Epigenetic Loci Research Articles

Mapping DNA Methylation to Cardiac Pathologies Induced by Beta-Adrenergic Stimulation in a Large Panel of Mice.

Heart failure (HF) is a leading cause of morbidity and mortality worldwide, with over 18 million deaths annually. Despite extensive research, genetic and environmental factors contributing to HF remain complex and poorly understood. Recent studies suggest that epigenetic modifications, such as DNA methylation, may play a crucial role in regulating HF-associated phenotypes. In this study, we leverage the Hybrid Mouse Diversity Panel (HMDP), a cohort of over 100 inbred mouse strains, to investigate the role of DNA methylation in HF progression. We aim to identify epigenetic modifications associated with HF by integrating DNA methylation data with gene expression and phenotypic traits. Using isoproterenol (ISO)-induced cardiac hypertrophy and failure in HMDP mice, we explore the relationship between methylation patterns and HF susceptibility. We performed reduced representational bisulfite sequencing (RRBS) to capture DNA methylation at single-nucleotide resolution in the left ventricles of 90 HMDP mouse strains under both control and ISO-treated conditions. We identified differentially methylated regions (DMRs) and performed an epigenome-wide association study (EWAS) using the MACAU algorithm. We identified likely candidate genes within each locus through integration of our results with previously reported sequence variation, gene expression, and HF-related phenotypes. In vitro approaches were employed to validate key findings, including gene knockdown experiments in neonatal rat ventricular myocytes (NRVMs). We also examined the effects of preventing DNA methyltransferase activity on HF progression. Our EWAS identified 56 CpG loci significantly associated with HF phenotypes, including 18 loci where baseline DNA methylation predicted post-ISO HF progression. Key candidate genes, such as Prkag2, Anks1, and Mospd3, were identified based on their epigenetic regulation and association with HF traits. In vitro follow-up on a number of genes confirmed that knockdown of Anks1 and Mospd3 in NRVMs resulted in significant alterations in cell size and blunting of ISO-induced hypertrophy, demonstrating their functional relevance in HF pathology.Furthermore, treatment with the DNA methyltransferase inhibitor RG108 in ISO-treated BTBRT mice significantly reduced cardiac hypertrophy and preserved ejection fraction compared to mice only treated with ISO, highlighting the therapeutic potential of targeting DNA methylation in HF. Differential expression analysis revealed that RG108 treatment restored the expression of several methylation-sensitive genes, further supporting the role of epigenetic regulation in HF. Our study demonstrates a clear interplay between DNA methylation, gene expression, and HF-associated phenotypes. We identified several novel epigenetic loci and candidate genes that contribute to HF progression, offering new insights into the molecular mechanisms of HF. These findings underscore the importance of epigenetic regulation in cardiac disease and suggest potential therapeutic strategies for modifying HF outcomes through targeting DNA methylation.

Environmental conditions modulate the effect of epigenetic factors controlling the response of Arabidopsis thaliana to Plasmodiophora brassicae.

The resistance of Arabidopsis thaliana to clubroot, a major disease of Brassicaceae caused by the obligate protist Plasmodiophora brassicae, is controlled in part by epigenetic factors. The detection of some of these epigenetic quantitative trait loci (QTLepi) has been shown to depend on experimental conditions. The aim of the present study was to assess whether and how temperature and/or soil water availability influenced both the detection and the extent of the effect of response QTLepi. The epigenetic recombinant inbred line (epiRIL) population, derived from the cross between ddm1-2 and Col-0 (partially resistant and susceptible to clubroot, respectively), was phenotyped for response to P. brassicae under four abiotic conditions including standard conditions, a 5°C temperature increase, drought, and flooding. The abiotic constraints tested had a significant impact on both the leaf growth of the epiRIL population and the outcome of the epiRIL-pathogen interaction. Linkage analysis led to the detection of a total of 31 QTLepi, 18 of which were specific to one abiotic condition and 13 common to at least two environments. EpiRIL showed significant plasticity under epigenetic control, which appeared to be specific to the traits evaluated and to the abiotic conditions. These results highlight that the environment can affect the epigenetic architecture of plant growth and immune responses and advance our understanding of the epigenetic factors underlying plasticity in response to climate change.

Neuroimaging and epigenetic analysis reveal novel epigenetic loci in major depressive disorder.

Epigenetic modifications, such as DNA methylation, contribute to the pathophysiology of major depressive disorder (MDD). This study aimed to identify novel MDD-associated epigenetic loci using DNA methylation profiles and explore the correlations between epigenetic loci and cortical thickness changes in patients with MDD. A total of 350 patients with MDD and 161 healthy controls (HCs) were included in the epigenome-wide association studies (EWAS). We analyzed methylation, copy number alteration (CNA), and gene network profiles in the MDD group. A total of 234 patients with MDD and 135 HCs were included in neuroimaging methylation analysis. Pearson's partial correlation analysis was used to estimate the correlation between cortical thickness of brain regions and DNA methylation levels of the loci. In total, 2018 differentially methylated probes (DMPs) and 351 differentially methylated regions (DMRs) were identified. DMP-related genes were enriched in two networks involved in the central nervous system. In neuroimaging analysis, patients with MDD showed cortical thinning in the prefrontal regions and cortical thickening in several occipital regions. Cortical thickness of the left ventrolateral prefrontal cortex (VLPFC, i.e. pars triangularis) was negatively correlated with eight DMPs associated with six genes (EML6, ZFP64, CLSTN3, KCNMA1, TAOK2, and NT5E). Through combining DNA methylation and neuroimaging analyses, negative correlations were identified between the cortical thickness of the left VLPFC and DNA methylation levels of eight DMPs. Our findings could improve our understanding of the pathophysiology of MDD.

Climate-related naturally occurring epimutation and their roles in plant adaptation in A. thaliana.

DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.

Disruption of the Uty epigenetic regulator locus in hematopoietic cells phenocopies the profibrotic attributes of Y chromosome loss in heart failure.

Heart failure affects millions of people worldwide, with men exhibiting a higher incidence than women. Our previous work has shown that mosaic loss of the Y chromosome (LOY) in leukocytes is causally associated with an increased risk for heart failure. Here, we show that LOY macrophages from the failing hearts of humans with dilated cardiomyopathy exhibit widespread changes in gene expression that correlate with cardiac fibroblast activation. Moreover, we identify the ubiquitously transcribed t et ratricopeptide Y-linked (Uty) gene in leukocytes as a causal locus for an accelerated progression of heart failure in male mice with LOY. We demonstrate that Uty disruption leads to epigenetic alterations in both monocytes and macrophages, increasing the propensity of differentiation into profibrotic macrophages. Treatment with a transforming growth factor-β-neutralizing antibody prevented the cardiac pathology associated with Uty deficiency in leukocytes. These findings shed light on the mechanisms that contribute to the higher incidence of heart failure in men.

Comparing feature selection and machine learning approaches for predicting CYP2D6 methylation from genetic variation.

Pharmacogenetics currently supports clinical decision-making on the basis of a limited number of variants in a few genes and may benefit paediatric prescribing where there is a need for more precise dosing. Integrating genomic information such as methylation into pharmacogenetic models holds the potential to improve their accuracy and consequently prescribing decisions. Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene conventionally associated with the metabolism of commonly used drugs and endogenous substrates. We thus sought to predict epigenetic loci from single nucleotide polymorphisms (SNPs) related to CYP2D6 in children from the GUSTO cohort. Buffy coat DNA methylation was quantified using the Illumina Infinium Methylation EPIC beadchip. CpG sites associated with CYP2D6 were used as outcome variables in Linear Regression, Elastic Net and XGBoost models. We compared feature selection of SNPs from GWAS mQTLs, GTEx eQTLs and SNPs within 2 MB of the CYP2D6 gene and the impact of adding demographic data. The samples were split into training (75%) sets and test (25%) sets for validation. In Elastic Net model and XGBoost models, optimal hyperparameter search was done using 10-fold cross validation. Root Mean Square Error and R-squared values were obtained to investigate each models' performance. When GWAS was performed to determine SNPs associated with CpG sites, a total of 15 SNPs were identified where several SNPs appeared to influence multiple CpG sites. Overall, Elastic Net models of genetic features appeared to perform marginally better than heritability estimates and substantially better than Linear Regression and XGBoost models. The addition of nongenetic features appeared to improve performance for some but not all feature sets and probes. The best feature set and Machine Learning (ML) approach differed substantially between CpG sites and a number of top variables were identified for each model. The development of SNP-based prediction models for CYP2D6 CpG methylation in Singaporean children of varying ethnicities in this study has clinical application. With further validation, they may add to the set of tools available to improve precision medicine and pharmacogenetics-based dosing.

Maternal ploidy shapes reproductive pathways in the triploid hybrid Chrosomus eos × eos-neogaeus.

Elements transferred from a mother to her eggs may strongly influence the phenotype of her offspring. Such maternal effects depend on the genotype of the mother, and while multiple ploidy levels occur naturally in some vertebrate species, studies evaluating the impact of maternal ploidy on offspring are scarce. This paper aimed to test whether maternal ploidy is responsible for the two reproductive phenotypes observed in the triploid fish Chrosomus eos × eos-neogaeus. Indeed, these hybrids have two different maternal origins (diploid or triploid) and display two reproductive phenotypes, ameiotic and meiotic hybridogenesis, resulting in diploid and haploid eggs, respectively. To this end, we first conducted a genomic survey to identify epigenetic variations in triploid larvae reared under common garden conditions, concordantly with their maternal origin. The results revealed that the polymorphic epigenetic loci of the larvae clustered into two highly distinct groups consistently with the ploidy of their mother. Diagnostic epigenetic loci were then tested in triploid adult females whose reproductive pathways were already known, to infer their own maternal origin. Altogether, the results suggest that triploid larvae from diploid and triploid mothers will develop the ameiotic and meiotic hybridogenesis pathway, respectively. This confirms that the development of a given reproductive pathway in triploid females results from the ploidy of their mother. Overall, this study supports a strong maternal effect, introducing maternal ploidy and reproductive pathways as additional cause and effect of maternal effects, respectively.

Epigenomic and epigenetic investigations of food allergy.

As a potential link between genetic predisposition, environmental exposures, and food allergy outcomes, epigenetics has been a molecular variable of interest in ongoing efforts to understand food allergy mechanisms and outcomes. Here we review population-based investigations of epigenetic loci associated with food allergy, focusing on established clinical food allergy. We first provide an overview of epigenetic mechanisms that have been studied in cohorts with food allergy, predominantly DNA methylation but also microRNA. We then discuss investigations that have implemented epigenome-wide approaches aimed at genome-wide profiling and discovery. Such epigenome-wide studies have collectively identified differentially methylated and differentially regulated loci associated with T cell development, antigen presentation, reaction severity, and causal mediation in food allergy. We then discuss candidate-gene investigations that have honed in on Th1, Th2, T regulatory, and innate genes of a priori interest in food allergy. These studies have highlighted methylation changes in specific candidate genes as associated with T regulatory cell activity as well as differential methylation of Type 1 and Type 2 cytokine genes associated with various food allergies. Intriguingly, epigenetic loci associated with food allergy have also been explored as potential biomarkers for the clinical management of food allergy. We conclude by highlighting several priority directions for advancing population-based epigenomic and epigenetic understandings of food allergy.

Associations between Epigenetic Age Acceleration and Psychoneurological Symptoms in Sickle Cell Disease

Introduction: Sickle cell disease (SCD) affects approximately 100,000 predominantly Black or African American individuals in the United States. The disease has several acute and chronic complications that lead to a reduced median lifespan of 42 years, which is significantly shorter than the general US population. In this shortened lifespan, people experience deleterious psychoneurological symptoms including pain, sleep disturbances, depressive symptoms, and cognitive impairment. The high occurrence of these symptoms has negative effects on quality of life and function, and contributes to health disparities in this population. Evidence suggests a person's epigenetic age may be associated with inter-individual variability in psychoneurological symptoms in SCD. Epigenetic age is a promising biomarker because it reflects the cumulative effects of exposures to stressors at the psychosocial, physical and environmental level, by capturing the molecular processes occurring with declining tissue function through globally assessing DNA methylation patterns that account for the pace of cellular aging. Epigenetic age and age acceleration in relation to disease characteristics and symptom burden has been assessed in several chronic conditions such as cancer, obesity and Alzheimer's. None have assessed this association in SCD. To address this gap, our study aims to determine whether epigenetic age acceleration is associated with psychoneurological symptom burden (pain impact, emotional impact, sleep impact, and cognition) in SCD. Methods: Psychoneurological symptoms and DNA methylation were assessed in a subset of participants aged between 18 - 45 years enrolled in one of the Sickle Cell Disease Implementation Consortium sites. DNA methylation data were generated on the Infinium MethylationEPIC beadchip (Illumina) from the extracted DNA of blood specimens and used to calculate epigenetic age using five epigenetic clocks (Horvath, Hannum, PhenoAge, GrimAge, & DunedinPACE). Psychoneurological symptoms were evaluated using validated instruments: the Adult Sickle Cell Quality of Life Measurement Information System (ASCQ-Me), and Quality of Life in Neurological Disorders (NeuroQoL). Data were converted to T-scores and were used to determine associations with epigenetic age acceleration for each of the epigenetic clocks. Higher T-scores in ASCQ-Me and NeuroQoL indicate more desirable (better) outcomes. Results: Among participants (n=89) included in the analysis, the mean (SD) chronologic age was 30.6 (8.0) years. A majority identified as female (60.7%), non-Hispanic Black or African American (92%), never married (76.4%), had Hb SS genotype (68.5%), were taking hydroxyurea (60.5%), and had at least 4 pain events in past year (53.5%). Two epigenetic clocks showed mean age acceleration (Horvath: 0.2 ±4.6 years; GrimAge: 12.6 ±4.0 years, whereas two clocks showed mean age deceleration (Hannum: -4.27 ±3.91 years; PhenoAge: -8.43 ±6.0 years). The DunedinPACE clock is on a different scale than other clocks, but also demonstrated evidence for accelerated aging whereby the epigenetic age increased 1.14 years for every chronologic year. Increased age acceleration was associated with worse pain impact scores (GrimAge β=-0.25, p= 0.02), worse emotional impact scores (GrimAge β=-0.24, p=0.03; Dunedin β= -0.30, p=0.01) greater sleep disturbance (Dunedin β=-0.22, p=0.04) and more depressive symptoms (Dunedin β=0.29, p=0.01) (Table 1). Conclusion: This was the first study, to our knowledge, that explored the relationship between epigenetic age and psychoneurological symptoms in SCD. Epigenetic age acceleration was associated with worse symptom scores. Our preliminary findings identified several variations in the associations between symptom outcomes and epigenetic age across the five clocks. These variations may be due to the differences in the models used to develop the clocks, as well as inherent differences in epigenetic loci used to calculate epigenetic age for each clock. Future assessment of those discrepancies is warranted to effectively characterize individuals at higher risk of age acceleration and higher symptom burden in SCD. Our findings also highlight the potential use of epigenetic age acceleration as a biological target for interventions aimed towards preventing age acceleration and symptom development, improving the quality of life of individuals with SCD.

Epigenetic Gene-Regulatory Loci in Alu Elements Associated with Autism Susceptibility in the Prefrontal Cortex of ASD.

Alu elements are transposable elements that can influence gene regulation through several mechanisms; nevertheless, it remains unclear whether dysregulation of Alu elements contributes to the neuropathology of autism spectrum disorder (ASD). In this study, we characterized transposable element expression profiles and their sequence characteristics in the prefrontal cortex tissues of ASD and unaffected individuals using RNA-sequencing data. Our results showed that most of the differentially expressed transposable elements belong to the Alu family, with 659 loci of Alu elements corresponding to 456 differentially expressed genes in the prefrontal cortex of ASD individuals. We predicted cis- and trans-regulation of Alu elements to host/distant genes by conducting correlation analyses. The expression level of Alu elements correlated significantly with 133 host genes (cis-regulation, adjusted p < 0.05) associated with ASD as well as the cell survival and cell death of neuronal cells. Transcription factor binding sites in the promoter regions of differentially expressed Alu elements are conserved and associated with autism candidate genes, including RORA. COBRA analyses of postmortem brain tissues showed significant hypomethylation in global methylation analyses of Alu elements in ASD subphenotypes as well as DNA methylation of Alu elements located near the RNF-135 gene (p < 0.05). In addition, we found that neuronal cell density, which was significantly increased (p = 0.042), correlated with the expression of genes associated with Alu elements in the prefrontal cortex of ASD. Finally, we determined a relationship between these findings and the ASD severity (i.e., ADI-R scores) of individuals with ASD. Our findings provide a better understanding of the impact of Alu elements on gene regulation and molecular neuropathology in the brain tissues of ASD individuals, which deserves further investigation.

DNA Methylation Analysis Identifies Novel Epigenetic Loci in Dilated Murine Heart upon Exposure to Volume Overload

Left ventricular (LV) dilatation, a prominent risk factor for heart failure (HF), precedes functional deterioration and is used to stratify patients at risk for arrhythmias and cardiac mortality. Aberrant DNA methylation contributes to maladaptive cardiac remodeling and HF progression following pressure overload and ischemic cardiac insults. However, no study has examined cardiac DNA methylation upon exposure to volume overload (VO) despite being relatively common among HF patients. We carried out global methylome analysis of LV harvested at a decompensated HF stage following exposure to VO induced by aortocaval shunt. VO resulted in pathological cardiac remodeling, characterized by massive LV dilatation and contractile dysfunction at 16 weeks after shunt. Although methylated DNA was not markedly altered globally, 25 differentially methylated promoter regions (DMRs) were identified in shunt vs. sham hearts (20 hypermethylated and 5 hypomethylated regions). The validated hypermethylated loci in Junctophilin-2 (Jph2), Signal peptidase complex subunit 3 (Spcs3), Vesicle-associated membrane protein-associated protein B (Vapb), and Inositol polyphosphate multikinase (Ipmk) were associated with the respective downregulated expression and were consistently observed in dilated LV early after shunt at 1 week after shunt, before functional deterioration starts to manifest. These hypermethylated loci were also detected peripherally in the blood of the shunt mice. Altogether, we have identified conserved DMRs that could be novel epigenetic biomarkers in dilated LV upon VO exposure.

The impact of alcoholic drinks and dietary factors on epigenetic markers associated with triglyceride levels.

Background: Many epigenetic loci have been associated with plasma triglyceride (TG) levels, but epigenetic connections between those loci and dietary exposures are largely unknown. This study aimed to characterize the epigenetic links between diet, lifestyle, and TG. Methods: We first conducted an epigenome-wide association study (EWAS) for TG in the Framingham Heart Study Offspring population (FHS, n = 2,264). We then examined relationships between dietary and lifestyle-related variables, collected four times in 13years, and differential DNA methylation sites (DMSs) associated with the last TG measures. Third, we conducted a mediation analysis to evaluate the causal relationships between diet-related variables and TG. Finally, we replicated three steps to validate identified DMSs associated with alcohol and carbohydrate intake in the Genetics of Lipid-Lowering Drugs and Diet Network (GOLDN) study (n = 993). Results: In the FHS, the EWAS revealed 28TG-associated DMSs at 19 gene regions. We identified 102 unique associations between these DMSs and one or more dietary and lifestyle-related variables. Alcohol and carbohydrate intake showed the most significant and consistent associations with 11TG-associated DMSs. Mediation analyses demonstrated that alcohol and carbohydrate intake independently affect TG via DMSs as mediators. Higher alcohol intake was associated with lower methylation at seven DMSs and higher TG. In contrast, increased carbohydrate intake was associated with higher DNA methylation at two DMSs (CPT1A and SLC7A11) and lower TG. Validation in the GOLDN further supports the findings. Conclusion: Our findings imply that TG-associated DMSs reflect dietary intakes, particularly alcoholic drinks, which could affect the current cardiometabolic risk via epigenetic changes. This study illustrates a new method to map epigenetic signatures of environmental factors for disease risk. Identification of epigenetic markers of dietary intake can provide insight into an individual's risk of cardiovascular disease and support the application of precision nutrition. Clinical Trial Registration: www.ClinicalTrials.gov, the Framingham Heart Study (FHS), NCT00005121; the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN), NCT01023750.

(Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions.

Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (Ciona intestinalis) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of divergent selection. In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating the strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, Gene Ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.

Hypomethylation of miR-17-92 cluster in lupus T cells and no significant role for genetic factors in the lupus-associated DNA methylation signature

ObjectivesLupus T cells demonstrate aberrant DNA methylation patterns dominated by hypomethylation of interferon-regulated genes. The objective of this study was to identify additional lupus-associated DNA methylation changes and determine the...

GH Responsiveness Is not Correlated to IGF1 P2 Promoter Methylation in Children With Turner Syndrome, GHD and SGA Short Stature.

BackgroundThe methylation of IGF1 promoter P2 was reported to negatively correlate with serum IGF-1 concentration and rhGH treatment response in children with idiopathic short stature. These findings have not yet been confirmed.ObjectiveThis study aimed to determine IGF1 promoter P2 methylation in short children treated with rhGH and correlate clinical parameters with the methylation status. In addition, long-term stability of methylation during rhGH treatment was studied.DesignThis was a single tertiary center study analyzing clinical GH response and IGF-1 serum concentration changes in patients with GHD (n=40), SGA short stature (n=36), and Turner syndrome (n=16) treated with rhGH. Data were correlated to the methylation of two cytosine residues (-137, +97) of the P2 promoter of IGF1 in blood cells measured by pyrosequencing in 443 patient samples.ResultsBasal and stimulated IGF-1 concentrations, first year increment in height velocity and studentized residuals of a prediction model did not correlate to the methylation of -137 und +97 in IGF1 P2 promoter. The methylation of these two sites was relatively stable during treatment.ConclusionsThis study did not confirm IGF1 P2 promotor being a major epigenetic locus for GH responsiveness in patients treated with a normal dose of rhGH. Additional studies are warranted.

Triglyceride-Associated Epigenetic Markers and Diet and Lifestyle Habits in the Framingham Heart Study

ObjectivesThe current evidence has shown that environmental and lifestyle factors (e.g., diet, physical activity, tobacco smoking, alcohol) are associated with DNA methylation patterns. However, the mechanisms underlying the relation between diet and other exposures and epigenetic profiles are not well understood. To reduce such knowledge gap, we investigated the links between lifestyle, including diet, and methylation marks with plasma triglyceride concentrations (TG).MethodsWe first conducted an epigenome-wide association study (EWAS) (Illumina HumanMethylation450 BeadChip) for TG in the Framingham Heart Study Offspring population (n = 2,178). We then examined the relationships between dietary and lifestyle-related variables, collected over 13 years, and differential DNA methylation marks associated with the last TG measures (exam 8). Second, we conducted a mediation analysis to examine the potential causal relationship between diet-related variables and TG.ResultsThe EWAS analyses revealed 28 TG-associated DNA methylation sites at 19 regions (e.g., ABCG1, CPT1A, DHCR24, PHGDH, SLC7A11, SLC43A1, SREBF1, TXNIP). Within those methylation sites, we identified 427 significant associations between these DNA methylation sites and one or more dietary and lifestyle-related variables after accounting for multiple testing. The two most significant and consistent associations between TG-associated DNA methylation markers and diet were alcohol (g/day) and carbohydrate intake (% total energy), with P-values ranging from 10^(−4) to 10^(−56). Mediation analyses demonstrated that alcohol and carbohydrate intake independently affect TG via DNA methylation markers as mediators. For seven of the 19 identified differential DNA-methylation regions, higher alcohol intake was associated with decreased methylation and higher TG. In contrast, increased carbohydrate intake was associated with higher DNA methylation at two epigenetic loci (CPT1A and SLC7A11) and lower TG.ConclusionsOur findings indicate that dietary factors (i.e., alcohol and carbohydrate) are associated with specific DNA methylation markers that could mediate some of the observed associations between diet and cardiometabolic risk factors.Funding SourcesThis work was funded by the US Department of Agriculture, under agreement no. 8050-51,000-107-000D.

Complementary genomic and epigenomic adaptation to environmental heterogeneity.

While adaptation is commonly thought to result from selection on DNA sequence-based variation, recent studies have highlighted an analogous epigenetic component as well. However, the relative roles of these mechanisms in facilitating population persistence under environmental heterogeneity remain unclear. To address the underlying genetic and epigenetic mechanisms and their relationship during environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, Botryllus schlosseri. We detected clear population differentiation at the genetic and epigenetic levels. Patterns of genetic and epigenetic structure were significantly influenced by local environmental variables. Among these variables, minimum annual sea surface temperature was identified as the top explanatory variable for both genetic and epigenetic variation. However, patterns of population structure driven by genetic and epigenetic variation were somewhat distinct, suggesting possible autonomy of epigenetic variation. We found both shared and specific genes and biological pathways among genetic and epigenetic loci associated with environmental factors, consistent with complementary and independent contributions of genetic and epigenetic variation to environmental adaptation in this system. Collectively, these mechanisms may facilitate population persistence under environmental change and sustain successful invasions across novel environments.

Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure

Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.

Abstract P178: Methylation Sites Associated With Cumulative Socioeconomic Status And Body Mass Index Among African American Adults From The Atherosclerosis Risk In Communities Study

Background: Obesity increases the risk of multiple morbidities and is patterned by socioeconomic status (SES). Lower SES is associated with greater burden of obesity, especially among African American adults. Epigenetic research has provided novel insights into human biology and health; however, few studies have examined whether epigenetic loci mediate the association between SES and obesity. Objective: We sought to determine the union of epigenetic sites associated with cumulative SES and body mass index (BMI) among African American adults from the Atherosclerosis Risk in Communities (ARIC) study, and to examine differences by sex. Hypothesis: Several Cytosine-phosphate-guanine (CpG) sites will be associated with both cumulative SES and BMI, which will provide suggestive evidence of epigenetic mechanisms mediating the association between SES and obesity. Also, sex differences will be detected. Methods: Methylation data from venous blood of 2,684 African American adults (1702 women, 982 men) in the ARIC study (mean age 56.61) was collected from either visit 2 (1990-1992) or visit 3 (1993-1995) using the Illumina HumanMethylation 450k array. For each participant, we created a cumulative SES score comprised of education, income, and occupation from visit 1 (1987-1989). Each SES indicator had 3 categories, which were given a score of 0 (low), 0.5 (medium), or 1 (high), then all SES indicator scores were summed (mean 1.47, SD 0.76, range: 0-3). BMI values (mean 30.12, SD 6.26, range 14.68-62.35) from the same visit as the methylation typing, were then inverse rank normalized. Linear regression analyses were used to test the association of cumulative SES scores and the association of BMI residuals with CpG sites, respectively. Analyses were stratified by sex and combined using inverse variance fixed-effect meta-analysis. The final model adjusted for age, age 2 , alcohol use, smoking, genetic principal components and time between visits. Statistical significance was determined as p &lt;2X10 -7 . Results: Among men and women combined, 3,843 CpG sites were associated with cumulative SES and 212 CpG sites were associated with BMI. Thirty (n=30) CpG sites were statistically significant for both cumulative SES and BMI. Of the 30 sites, 15 sites were previously identified in epigenetic studies of obesity/BMI, and 11 sites were previously identified for other cardiometabolic traits. Sites were statistically more significant among women. Conclusion: Our findings suggest shared patterns of epigenetic variation between SES and BMI and differences by sex. As a follow up, we will replicate our study findings in other cohort studies and test the hypothesis that the effect of SES on obesity is mediated through methylation. Indeed, such findings could reveal how SES gets “under the skin” to influence obesity. Such knowledge could help us better identify therapeutic targets for intervention.

Genome- and epigenome-wide studies of plasma protein biomarkers for Alzheimer's disease implicate TBCA and TREM2 in disease risk.

IntroductionThe levels of many blood proteins are associated with Alzheimer's disease (AD) or its pathological hallmarks. Elucidating the molecular factors that control circulating levels of these proteins may help to identify proteins associated with disease risk mechanisms.MethodsGenome‐wide and epigenome‐wide studies (nindividuals ≤1064) were performed on plasma levels of 282 AD‐associated proteins, identified by a structured literature review. Bayesian penalized regression estimated contributions of genetic and epigenetic variation toward inter‐individual differences in plasma protein levels. Mendelian randomization (MR) and co‐localization tested associations between proteins and disease‐related phenotypes.ResultsSixty‐four independent genetic and 26 epigenetic loci were associated with 45 proteins. Novel findings included an association between plasma triggering receptor expressed on myeloid cells 2 (TREM2) levels and a polymorphism and cytosine‐phosphate‐guanine (CpG) site within the MS4A4A locus. Higher plasma tubulin‐specific chaperone A (TBCA) and TREM2 levels were significantly associated with lower AD risk.DiscussionOur data inform the regulation of biomarker levels and their relationships with AD.