Epigenome-Wide Association Study of Asthma Exacerbations in Europeans.

Epigenetics in health and disease: heralding the EWAS era

Calorie restriction (CR) increases healthy life span and is accompanied by slowing or reversal of aging-associated DNA methylation (DNAm) changes in animal models. In the Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy (CALERIETM) human trial, we evaluated associations of CR and changes in whole-blood DNAm. CALERIETM randomized 220 healthy, nonobese adults in a 2:1 allocation to 2 years of CR or ad libitum (AL) diet. The average CR in the treatment group through 24 months of follow-up was 12%. Whole blood (baseline, 12, and 24 months) DNAm profiles were measured. Epigenome-wide association study (EWAS) analysis tested CR-induced changes from baseline to 12 and 24 months in the n = 197 participants with available DNAm data. CR treatment was not associated with epigenome-wide significant (false discovery rate [FDR] < 0.05) DNAm changes at the individual-CpG-site level. Secondary analysis of sets of CpG sites identified in published EWAS revealed that CR induced DNAm changes opposite to those associated with higher body mass index and cigarette smoking (p < .003 at 12- and 24-month follow-ups). In contrast, CR altered DNAm at chronological-age-associated CpG sites in the direction of older age (p < .003 at 12- and 24-month follow-ups). Although individual CpG site DNAm changes in response to CR were not identified, analyses of sets CpGs identified in prior EWAS revealed CR-induced changes to blood DNAm. Altered CpG sets were enriched for insulin production, glucose tolerance, inflammation, and DNA-binding and DNA-regulation pathways, several of which are known to be modified by CR. DNAm changes may contribute to CR effects on aging.

Background:The identification of expression quantitative trait methylation (eQTMs), defined as associations between DNA methylation levels and gene expression, might help the biological interpretation of epigenome-wide association studies (EWAS). We aimed to identify autosomal cis eQTMs in children’s blood, using data from 832 children of the Human Early Life Exposome (HELIX) project.Methods:Blood DNA methylation and gene expression were measured with the Illumina 450K and the Affymetrix HTA v2 arrays, respectively. The relationship between methylation levels and expression of nearby genes (1 Mb window centered at the transcription start site, TSS) was assessed by fitting 13.6 M linear regressions adjusting for sex, age, cohort, and blood cell composition.Results:We identified 39,749 blood autosomal cis eQTMs, representing 21,966 unique CpGs (eCpGs, 5.7% of total CpGs) and 8,886 unique transcript clusters (eGenes, 15.3% of total transcript clusters, equivalent to genes). In 87.9% of these cis eQTMs, the eCpG was located at <250 kb from eGene’s TSS; and 58.8% of all eQTMs showed an inverse relationship between the methylation and expression levels. Only around half of the autosomal cis-eQTMs eGenes could be captured through annotation of the eCpG to the closest gene. eCpGs had less measurement error and were enriched for active blood regulatory regions and for CpGs reported to be associated with environmental exposures or phenotypic traits. In 40.4% of the eQTMs, the CpG and the eGene were both associated with at least one genetic variant. The overlap of autosomal cis eQTMs in children’s blood with those described in adults was small (13.8%), and age-shared cis eQTMs tended to be proximal to the TSS and enriched for genetic variants.Conclusions:This catalogue of autosomal cis eQTMs in children’s blood can help the biological interpretation of EWAS findings and is publicly available at https://helixomics.isglobal.org/ and at Dryad (doi:10.5061/dryad.fxpnvx0t0).Funding:The study has received funding from the European Community’s Seventh Framework Programme (FP7/2007-206) under grant agreement no 308333 (HELIX project); the H2020-EU.3.1.2. - Preventing Disease Programme under grant agreement no 874583 (ATHLETE project); from the European Union’s Horizon 2020 research and innovation programme under grant agreement no 733206 (LIFECYCLE project), and from the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL and Instituto de Salud Carlos III) under the grant agreement no AC18/00006 (NutriPROGRAM project). The genotyping was supported by the projects PI17/01225 and PI17/01935, funded by the Instituto de Salud Carlos III and co-funded by European Union (ERDF, “A way to make Europe”) and the Centro Nacional de Genotipado-CEGEN (PRB2-ISCIII). BiB received core infrastructure funding from the Wellcome Trust (WT101597MA) and a joint grant from the UK Medical Research Council (MRC) and Economic and Social Science Research Council (ESRC) (MR/N024397/1). INMA data collections were supported by grants from the Instituto de Salud Carlos III, CIBERESP, and the Generalitat de Catalunya-CIRIT. KANC was funded by the grant of the Lithuanian Agency for Science Innovation and Technology (6-04-2014_31V-66). The Norwegian Mother, Father and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. The Rhea project was financially supported by European projects (EU FP6-2003-Food-3-NewGeneris, EU FP6. STREP Hiwate, EU FP7 ENV.2007.1.2.2.2. Project No 211250 Escape, EU FP7-2008-ENV-1.2.1.4 Envirogenomarkers, EU FP7-HEALTH-2009- single stage CHICOS, EU FP7 ENV.2008.1.2.1.6. Proposal No 226285 ENRIECO, EU- FP7- HEALTH-2012 Proposal No 308333 HELIX), and the Greek Ministry of Health (Program of Prevention of obesity and neurodevelopmental disorders in preschool children, in Heraklion district, Crete, Greece: 2011-2014; “Rhea Plus”: Primary Prevention Program of Environmental Risk Factors for Reproductive Health, and Child Health: 2012-15). We acknowledge support from the Spanish Ministry of Science and Innovation through the “Centro de Excelencia Severo Ochoa 2019-2023” Program (CEX2018-000806-S), and support from the Generalitat de Catalunya through the CERCA Program. MV-U and CR-A were supported by a FI fellowship from the Catalan Government (FI-DGR 2015 and #016FI_B 00272). MC received funding from Instituto Carlos III (Ministry of Economy and Competitiveness) (CD12/00563 and MS16/00128).

Depressive disorders arise from a combination of genetic and environmental risk factors. Epigenetic disruption provides a plausible mechanism through which gene-environment interactions lead to depression. Large-scale, epigenome-wide studies on depression are missing, hampering the identification of potentially modifiable biomarkers. To identify epigenetic mechanisms underlying depression in middle-aged and elderly persons, using DNA methylation in blood. To date, the first cross-ethnic meta-analysis of epigenome-wide association studies (EWAS) within the framework of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium was conducted. The discovery EWAS included 7948 individuals of European origin from 9 population-based cohorts. Participants who were assessed for both depressive symptoms and whole-blood DNA methylation were included in the study. Results of EWAS were pooled using sample-size weighted meta-analysis. Replication of the top epigenetic sites was performed in 3308 individuals of African American and European origin from 2 population-based cohorts. Whole-blood DNA methylation levels were assayed with Illumina-Infinium Human Methylation 450K BeadChip and depressive symptoms were assessed by questionnaire. The discovery cohorts consisted of 7948 individuals (4104 [51.6%] women) with a mean (SD) age of 65.4 (5.8) years. The replication cohort consisted of 3308 individuals (2456 [74.2%] women) with a mean (SD) age of 60.3 (6.4) years. The EWAS identified methylation of 3 CpG sites to be significantly associated with increased depressive symptoms: cg04987734 (P = 1.57 × 10-08; n = 11 256; CDC42BPB gene), cg12325605 (P = 5.24 × 10-09; n = 11 256; ARHGEF3 gene), and an intergenic CpG site cg14023999 (P = 5.99 × 10-08; n = 11 256; chromosome = 15q26.1). The predicted expression of the CDC42BPB gene in the brain (basal ganglia) (effect, 0.14; P = 2.7 × 10-03) and of ARHGEF3 in fibroblasts (effect, -0.48; P = 9.8 × 10-04) was associated with major depression. This study identifies 3 methylated sites associated with depressive symptoms. All 3 findings point toward axon guidance as the common disrupted pathway in depression. The findings provide new insights into the molecular mechanisms underlying the complex pathophysiology of depression. Further research is warranted to determine the utility of these findings as biomarkers of depression and evaluate any potential role in the pathophysiology of depression and their downstream clinical effects.

Background: Maternal smoking during pregnancy is associated with significant infant morbidity and mortality, and may influence later disease risk. One mechanism by which smoking (and other environmental factors) might have long-lasting effects is through epigenetic modifications such as DNA methylation.Objectives: We conducted an epigenome-wide association study (EWAS) investigating alterations in DNA methylation in infants exposed in utero to maternal tobacco smoke, using the Norway Facial Clefts Study.Methods: The Illumina HumanMethylation450 BeadChip was used to assess DNA methylation in whole blood from 889 infants shortly after delivery. Of 889 mothers, 287 reported smoking—twice as many smokers as in any previous EWAS of maternal smoking. CpG sites related to maternal smoking during the first trimester were identified using robust linear regression.Results: We identified 185 CpGs with altered methylation in infants of smokers at genome-wide significance (q-value < 0.05; mean Δβ = ± 2%). These correspond to 110 gene regions, of which 7 have been previously reported and 10 are newly confirmed using publicly available results. Among these 10, the most noteworthy are FRMD4A, ATP9A, GALNT2, and MEG3, implicated in processes related to nicotine dependence, smoking cessation, and placental and embryonic development.Conclusions: Our study identified 10 genes with newly established links to maternal smoking. Further, we note differences between smoking-related methylation changes in newborns and adults, suggesting possible distinct effects of direct versus indirect tobacco smoke exposure as well as potential differences due to age. Further work would be needed to determine whether these small changes in DNA methylation are biologically or clinically relevant. The methylation changes identified in newborns may mediate the association between in utero maternal smoking exposure and later health outcomes.Citation: Markunas CA, Xu Z, Harlid S, Wade PA, Lie RT, Taylor JA, Wilcox AJ. 2014. Identification of DNA methylation changes in newborns related to maternal smoking during pregnancy. Environ Health Perspect 122:1147–1153; http://dx.doi.org/10.1289/ehp.1307892

Early patterning of DNA methylation (DNAm) may play an important role in later disease development. To better understand intergenerational epigenetic inheritance, we investigated the correlation between DNAm in blood in mother-newborn and in father-newborn pairs in the Isle of Wight (IoW) birth cohort. For parent-newborn pairs (n = 48), offspring DNAm was measured in cord blood and the parent’s DNAm in whole blood. Mothers’ DNAm was analyzed at birth (Guthrie card), age 18, early and late pregnancy respectively, and fathers’ DNAm was measured during the mother’s pregnancy. Linear regressions were applied to assess the intergenerational correlation of parental DNAm with that of offspring. Among various pairs of mother-newborn and father-newborn DNAm, the pairs where the mothers’ DNAm was measured at age 18 years exhibited the highest number of CpGs with significant intergenerational correlation in DNAm, with 1829 CpGs (0.54%) of the 338,526 CpGs studied (FDR < 0.05). Amongst these 1829 CpGs, 986 (54%) are known quantitative trait loci (QTL) for CpG methylation (methQTL). When the mother’s DNAm was assessed at early pregnancy, the number of CpGs showing intergenerational correlation was the smallest (384 CpGs, 0.11%). The second smallest number of such CpGs (559 CpGs, 0.17%) was found when investigating DNAm in offspring cord blood and father pairs. The low proportions of intergenerationally correlated CpGs suggest that epigenetic inheritance is limited.

<b>Introduction:</b> Asthma affects African Americans disproportionally. Although the contribution of DNA methylation (DNAm) to asthma has been explored, epigenome-wide association studies (EWAS) in African Americans are scarce. <b>Aim:</b> To identify CpG sites and processes with differential methylation patterns in whole blood associated with asthma in African American children. <b>Methods:</b> We performed an EWAS in 250 patients with asthma and 233 healthy subjects from the Study of Asthma, Genes and the Environment (SAGE). Whole-blood DNAm was profiled with the Illumina EPIC array. The association of DNAm at 802,185 CpGs and asthma was tested via robust linear regression models adjusted by age, sex, ancestry, and tissue heterogeneity. An empirical genome-wide significance threshold of p&lt;9x10^-8 was adopted and enrichment analysis was performed for probes with a false discovery rate (FDR)&lt;5%. <b>Results:</b> Participants’ mean age was 15.1±3.9 years, and 49.7% were females. Nine CpGs were genome-wide significantly associated with asthma, which were annotated to genes participating in airway remodelling, inflammation, immunoregulation, and corticosteroid response (e.g., <i>CCL4</i>, <i>MAPK1</i>, <i>GLCCI1</i>, and <i>GRAMD3</i>). Based on 154 probes with FDR&lt;5%, significant enrichment was found for chemokine signalling pathway, viral protein interaction, and previous EWAS associations, such as smoking, nitrogen dioxide, and fractional exhaled nitric oxide. <b>Conclusions:</b> We identified several DNAm markers associated with paediatric asthma among African Americans related to key asthma processes and environmental exposures. Supported by NIH R01HL155024, R01MD010443, R56MD013312 and MCIN/AEI/10.13039/501100011033 PID2020-116274RB-I00.

BackgroundBetween 1962 and 1971, the US Air Force sprayed Agent Orange across Vietnam, exposing many soldiers to this dioxin-containing herbicide. Several negative health outcomes have been linked to Agent Orange exposure, but data is lacking on the effects this chemical has on the genome. Therefore, we sought to characterize the impact of Agent Orange exposure on DNA methylation in the whole blood and adipose tissue of veterans enrolled in the Air Force Health Study (AFHS).MethodsWe received adipose tissue (n = 37) and whole blood (n = 42) from veterans in the AFHS. Study participants were grouped as having low, moderate, or high TCDD body burden based on their previously measured serum levels of dioxin. DNA methylation was assessed using the Illumina 450 K platform.ResultsEpigenome-wide analysis indicated that there were no FDR-significantly methylated CpGs in either tissue with TCDD burden. However, 3 CpGs in the adipose tissue (contained within SLC9A3, LYNX1, and TNRC18) were marginally significantly (q < 0.1) hypomethylated, and 1 CpG in whole blood (contained within PTPRN2) was marginally significantly (q < 0.1) hypermethylated with high TCDD burden. Analysis for differentially methylated DNA regions yielded SLC9A3, among other regions in adipose tissue, to be significantly differentially methylated with higher TCDD burden. Comparing whole blood data to a study of dioxin exposed adults from Alabama identified a CpG within the gene SMO that was hypomethylated with dioxin exposure in both studies.ConclusionWe found limited evidence of dioxin associated DNA methylation in adipose tissue and whole blood in this pilot study of Vietnam War veterans. Nevertheless, loci in the genes of SLC9A3 in adipose tissue, and PTPRN2 and SMO in whole blood, should be included in future exposure analyses.

Bronchial asthma is a common chronic airway disease marked by reversible obstruction and bronchial hyperresponsiveness. Effective management relies on patient understanding of the condition and available treatments. This study aimed to assess awareness of asthma risk factors, exacerbations, and disease severity among the population in the Jazan region of Saudi Arabia. A cross-sectional observational study was conducted through social media platforms, targeting individuals from various cities in the Jazan region. A total of 633 participants completed structured questionnaires designed to assess their knowledge of asthma and its environmental risk factors. Data were analyzed using Statistical Package for the Social Sciences software. Out of the 633 participants, 506 (79.9%) demonstrated good awareness of the relationship between environmental risk factors and asthma exacerbations, while 127 (20.1%) exhibited poor awareness. Nearly all participants (99.2%) had prior knowledge of asthma, and 437 (69%) were aware of the link between environmental factors and exacerbations, making efforts to reduce exposure. House dust mites were identified as the most frequently reported cause of asthma exacerbations (69.5%), followed by respiratory infections (67.1%). A significant association was found between educational level and awareness of asthma’s environmental triggers (P = .020), with participants holding bachelor’s and diploma degrees showing higher levels of awareness compared to other educational groups. The overall level of awareness regarding environmental risk factors associated with asthma exacerbations was satisfactory, though gaps remain in understanding specific triggers such as respiratory infections, cold weather, and exercise. Educational attainment and a formal asthma diagnosis were significantly associated with greater awareness. Targeted educational interventions may help bridge these knowledge gaps, enhancing asthma management, and reducing exacerbations in the region.

1461-P: HbA1c-Independent Association between DNA Methylation (DNAm) and 28-Year Risk of Microvascular Complications in Type 1 Diabetes (T1D)

Both genome-wide association studies (GWAS) and epigenome-wide association studies (EWAS) are aiming to discover molecular signs for diseases, which possibly can be helpful for future therapeutic intervention strategies. The most prominently used tissue in association studies on humans is venous blood. In contrast to the unchangeable genotype, epigenetic DNA methylation is more variable. Methylation is affected not only by a subject's constitution such as age, gender, ethnicity, genotype, lifestyle and health status, but is also determined by tissue-specific cell types. PubMed, published before 2017, was researched, documenting the importance of epigenetic analyses on single cell types instead of whole blood in EWAS. Initial studies documented that stressor-induced, mostly marginal, DNA methylation changes in whole-blood samples (< 5% methylation difference) may rely not on uniform distribution of that methylation shift among each blood cell type, but on strongly altered methylation (> 20%) in single cell types. The effect size in single cell types enables the performance of epigenome-wide studies on replicated smaller cohorts, in contrast to the requirement of larger international consortium-based approaches. Therefore, the identification of a specific cell type that is responsible for association between DNA methylation in whole blood with the phenotype of interest, has to be a prioritized experimental approach in association studies. This is a key prerequisite for constructive interpretation of epigenetic signs in the context of diverse biological function of the tissue blood, for detection of causality link between methylation and phenotype and for establishment of valuable clinical biomarkers and therapeutic targets.

Traffic-related air pollution (TRAP) exposure is associated with negative health outcomes. Changes in DNA methylation level may be an important mechanism through which air pollution can induce its effects. The objective of this study was to evaluate the association between DNA methylation in blood and personally measured TRAP exposure. Global DNA methylation in whole blood was analyzed with HPLC in a population of 55 healthy adults (average age 41 years). TRAP was assessed for each participant with a portable aethalometer measuring black carbon (BC). Exposure measurements were collected during one typical working week. These data were used in combination with ambient levels measured at a reference site to derive subchronic BC exposure. Urinary trans,trans-muconic acid (t,t-MA), a metabolite of benzene, was used as an internal proxy of traffic exposure. DNA methylation levels were associated with short- and subchronic BC exposure. An IQR increase in BC exposure on lag 24 h (477 ng/m3), lag 48 h (491 ng/m3), lag 1 week (314 ng/m3) and subchronic exposure (618 ng/m3) were associated with a decrease in DNA methylation levels of respectively 0.0020% (− 0.0040 to − 0.0001, p = 0.047), 0.0028% (− 0.0054 to − 0.0001, p = 0.043), 0.0024% (− 0.0043 to − 0.0005, p = 0.019), and 0.025% (− 0.048 to − 0.0015, p = 0.044). In addition, an IQR increase in t,t-MA (0.135 mg/l) was associated with a 0.0021% (− 0.0033 to − 0.0008, p = 0.0019) decrease in global DNA methylation levels. Analysis of a panel of cytokines in blood samples failed to demonstrate an association between inflammatory and oxidative stress biomarkers and TRAP or DNA methylation. In a panel of healthy adults, we found negative associations between total DNA methylation and markers of TRAP exposure. Considering that change in DNA methylation concentration is a biological marker connecting environmental and lifestyle exposures and disease development trajectories, our results warrant further study.

DNA methylation has been proposed as an epigenetic mechanism by which the childhood neighborhood environment may have implications for the genome that compromise adult health. To ascertain whether childhood neighborhood socioeconomic disadvantage is associated with differences in DNA methylation by age 18 years. This longitudinal cohort study analyzed data from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally representative birth cohort of children born between 1994 and 1995 in England and Wales and followed up from age 5 to 18 years. Data analysis was performed from March 15, 2019, to June 30, 2019. High-resolution neighborhood data (indexing deprivation, dilapidation, disconnection, and dangerousness) collected across childhood. DNA methylation in whole blood was drawn at age 18 years. Associations between neighborhood socioeconomic disadvantage and methylation were tested using 3 prespecified approaches: (1) testing probes annotated to candidate genes involved in biological responses to growing up in socioeconomically disadvantaged neighborhoods and investigated in previous epigenetic research (stress reactivity-related and inflammation-related genes), (2) polyepigenetic scores indexing differential methylation in phenotypes associated with growing up in disadvantaged neighborhoods (obesity, inflammation, and smoking), and (3) a theory-free epigenome-wide association study. A total of 1619 participants (806 female individuals [50%]) had complete neighborhood and DNA methylation data. Children raised in socioeconomically disadvantaged neighborhoods exhibited differential DNA methylation in genes involved in inflammation (β = 0.12; 95% CI, 0.06-0.19; P < .001) and smoking (β = 0.18; 95% CI, 0.11-0.25; P < .001) but not obesity (β = 0.05; 95% CI, -0.01 to 0.11; P = .12). An epigenome-wide association study identified multiple CpG sites at an arraywide significance level of P < 1.16 × 10-7 in genes involved in the metabolism of hydrocarbons. Associations between neighborhood disadvantage and methylation were small but robust to family-level socioeconomic factors and to individual-level tobacco smoking. Children raised in more socioeconomically disadvantaged neighborhoods appeared to enter young adulthood epigenetically distinct from their less disadvantaged peers. This finding suggests that epigenetic regulation may be a mechanism by which the childhood neighborhood environment alters adult health.

Pregnancy exposure to atmospheric pollution and meteorological conditions and placental DNA methylation

Anxiety disorders (ANX) are a prevalent public health burden that significantly impair daily functioning and decrease quality of life. A growing body of research suggests that DNA methylation (DNAm), an epigenetic modification that can impact gene expression, may be altered in ANX. The current review used a systematic approach to identify and synthesize the literature regarding methylome-wide association studies (MWASs) of ANX in humans. We screened 804 articles returned by a search in PubMed in May 2025 and identified 12 studies for inclusion. All included studies examined ANX-associated DNAm in blood. In total, 2,023 DNAm sites corresponding to 985 genes were significantly associated with ANX. No DNAm sites significantly replicated across studies and four nominally replicated. This is likely a result of a lack of replication attempts, small sample sizes, and differences in data analysis choices. Findings suggest that ANX-associated DNAm may promote dysregulation of immune and inflammatory processes, some possibly sex-dependent. Collectively, the findings from studies included in this review provide preliminary evidence of ANX-related alterations to DNAm in whole blood and multiple blood cell-types. Future MWASs of ANX could benefit from larger sample sizes, a standardized analytic pipeline, longitudinal study designs, and the examination of DNAm in additional cell-types and tissues.