for adult packyears score and batch effects. Score-15 was positively associated with lung cancer (per standard deviation, OR = 1.40, 95% CI = 1.10-1.79, P-trend = .006), especially in the 1930-1938 birth cohort (OR = 3.43, 95% CI = 1.55-7.60, P-trend = .002). Score-19 was associated only in the 1930-1938 birth cohort (OR = 2.12, 95% CI = 1.15-3.91). Participants with both prenatal scores below the median (vs all other combinations) had lower risk (OR = 0.44, 95% CI = 0.27-0.72), especially in the 1930-1938 birth cohort (OR = 0.16, 95% CI = 0.04-0.62). Among ever smokers, participants with higher prenatal smoking scores had higher risk, irrespective of adult packyears (low: OR = 2.81, 95% CI = 1.38-5.72, high: OR = 2.67, 95% CI = 1.03-6.95). This prospective study suggests a positive association between prenatal smoking exposure and adult lung cancer risk, especially in the 1930-1938 birth cohort, independent of active smoking. Future studies with multiple birth cohorts are needed.

From womb to wellness: early environmental exposures, cord blood DNA methylation and disease origins

Fetal exposures can induce epigenetic modifications, particularly DNA methylation, potentially predisposing individuals to later health issues. Cord blood (CB) DNA methylation provides a unique window into the fetal epigenome, reflecting the intrauterine environment's impact. Maternal factors, including nutrition, smoking and toxin exposure, can alter CB DNA methylation patterns, associated with conditions from obesity to neurodevelopmental disorders. These epigenetic changes underscore prenatal exposures' enduring effects on health trajectories. Technical challenges include tissue specificity issues, limited coverage of current methylation arrays and confounding factors like cell composition variability. Emerging technologies, such as single-cell sequencing, promise to overcome some of these limitations. Longitudinal studies are crucial to elucidate exposure-epigenome interactions and develop prevention strategies. Future research should address these challenges, advance public health initiatives to reduce teratogen exposure and consider ethical implications of epigenetic profiling. Progress in CB epigenetics research promises personalized medicine approaches, potentially transforming our understanding of developmental programming and offering novel interventions to promote lifelong health from the earliest stages of life.

An epigenome-wide study of a needs-based family intervention for offspring of trauma-exposed mothers in Kosovo

INTRODUCTION

Maternal stress and trauma during pregnancy have been shown to influence cortisol levels and epigenetic patterns, including DNA methylation, in the offspring. This study aimed to determine whether a tailor-made family intervention could help reduce cortisol levels in children born to traumatized mothers, and to determine whether it effected offspring DNA methylation. The secondary aim was to determine whether the family intervention influenced DNA methylation aging, a marker of biological aging.

METHODS

A needs-based family intervention was designed to help address relational difficulties and family functioning, and included a focus on family strengths and problem-solving patterns. Women survivors of sexual violence during the Kosovar war in 1998-1999, and their families (children with or without partners) were randomly assigned to 10 sessions of a family therapy over a 3-5-month period, or to a waitlist control group. Both mothers and children completed assessments prior to and after the intervention phase. Children's blood samples collected at these two time points were used to measure cortisol and epigenome-wide DNA methylation patterns (Illumina EPIC array). Cortisol levels, and genome-wide DNA methylation changes pre-/postintervention were compared between children in the intervention and the waitlist groups. DNA methylation age and accelerated biological aging were calculated.

RESULTS

Sixty-two women-child dyads completed the study, 30 were assigned first to the intervention group, and 32 to the waitlist control group. In adjusted linear regression, the family intervention was associated with a significant decline in cortisol levels compared to the waitlist control (β = -124.72, 95% confidence interval [CI]: -197.4 to -52.1, p = .001). Children in the intervention group, compared to the waitlist control group, showed >1% differential methylation degree at 5819 CpG (5'-C-phosphate-G-3') sites across the genome (p < .01), with the largest methylation difference being 21%. However, none of these differences reached genome-wide significant levels. There was no significant difference in DNA methylation aging between the two groups.

CONCLUSION

We find evidence that a tailored family-based intervention reduced stress levels in the children (based on cortisol levels), and modified DNA methylation levels at a number of sites across the genome. This study provides some preliminary evidence to suggest the potential for tailored interventions to help break the intergenerational transmission of trauma, however, large studies powered to detect associations at genome-wide significant levels are needed.

Contributions of prenatal risk factors and neonatal epigenetics to cognitive outcome in children born very preterm

Children born less than 30 weeks gestational age (GA) are at high risk for neurodevelopmental delay compared to term peers. Prenatal risk factors and neonatal epigenetics could help identify preterm children at highest risk for poor cognitive outcomes. We aimed to understand the associations among cumulative prenatal risk, neonatal DNA methylation, and child cognitive ability at age 3 years, including whether DNA methylation mediates the association between prenatal risk and cognitive ability. We studied 379 neonates (54% male) born less than 30 weeks GA who had DNA methylation measured at neonatal intensive care unit discharge along with 3-year follow-up data. Cumulative prenatal risk was calculated from 24 risk factors obtained from maternal report and medical record and epigenome-wide neonatal DNA methylation was assayed from buccal swabs. At 3-year follow-up, child cognitive ability was assessed using the Bayley Scales of Infant and Toddler Development (third edition). Cumulative prenatal risk and DNA methylation at two cytosine-phosphate-guanines (CpGs) were uniquely associated with child cognitive ability. Using high-dimensional mediation analysis, we also identified differential methylation of 309 CpGs that mediated the association between cumulative prenatal risk and child cognitive ability. Many of the associated CpGs were located in genes (TNS3, TRAPPC4, MAD1L1, APBB2, DIP2C, TRAPPC9, DRD2) that have previously been associated with prenatal exposures and/or neurodevelopmental phenotypes. Our findings suggest a role for both prenatal risk factors and DNA methylation in explaining outcomes for children born preterm and suggest we should further study DNA methylation as a potential mechanism underlying the association between prenatal risk and child neurodevelopment. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Gestational epigenetic age and ADHD symptoms in childhood: a prospective, multi-cohort study

Epigenetic age acceleration (EAA), defined as the difference between chronological age and epigenetically predicted age, was calculated from multiple gestational epigenetic clocks (Bohlin, EPIC overlap, and Knight) using DNA methylation levels from cord blood in three large population-based birth cohorts: the Generation R Study (The Netherlands), the Avon Longitudinal Study of Parents and Children (United Kingdom), and the Norwegian Mother, Father and Child Cohort Study (Norway). We hypothesized that a lower EAA associates prospectively with increased ADHD symptoms. We tested our hypotheses in these three cohorts and meta-analyzed the results (n = 3383). We replicated previous research on the association between gestational age (GA) and ADHD. Both clinically measured gestational age as well as epigenetic age measures at birth were negatively associated with ADHD symptoms at ages 5-7 years (clinical GA: β = -0.04, p < 0.001, Bohlin: β = -0.05, p = 0.01; EPIC overlap: β = -0.05, p = 0.01; Knight: β = -0.01, p = 0.26). Raw EAA (difference between clinical and epigenetically estimated gestational age) was positively associated with ADHD in our main model, whereas residual EAA (raw EAA corrected for clinical gestational age) was not associated with ADHD symptoms across cohorts. Overall, findings support a link between lower gestational age (either measured clinically or using epigenetic-derived estimates) and ADHD symptoms. Epigenetic age acceleration does not, however, add unique information about ADHD risk independent of clinically estimated gestational age at birth.