Associations between DNA methylation and BMI vary by metabolic health status: a potential link to disparate cardiovascular outcomes

Abstract Background Body mass index (BMI), a well-known risk factor for poor cardiovascular outcomes, is associated with differential DNA methylation (DNAm). Similarly, metabolic health has also been associated with changes in DNAm. It is unclear how overall metabolic health outside of BMI may modify the relationship between BMI and methylation profiles, and what consequences this may have on downstream cardiovascular disease. The purpose of this study was to identify cytosine-phosphate-guanine (CpG) sites at which the association between BMI and DNAm could be modified by overall metabolic health. Results The discovery study population was derived from three Women’s Health Initiative (WHI) ancillary studies (n = 3977) and two Atherosclerosis Risk in Communities (ARIC) ancillary studies (n = 3520). Findings were validated in the Multi-Ethnic Study of Atherosclerosis (MESA) cohort (n = 1200). Generalized linear models regressed methylation β values on the interaction between BMI and metabolic health Z score (BMI × MHZ) adjusted for BMI, MHZ, cell composition, chip number and location, study characteristics, top three ancestry principal components, smoking, age, ethnicity (WHI), and sex (ARIC). Among the 429,566 sites examined, differential associations between BMI × MHZ and DNAm were identified at 22 CpG sites (FDR q < 0.05), with one site replicated in MESA (cg18989722, in the TRAPPC9 gene). Three of the 22 sites were associated with incident coronary heart disease (CHD) in WHI. For each 0.01 unit increase in DNAm β value, the risk of incident CHD increased by 9% in one site and decreased by 6–10% in two sites over 25 years. Conclusions Differential associations between DNAm and BMI by MHZ were identified at 22 sites, one of which was validated (cg18989722) and three of which were predictive of incident CHD. These sites are located in several genes related to NF-kappa-B signaling, suggesting a potential role for inflammation between DNA methylation and BMI-associated metabolic health.

Download Full-text

Abstract 052: Genome-wide Methylation Study of Body Mass Index (BMI) in African American Adults: Preliminary Data from the ARIC Study

Circulation ◽

10.1161/circ.127.suppl_12.a052 ◽

2013 ◽

Vol 127 (suppl_12) ◽

Author(s):

Ellen W Demerath ◽

Weihua Guan ◽

James S Pankow ◽

Megan L Grove ◽

Kari E North ◽

...

Keyword(s):

Dna Methylation ◽

African American ◽

Statistical Testing ◽

P Value ◽

Genetic Associations ◽

Cross Sectional ◽

Atherosclerosis Risk In Communities ◽

African American Adults ◽

Cpg Sites ◽

Aric Study

Background and Objective: DNA methylation patterns are influenced by environmental factors, alter gene expression, and can point to genomic regions affected by behavioral and lifestyle factors, such as obesity. However, analytic strategies for high dimensional methylation data are still evolving. Here we present preliminary analyses examining cross-sectional associations between DNA methylation level and BMI in African-American adults enrolled in the Atherosclerosis Risk in Communities (ARIC) study. Methods: BMI was measured at the same study visit as the DNA sample used for analysis. We used the Illumina Infinium HumanMethylation450 BeadChip to measure average methylation levels (beta values) in bisulfite-converted peripheral blood DNA obtained from participants from the Jackson, MS and Forsyth County, NC field centers. After excluding outlier samples and CpG sites using quality control filters, a model adjusting BMI (continuous) for batch (plate) and a model additionally adjusting for a small set of potential confounders (age, sex, center, smoking) were tested, with average beta value as the dependent variable. Robust standard errors were used for statistical testing and Bonferroni-corrected p value for significance was p<1 x 10 -7 . Results: A total of 2,873 individuals and 473,788 CpG sites entered the analysis. In the minimally-adjusted analysis, there were over 300 regions distributed across all 22 autosomes with at least one significant association between BMI and CpG methylation. Adjusting for confounders sharply reduced the evidence for association to a total of approximately 20 regions on 11 autosomes. Conclusion: Use of the 450K methylation BeadChip in large epidemiologic cohorts has potential to help identify genes that are transcriptionally altered by common behavioral factors such as obesity, leading to improved understanding of related diseases. However, whereas genetic associations with disease are generally unconfounded by demographic and other covariate factors, methylation associations can be strongly affected by selection of covariates as well as other analytic choices.

Download Full-text

EPIGENETIC ALTERATIONS ASSOCIATED WITH PREMATURE OVARIAN FAILURE

Clinical & Investigative Medicine ◽

10.25011/cim.v31i4.4804 ◽

2008 ◽

Vol 31 (4) ◽

pp. 11

Author(s):

Manda Ghahremani ◽

Courtney W Hannah ◽

Maria Peneherrera ◽

Karla L Bretherick ◽

Margo R Fluker ◽

...

Keyword(s):

Dna Methylation ◽

Premature Ovarian Failure ◽

Promoter Region ◽

Gene Promoter ◽

Ovarian Failure ◽

P Value ◽

Epigenetic Alterations ◽

Methylation Array ◽

Cpg Sites ◽

Deficient Mice

Background/Purpose: Premature ovarian failure (POF) affects 1% of women with a largely idiopathic and poorly understood etiology. The objective of this study was to identify specific epigenetic alterations by measuring DNA methylation of gene regulatory regions in women with POF vs. controls. Methods: Blood samples were collected from idiopathic POFpatients (Amenorrhea for at least 3 months and 2 serum FSH levels of > 40mIU/ml obtained > 1 month apart prior to age 40) and control women (CW) (healthy pregnancy after age 37 with out a pregnancy loss). Genomic DNA was extracted from EDTA anticoagulated blood and bisulfite converted for analysis using the Illumina Golden Gate Methylation Panel which measures DNA methylation at 1506 CpG sites in the promoter regions of 807 genes in 10 POF and 12 CW. Candidate genes with altered epigenetic marks between POF and CW at a nominal P-value < 0.05 were identified using a t-testcomparison within the Illumina bead studio software. Genes of interest were further analyzed for quantitative methylation at specific CpG sites using pyrosequencing in 30 POF and 30 CW. Results: Comparison of DNA methylation profiles of our initial POF and CW groups identified several genes with statistically significanthyper- or hypo- methylation in the POF group (P < 0.05), including the Androgen Receptor (AR)promoter region, which was significantly hypermethylated. To further validate these results, DNA methylation of the AR gene promoter was quantified bypryosequencing in a larger group of POF and CW. Pyrosequencing further confirmed a significantly higher DNA methylation of the AR promoter region inPOF vs. CW (P=0.007). Conclusions: This is a novel study identifying epigenetic alterations in POF. The hypermethylation of the AR gene in POF patients may cause decreased level of the AR in these women. This is especially interesting given a recent report of induced POF in AR deficient mice^1. Specific epigenetic markers, as identified by DNA methylation array profiling in blood, may serve as useful biomarkers for POF and other fertility disorders. However, it will need to be determined if these methylation changes are present prior to diagnosis, or are a consequence of menopause itself. Reference: 1.Hiroko S. et al. Premature ovarian failure in androgenreceptor deficient mice. PNAS;103:224-9

Download Full-text

Birthweight DNA methylation signatures in infant saliva

Clinical Epigenetics ◽

10.1186/s13148-021-01053-1 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Chiara Moccia ◽

Maja Popovic ◽

Elena Isaevska ◽

Valentina Fiano ◽

Morena Trevisan ◽

...

Keyword(s):

Dna Methylation ◽

Cord Blood ◽

Gestational Age ◽

Low Birthweight ◽

Continuous Variable ◽

Linear Regression Models ◽

Association Analyses ◽

Cpg Sites ◽

Adverse Health Outcomes ◽

The Look

Abstract Background Low birthweight has been repeatedly associated with long-term adverse health outcomes and many non-communicable diseases. Our aim was to look-up cord blood birthweight-associated CpG sites identified by the PACE Consortium in infant saliva, and to explore saliva-specific DNA methylation signatures of birthweight. Methods DNA methylation was assessed using Infinium HumanMethylation450K array in 135 saliva samples collected from children of the NINFEA birth cohort at an average age of 10.8 (range 7–17) months. The association analyses between birthweight and DNA methylation variations were carried out using robust linear regression models both in the exploratory EWAS analyses and in the look-up of the PACE findings in infant saliva. Results None of the cord blood birthweight-associated CpGs identified by the PACE Consortium was associated with birthweight when analysed in infant saliva. In saliva EWAS analyses, considering a false discovery rate p-values < 0.05, birthweight as continuous variable was associated with DNA methylation in 44 CpG sites; being born small for gestational age (SGA, lower 10th percentile of birthweight for gestational age according to WHO reference charts) was associated with DNA methylation in 44 CpGs, with only one overlapping CpG between the two analyses. Despite no overlap with PACE results at the CpG level, two of the top saliva birthweight CpGs mapped at genes associated with birthweight with the same direction of the effect also in the PACE Consortium (MACROD1 and RPTOR). Conclusion Our study provides an indication of the birthweight and SGA epigenetic salivary signatures in children around 10 months of age. DNA methylation signatures in cord blood may not be comparable with saliva DNA methylation signatures at about 10 months of age, suggesting that the birthweight epigenetic marks are likely time and tissue specific.

Download Full-text

Age-related differences in monocyte DNA methylation and immune function in healthy Kenyan adults and children

Immunity & Ageing ◽

10.1186/s12979-021-00223-2 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Katherine R. Dobbs ◽

Paula Embury ◽

Emmily Koech ◽

Sidney Ogolla ◽

Stephen Munga ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Young Adults ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Innate Immune ◽

Inflammatory Gene Expression ◽

Cpg Sites ◽

Age Related ◽

Adults And Children

Abstract Background Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profiles in monocytes from young adults and children from western Kenya. Results We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles. Conclusions These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.

Download Full-text

DNA Methylation in LIME1 and SPTBN2 Genes Is Associated with Attention Deficit in Children

Children ◽

10.3390/children8020092 ◽

2021 ◽

Vol 8 (2) ◽

pp. 92

Author(s):

Sung-Chou Li ◽

Ho-Chang Kuo ◽

Lien-Hung Huang ◽

Wen-Jiun Chou ◽

Sheng-Yu Lee ◽

...

Keyword(s):

Dna Methylation ◽

Attention Deficit ◽

Performance Test ◽

Neurodevelopmental Disorder ◽

Continuous Performance Test ◽

Attention Deficits ◽

Clinical Settings ◽

Hyperactivity Disorder ◽

Cpg Sites ◽

Healthy Control

DNA methylation levels are associated with neurodevelopment. Attention-deficit/hyperactivity disorder (ADHD), characterized by attention deficits, is a common neurodevelopmental disorder. We used methylation microarray and pyrosequencing to detect peripheral blood DNA methylation markers of ADHD. DNA methylation profiling data from the microarray assays identified potential differentially methylated CpG sites between 12 ADHD patients and 9 controls. Five candidate CpG sites (cg00446123, cg20513976, cg07922513, cg17096979, and cg02506324) in four genes (LIME1, KCNAB2, CAPN9, and SPTBN2) were further examined with pyrosequencing. The attention of patients were tested using the Conners’ Continuous Performance Test (CPT). In total, 126 ADHD patients with a mean age of 9.2 years (78.6% males) and 72 healthy control subjects with a mean age of 9.3 years (62.5% males) were recruited. When all participants were categorized by their CPT performance, the DNA methylation levels in LIME1 (cg00446123 and cg20513976) were found to be significantly higher and those in SPTBN2 (cg02506324) were significantly lower in children with worse CPT performance. Therefore, DNA methylation of two CpG sites in LIME1 and one CpG site in SPTBN2 is associated with attention deficits in children. DNA methylation biomarkers may assist in identifying attention deficits of children in clinical settings.

Download Full-text

DNA methylation and lipid metabolism: an EWAS of 226 metabolic measures

Clinical Epigenetics ◽

10.1186/s13148-020-00957-8 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Monica del C. Gomez-Alonso ◽

Anja Kretschmer ◽

Rory Wilson ◽

Liliane Pfeiffer ◽

Ville Karhunen ◽

...

Keyword(s):

Dna Methylation ◽

Lipid Metabolism ◽

Population Based ◽

Total Serum ◽

Resonance Spectroscopy ◽

Metabolic Disturbances ◽

Cpg Sites ◽

Gene Transcripts

Abstract Background The discovery of robust and trans-ethnically replicated DNA methylation markers of metabolic phenotypes, has hinted at a potential role of epigenetic mechanisms in lipid metabolism. However, DNA methylation and the lipid compositions and lipid concentrations of lipoprotein sizes have been scarcely studied. Here, we present an epigenome-wide association study (EWAS) (N = 5414 total) of mostly lipid-related metabolic measures, including a fine profiling of lipoproteins. As lipoproteins are the main players in the different stages of lipid metabolism, examination of epigenetic markers of detailed lipoprotein features might improve the diagnosis, prognosis, and treatment of metabolic disturbances. Results We conducted an EWAS of leukocyte DNA methylation and 226 metabolic measurements determined by nuclear magnetic resonance spectroscopy in the population-based KORA F4 study (N = 1662) and replicated the results in the LOLIPOP, NFBC1966, and YFS cohorts (N = 3752). Follow-up analyses in the discovery cohort included investigations into gene transcripts, metabolic-measure ratios for pathway analysis, and disease endpoints. We identified 161 associations (p value < 4.7 × 10−10), covering 16 CpG sites at 11 loci and 57 metabolic measures. Identified metabolic measures were primarily medium and small lipoproteins, and fatty acids. For apolipoprotein B-containing lipoproteins, the associations mainly involved triglyceride composition and concentrations of cholesterol esters, triglycerides, free cholesterol, and phospholipids. All associations for HDL lipoproteins involved triglyceride measures only. Associated metabolic measure ratios, proxies of enzymatic activity, highlight amino acid, glucose, and lipid pathways as being potentially epigenetically implicated. Five CpG sites in four genes were associated with differential expression of transcripts in blood or adipose tissue. CpG sites in ABCG1 and PHGDH showed associations with metabolic measures, gene transcription, and metabolic measure ratios and were additionally linked to obesity or previous myocardial infarction, extending previously reported observations. Conclusion Our study provides evidence of a link between DNA methylation and the lipid compositions and lipid concentrations of different lipoprotein size subclasses, thus offering in-depth insights into well-known associations of DNA methylation with total serum lipids. The results support detailed profiling of lipid metabolism to improve the molecular understanding of dyslipidemia and related disease mechanisms.

Download Full-text

Age Prediction of Human Based on DNA Methylation by Blood Tissues

Genes ◽

10.3390/genes12060870 ◽

2021 ◽

Vol 12 (6) ◽

pp. 870

Author(s):

Jiansheng Zhang ◽

Hongli Fu ◽

Yan Xu

Keyword(s):

Dna Methylation ◽

Pearson Correlation ◽

Close Correlation ◽

Gradient Boosting ◽

Tissue Samples ◽

Regression Methods ◽

Cpg Sites ◽

Testing Dataset ◽

Age Related ◽

Better Than

In recent years, scientists have found a close correlation between DNA methylation and aging in epigenetics. With the in-depth research in the field of DNA methylation, researchers have established a quantitative statistical relationship to predict the individual ages. This work used human blood tissue samples to study the association between age and DNA methylation. We built two predictors based on healthy and disease data, respectively. For the health data, we retrieved a total of 1191 samples from four previous reports. By calculating the Pearson correlation coefficient between age and DNA methylation values, 111 age-related CpG sites were selected. Gradient boosting regression was utilized to build the predictive model and obtained the R2 value of 0.86 and MAD of 3.90 years on testing dataset, which were better than other four regression methods as well as Horvath’s results. For the disease data, 354 rheumatoid arthritis samples were retrieved from a previous study. Then, 45 CpG sites were selected to build the predictor and the corresponded MAD and R2 were 3.11 years and 0.89 on the testing dataset respectively, which showed the robustness of our predictor. Our results were better than the ones from other four regression methods. Finally, we also analyzed the twenty-four common CpG sites in both healthy and disease datasets which illustrated the functional relevance of the selected CpG sites.

Download Full-text

Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus)

Genetics ◽

10.1093/genetics/iyab001 ◽

2021 ◽

Vol 217 (1) ◽

Author(s):

Juntao Hu ◽

Sara J S Wuitchik ◽

Tegan N Barry ◽

Heather A Jamniczky ◽

Sean M Rogers ◽

...

Keyword(s):

Dna Methylation ◽

Genetic Architecture ◽

Gasterosteus Aculeatus ◽

Additive Genetic Variance ◽

Natural Populations ◽

Threespine Stickleback ◽

Phenotypic Change ◽

Cpg Sites ◽

Cis And Trans ◽

Methylation Variation

Abstract Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24–35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.

Download Full-text

Kidney Measures with Diabetes and Hypertension on Cardiovascular Disease: The Atherosclerosis Risk in Communities Study

American Journal of Nephrology ◽

10.1159/000433450 ◽

2015 ◽

Vol 41 (4-5) ◽

pp. 409-417 ◽

Cited By ~ 6

Author(s):

Nadine Alexander ◽

Kunihiro Matsushita ◽

Yingying Sang ◽

Shoshana Ballew ◽

Bakhtawar K. Mahmoodi ◽

...

Keyword(s):

Cardiovascular Risk ◽

Regression Models ◽

Estimated Glomerular Filtration Rate ◽

Cox Regression ◽

Cardiovascular Outcomes ◽

Creatinine Ratio ◽

Atherosclerosis Risk In Communities ◽

Atherosclerosis Risk ◽

Lower Egfr

Background: Whether the association of chronic kidney disease (CKD) with cardiovascular risk differs based on diabetes mellitus (DM) and hypertension (HTN) status remains unanswered. Methods: We investigated 11,050 participants from the Atherosclerosis Risk in Communities Study (fourth examination (1996-1998)) with follow-up for cardiovascular outcomes (coronary disease, heart failure and stroke) through 2009. Using the Cox regression models, we quantified cardiovascular risk associated with estimated glomerular filtration rate (eGFR) and urinary albumin-to-creatinine ratio (ACR) in individuals with and without DM and/or HTN and assessed their interactions. Results: Individuals with DM and HTN generally had higher cardiovascular risk relative to those without at all the levels of eGFR and ACR. Cardiovascular risk increased with lower eGFR and higher ACR regardless of DM and HTN status (e.g. adjusted hazards ratio (HR) for eGFR 30-44 vs. 90-104 ml/min/1.73 m2, 2.32 (95% CI, 1.66-3.26) in non-diabetics vs. 1.83 (1.25-2.67) in diabetics and 2.45 (2.20-5.01) in non-hypertensives vs. 1.51 (1.27-1.81) in hypertensives and corresponding adjusted HR for ACR 30-299 vs. <10 mg/g, 1.70 (1.45-2.00) vs. 1.34 (1.10-1.64) and 1.42 (1.10-1.85) vs. 1.57 (1.36-1.81), respectively). Only the ACR-DM interaction reached significance, with a shallower relative risk gradient among diabetics than among non-diabetics (p = 0.02). Analysis of individual cardiovascular outcomes showed similar results. Conclusion: Although individuals with DM and HTN generally had higher cardiovascular risk relative to those without these complications, both low eGFR and high ACR were associated with cardiovascular diseases regardless of the presence or absence of DM and HTN. These findings reinforce the importance of CKD in cardiovascular outcomes.

Download Full-text

Abstract MP42: Adherence To Healthy Dietary Patterns In Pregnancy And Placental Dna Methylation- An Epigenome Wide Association Study

Circulation ◽

10.1161/circ.143.suppl_1.mp42 ◽

2021 ◽

Vol 143 (Suppl_1) ◽

Author(s):

Cuilin Zhang ◽

Jing Wu ◽

Marion Ouidir ◽

Stefanie Hinkle ◽

Fasil Ayele

Keyword(s):

Dna Methylation ◽

Dietary Patterns ◽

First Trimester ◽

Healthy Eating Index ◽

Nervous System Development ◽

Dietary Quality ◽

Analysis Tool ◽

Linear Regression Models ◽

Cpg Sites ◽

In Pregnancy

Background: Accumulating evidence support the intergenerational impacts of diet in pregnancy. The underlying mechanisms, however, remain unclear. Placental epigenetic mechanisms may be involved although data from human epidemiological studies are sparse. We aimed to investigate associations of dietary quality in pregnancy with epigenome-wide placental DNA methylation in a multiracial pregnancy cohort. Methods: DNA methylation was measured using the Illumina Infinium Human Methylation450 Beadchip on placentas obtained at delivery from 301 pregnant women who participated in the Eunice Kennedy Shriver National Institute of Child Health and Human Development Fetal Growth Studies-Singleton cohort. Dietary information during periconception and early first trimester was collected using food frequency questionnaires, and diet in the second and third trimester was collected using a 24-hour dietary recall during four study visits. Scores for adherence to three healthy dietary patterns, alternate Healthy Eating Index (aHEI), alternate Mediterranean Diet (aMED), and Dietary Approaches to Stop Hypertension (DASH), were calculated. For associations of each dietary pattern score with methylation, we conducted analyses using robust linear regression models after the adjustment for age, pre-pregnancy body mass index, race/ethnicity, physical activity, total energy intakes, and population stratification. Genes annotating the top significant CpG sites (false discovery rate (FDR) adjusted P<0.05) were queried for enrichment of functional pathways using the Ingenuity Pathway Analysis tool. Results: Adherence to aHEI was significantly associated with methylation of 8 CpG sites, with the most significant association manifested in cg16724319- MDH1B (P=1.9x10 -10 ). Adherence to aMED was related to methylation of 14 CpG sites, with the most significant association manifested in cg07835181- CLCN7 (P=1.7x10 -11 ). DASH was significantly related to 33 CpG sites, with the most significant association manifested in cg26292547- REV3L (P=4.4x10 -10 ). Further, genes annotating the significant CpG sites were enriched in pathways related to cardiovascular and nervous system development and function, cancer, organismal injury and abnormalities, and reproductive system diseases. Conclusion: Findings from the epigenome wide study suggest that overall dietary quality in pregnancy is associated with placental DNA methylation changes at different loci potentially related to cardiovascular, neurological, reproductive, and cancer phenotypes.

Download Full-text