DNA Methylation Of Repetitive Elements Research Articles

Abstract 4045: Intragenic ATM methylation in peripheral blood DNA as a biomarker of breast cancer risk

Abstract DNA methylation is an important epigenetic modification that could affect cancer risk through direct effects on disease, and/or mediating effects of genetic and environmental factors. Global and gene-specific DNA methylation levels in white blood cells (WBC) have been related to risk of breast and other cancers, however, evidence is generally weak. We analysed WBC DNA methylation of two ATM intragenic loci (ATMmvp2a and ATMmvp2b) and genome-wide DNA methylation in LINE1 repetitive elements in three breast cancer studies with pre-diagnostic blood samples. Studies included a case-control study with cases derived from a prospective cohort of high-risk breast cancer families (KConFab), and nested case-control studies in two prospective cohorts: the Breakthrough Generations Study (BGS) and the European Prospective Investigation into Cancer and Nutrition (EPIC). Total sample size was 640 incident cases of invasive breast cancer and 741 controls. Bisulphite pyrosequencing was used to quantify methylation in WBC DNA. Quintile analyses of the combined data for ATMmvp2a showed an increased risk of breast cancer limited to women in the highest quintile of methylation (OR =1.89 (1.36-2.64), p= 1.64x10-4). We found no significant differences in estimates across studies, however, the largest differences in ATMmvp2a methylation levels were observed for familial cases in KConFab compared to controls. We observed no significant differences in LINE1 or ATMmvp2b methylation levels between cases and controls. These results indicate that WBC DNA methylation levels at ATM could be a marker of breast cancer risk and further support the pursuit of epigenome-wide association studies in peripheral blood DNA methylation. Funding: Breast Cancer Campaign Fellowship and Cancer Research UK Program C536/A6689. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4045. doi:1538-7445.AM2012-4045

DNA methylation in repetitive elements and post-traumatic stress disorder: a case-control study of US military service members.

We investigated serum DNA methylation patterns in genomic repetitive elements, LINE-1 and Alu, for post-traumatic stress disorder (PTSD) cases and controls who were US military service members recently deployed to Afghanistan or Iraq. Cases (n = 75) had a postdeployment diagnosis of PTSD. Controls (n = 75) were randomly selected service members with no postdeployment PTSD diagnosis. Pre- and post-deployment sera were accessed, DNA was extracted and DNA methylation (percentage 5-methyl cytosine) was quantified via pyrosequencing. Conditional and unconditional logistic regressions were used to compare: cases post- to pre-deployment; controls post- to pre-deployment; cases to controls predeployment; cases to controls postdeployment. LINE-1 was hypermethylated in controls post- versus pre-deployment (odds ratio [OR]: 1.33; 95% CI: 1.06-1.65) and hypomethylated in cases versus controls postdeployment (OR: 0.82; 95% CI: 0.67-1.01). Alu was hypermethylated for cases versus controls predeployment (OR: 1.46; 95% CI: 1.08-1.97). Patterns of hypermethylation of LINE-1 in controls postdeployment and of Alu in cases postdeployment are intriguing and may suggest resilience or vulnerability factors.

RNA interference in mammalian DNA methylation1This review is part of Special Issue entitled Asilomar Chromatin and has undergone the Journal’s usual peer review process.

RNAi and Dicer-dependent siRNAs are required for constitutive heterochromatin formation in fission yeast and for establishing DNA methylation at repetitive elements in plants. In the mammalian male germ line, DICER1-independent piRNAs are required for the full establishment of DNA methylation of dispersed repetitive transposable elements. However, in other mammalian cell types, no clear picture has yet emerged of the role of RNAi in establishing heterochromatin and DNA methylation. In mouse embryonic stem cells, which remain viable on loss of DICER1 and ablation of RNAi, while no firm evidence has been obtained for defective heterochromatin formation, there are indications of defective DNA methylation. The latter has been attributed to an indirect effect of reduced DNA methyltransferase (DNMT) activity due to a loss of miRNA-mediated gene regulation. However, it is unclear whether the reductions in DNMT activity were sufficient to affect DNA methylation. We consider it equally likely that the defects in DNA methylation that can be observed in DICER1-deficient embryonic stem cells are the result of nonspecific effects related to RNAi loss aside from reduced DNMT activity.

Commentary: Marking the epigenome—in search of the fingerprints of intrauterine nutritional deficiencies

Commentary: Marking the epigenome—in search of the fingerprints of intrauterine nutritional deficiencies

DNA methylation of stress-related genes and LINE-1 repetitive elements across the healthy human placenta

ObjectivesDNA methylation is known to play a critical role in regulating development of placental morphology and physiology. The methylation of genes mediated by glucocorticoid hormones may be particularly vulnerable to intrauterine stress in the placenta. However little is known about DNA methylation of stress-related genes within a healthy placenta, and particularly whether methylation occurs uniformly across different regions of the placenta, which is a critical question for researchers seeking to analyze methylation patterns. We examined DNA methylation across four regions of the placenta to evaluate methylation levels of stress-related genes within a healthy placenta, and to evaluate whether methylation patterns vary by sampling location. Study designWe evaluated levels of DNA methylation of three stress-related genes: NR3C1, BDNF, and 11B-HSD2 and of the repetitive element, LINE-1, in four different sample locations of 20 healthy placentas. Main outcome measuresPyrosequencing was used to quantify levels of methylation at CpG sites within the promoter regions of each of the three stress-related genes, and global methylation of LINE-1. ResultsVery low levels of methylation were found across all three stress-related genes; no gene showed a median methylation level greater than 4.20% across placental regions. Variation in methylation between placental regions for stress-related genes and for LINE-1 was minimal. ConclusionsOur data suggest that these frequently studied stress-related genes have low levels of methylation in healthy placenta tissue. Minimal variation between sites suggests that sampling location does not affect DNA methylation analyses of these genes or of LINE-1 repetitive elements.

Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts

DNA methylation changes in repetitive elements (REs) are associated with the regulation of gene transcription, embryonic development, differentiation and carcinogenesis. However, genome-wide analysis of DNA methylation of human REs is lacking. Here, we performed genome-wide methylation analysis of REs in nine repeat types in human embryonic stem cells (H1) and fetal fibroblasts (IMR90), and found that the potential for changes in the DNA methylation of REs was different among the nine repeat types and within different genomic regions. DNA methylation changes in the nine repeat types were related to the GC content and CpG density of the sequence contexts. The differentially methylated REs and targeted genes of different repeat types were associated with gene silencing in the transition from H1 to IMR90 cells. Our results suggest that a quarter of REs are involved in the reprogramming of DNA methylation which may play important epigenetic roles during cellular differentiation.

In Utero Exposures, Infant Growth, and DNA Methylation of Repetitive Elements and Developmentally Related Genes in Human Placenta

Background: Fetal programming describes the theory linking environmental conditions during embryonic and fetal development with risk of diseases later in life. Environmental insults in utero may lead to changes in epigenetic mechanisms potentially affecting fetal development.Objectives: We examined associations between in utero exposures, infant growth, and methylation of repetitive elements and gene-associated DNA in human term placenta tissue samples.Methods: Placental tissues and associated demographic and clinical data were obtained from subjects delivering at Women and Infants Hospital in Providence, Rhode Island (USA). Methylation levels of long interspersed nuclear element-1 (LINE-1) and the Alu element AluYb8 were determined in 380 placental samples from term deliveries using bisulfite pyrosequencing. Genomewide DNA methylation profiles were obtained in a subset of 184 samples using the Illumina Infinium HumanMethylation27 BeadArray. Multiple linear regression, model-based clustering methods, and gene set enrichment analysis examined the association between birth weight percentile, demographic variables, and repetitive element methylation and gene-associated CpG locus methylation.Results: LINE-1 and AluYb8 methylation levels were found to be significantly positively associated with birth weight percentile (p = 0.01 and p < 0.0001, respectively) and were found to differ significantly among infants exposed to tobacco smoke and alcohol. Increased placental AluYb8 methylation was positively associated with average methylation among CpG loci found in polycomb group target genes; developmentally related transcription factor binding sites were overrepresented for differentially methylated loci associated with both elements.Conclusions: Our results suggest that repetitive element methylation markers, most notably AluYb8 methylation, may be susceptible to epigenetic alterations resulting from the intrauterine environment and play a critical role in mediating placenta function, and may ultimately inform on the developmental basis of health and disease.

Birthweight, Maternal Weight Trajectories and Global DNA Methylation of LINE-1 Repetitive Elements

Low birthweight, premature birth, intrauterine growth retardation, and maternal malnutrition have been related to an increased risk of cardiovascular disease, type 2 diabetes mellitus, obesity, and neuropsychiatric disorders later in life. Conversely, high birthweight has been linked to future risk of cancer. Global DNA methylation estimated by the methylation of repetitive sequences in the genome is an indicator of susceptibility to chronic diseases. We used data and biospecimens from an epigenetic birth cohort to explore the association between trajectories of fetal and maternal weight and LINE-1 methylation in 319 mother-child dyads. Newborns with low or high birthweight had significantly lower LINE-1 methylation levels in their cord blood compared to normal weight infants after adjusting for gestational age, sex of the child, maternal age at delivery, and maternal smoking during pregnancy (p = 0.007 and p = 0.036, respectively), but the magnitude of the difference was small. Infants born prematurely also had lower LINE-1 methylation levels in cord blood compared to term infants, and this difference, though small, was statistically significant (p = 0.004). We did not find important associations between maternal prepregnancy BMI or gestational weight gain and global methylation of the cord blood or fetal placental tissue. In conclusion, we found significant differences in cord blood LINE-1 methylation among newborns with low and high birthweight as well as among prematurely born infants. Future studies may elucidate whether chromosomal instabilities or other functional consequences of these changes contribute to the increased risk of chronic diseases among individuals with these characteristics.

ARSENIC EXPOSURE AND DNA METHYLATION WITHIN REPETITIVE ELEMENTS IN ELDERLY MEN

Background and Aims: Arsenic (As) exposure has been linked to epigenetic modifications such as DNA methylation in in vitro and animal studies. This association has also being explored in highly exposed human populations, but studies among populations environmentally exposed to low As levels are lacking. We aimed to evaluate the association between As exposure and DNA methylation changes in repetitive elements in a population of community-dwelling elderly men. We also explored the possibility of effect modification by plasma folate, cobalamine (B12), and pyridoxine (B6). Methods: We measured toenail As levels by inductively coupled plasma mass spectrometry and DNA methylation in Alu and Long Interspersed Nucleotide Element-1 (LINE-1) repetitive elements by quantitative polymerase chain reaction-pyrosequencing of blood leukocytes. The study population was 581 participants from the Normative Aging Study in Boston, USA, with 434, 140, and 7 of them having 1, 2 and 3 visits, respectively, between 1999-2002 and 2006-2007. We used mixed effects models and included interaction terms to assess potential effect modification by plasma folate, B12, and B6. Results: There was a trend of increasing Alu and decreasing LINE-1 DNA methylation as arsenic exposure increased. In subjects with plasma folate below the median (less than 14.1 ng/ml), As was positively associated with Alu DNA methylation (b=0.08; 95%CI, 0.03 to 0.13 for one interquartile range [0.06 mcg/g] increase in As) while a negative association was observed in subjects with plasma folate above the median (b=-0.08; 95%CI, -0.17 to 0.01). Conclusions: In our study, the association between As exposure and DNA methylation in Alu repetitive elements varied by folate level, a factor that participates in one-carbon metabolism. This suggests a potential role for nutritional factors in As toxicity.

Prolonged Exposure to Particulate Pollution, Genes Associated with Glutathione Pathways, and DNA Methylation in a Cohort of Older Men

Background: DNA methylation is a potential pathway linking environmental exposures to disease. Exposure to particulate air pollution has been associated with increased cardiovascular morbidity and mortality, and lower blood DNA methylation has been found in processes related to cardiovascular morbidity.Objective: We hypothesized that prolonged exposure to particulate pollution would be associated with hypomethylation of repetitive DNA elements and that this association would be modified by genes involved in glutathione metabolism and other host characteristics.Methods: DNA methylation of the long interspersed nucleotide element–1 (LINE-1) and the short interspersed nucleotide element Alu were measured by quantitative polymerase chain reaction pyrosequencing in 1,406 blood samples from 706 elderly participants in the Normative Aging Study. We estimated changes in repetitive element DNA methylation associated with ambient particles (particulate matter ≤ 2.5 µm in aerodynamic diameter), black carbon (BC), and sulfates (SO4), with mixed models. We examined multiple exposure windows (1–6 months) before DNA methylation measurement. We investigated whether this association was modified by genotype and phenotype.Results: An interquartile range (IQR) increase in BC over a 90-day period was associated with a decrease of 0.31% 5-methylcytosine (5mC) (95% confidence interval, 0.12–0.50%) in Alu. An IQR increase in SO4 over a 90-day period was associated with a decrease of 0.27% 5mC (0.02–0.52%) in LINE-1. The glutathione S-transferase mu-1–null genotype strengthened the association between BC and Alu hypomethylation.Conclusion: Prolonged exposure to BC and SO4 particles was associated with hypomethylation of two types of repetitive elements.

DNA methylation in repetitive elements and Alzheimer disease

Epigenetics is believed to play a role in Alzheimer’s disease (AD). DNA methylation, the most investigated epigenetic hallmark, is a reversible mechanism that modifies genome function and chromosomal stability through the addition of methyl groups to cytosine located in CpG dinucleotides to form 5 methylcytosine (5mC). Methylation status of repetitive elements (i.e. Alu, LINE-1 and SAT-α) is a major contributor of global DNA methylation patterns and has been investigated in relation to a variety of human diseases. However, the role of methylation of repetitive elements in blood of AD patients has never been investigated so far. In the present study, a quantitative bisulfite-PCR pyrosequencing method was used to evaluate methylation of Alu, LINE-1 and SAT-α sequences in 43 AD patients and 38 healthy donors. In multivariate analysis adjusting for age and gender, LINE-1 was increased in AD patients compared with healthy volunteers (ADs: 83.6%5mC, volunteers: 83.1%5mC, p-value: 0.05). The group with best performances in mini mental state examination (MMSE) showed higher levels of LINE-1 methylation compared to the group with worst performances (MMSE>22: 83.9%5mC; MMSE⩽22: 83.2%5mC; p=0.05). Our data suggest that LINE-1 methylation may lead to a better understanding of AD pathogenesis and course, and may contribute to identify novel markers useful to assess risk stratification. Further prospective investigations are warranted to evaluate the dynamics of DNA methylation from early-stage AD to advanced phases of the disease.

Analysis of global methylation using a Zta-expressing nasopharyngeal carcinoma cell line

EBV infects more than 90% of the human population and persists in most individuals as a latent infection where the viral genome is silenced by host-driven methylation. The lytic cycle is initiated when the viral protein Zta binds to methylated BRLF1 and BRRF1 promoters. Although studies reveal the role of Zta and methylation changes in the viral genome upon EBV infection to reactivation, whether Zta plays any role in alteration of methylation in the host genome remains unknown. Using an inducible model, we demonstrate that global DNA methylation, based on whole-genome 5-methylcytosine content, and regional DNA methylation in repetitive elements, imprinting genes and the X chromosome, remains unchanged in response to Zta expression. Expression of DNA methyltransferases was also unaffected by ectopically expressed Zta. Our data imply that alteration of host gene expression following EBV reactivation may reflect methylation-independent Zta-mediated gene activation and not epigenetic modification of the host genome.

Repetitive element hypomethylation in blood leukocyte DNA and cancer incidence, prevalence, and mortality in elderly individuals: the Normative Aging Study

Global genomic hypomethylation is a common epigenetic event in cancer that mostly results from hypomethylation of repetitive DNA elements. Case-control studies have associated blood leukocyte DNA hypomethylation with several cancers. Because samples in case-control studies are collected after disease development, whether DNA hypomethylation is causal or just associated with cancer development is still unclear. In 722 elderly subjects from the Normative Aging Study cohort, we examined whether DNA methylation in repetitive elements (Alu, LINE-1) was associated with cancer incidence (30 new cases, median follow-up: 89 months), prevalence (205 baseline cases), and mortality (28 deaths, median follow-up: 85 months). DNA methylation was measured by bisulfite pyrosequencing. Individuals with low LINE-1 methylation (<median) had a 3.0-fold (95%CI 1.3-6.9) increased incidence of all cancers combined. LINE-1 and Alu methylation were not significantly associated with cancer prevalence at baseline (all cancers combined). However, individuals with low LINE-1 methylation (<median) had a 3.2-fold (95% CI 1.4-7.5) higher prevalence of lung cancer. Individuals with low LINE-1 or Alu methylation (<median) had increased cancer mortality (HR = 3.2, 95%CI 1.3-7.9 for LINE-1; HR = 2.5, 95%CI 1.1-5.8 for Alu). These findings suggest that individuals with lower repetitive element methylation are at high risk of developing and dying from cancer.

Repetitive element DNA methylation and circulating endothelial and inflammation markers in the VA normative aging study

BACKGROUND: Lower blood DNA methylation has been associated with atherosclerosis and high cardiovascular risk. Mechanisms linking DNA hypomethylation to increased cardiovascular risk are still largely unknown. In a population of community-dwelling elderly individuals, we evaluated whether DNA methylation in LINE-1 repetitive element, heavily methylated sequences dispersed throughout the human genome, was associated with circulating Vascular Cell Adhesion Molecule-1 (VCAM-1), Inter- Cellular Adhesion Molecule-1 (ICAM-1), and C-reactive protein (CRP). METHODS AND RESULTS: We measured LINE-1 methylation by bisulfite PCR-Pyrosequencing on 742 blood DNA samples from male participants in the Boston area Normative Aging Study (mean age=74.8 years). Mean serum VCAM-1 increased progressively in association with LINE-1 hypomethylation (from 975.2 to 1063.4 ng/ml in the highest vs. lowest methylation quintiles; ptrend= 0.004). The association between VCAM-1 and LINE-1 hypomethylation was significant in individuals without ischemic heart disease or stroke (n=480; p=0.001), but not in those with prevalent disease (n=262; p=0.57). Serum ICAM-1 and CRP were not associated with LINE-1 methylation (p-trend=>0.25). All results were confirmed by multivariable analyses adjusting for age, BMI, smoking, pack-years, and ischemic heart disease/stroke. CONCLUSIONS: LINE-1 element hypomethylation is associated with higher serum VCAM-1. Our data provide new insights into epigenetic events that may accompany the development of cardiovascular disease.

DNA methylation as a biomarker for cardiovascular disease risk.

BackgroundElevated serum homocysteine is associated with an increased risk of cardiovascular disease (CVD). This may reflect a reduced systemic remethylation capacity, which would be expected to cause decreased genomic DNA methylation in peripheral blood leukocytes (PBL).Methodology/Principal FindingsWe examined the association between prevalence of CVD (myocardial infarction, stroke) and its predisposing conditions (hypertension, diabetes) and PBL global genomic DNA methylation as represented by ALU and Satellite 2 (AS) repetitive element DNA methylation in 286 participants of the Singapore Chinese Health Study, a population-based prospective investigation of 63,257 men and women aged 45–74 years recruited during 1993–1998. Men exhibited significantly higher global DNA methylation [geometric mean (95% confidence interval (CI)): 159 (143, 178)] than women [133 (121, 147)] (P = 0·01). Global DNA methylation was significantly elevated in men with a history of CVD or its predisposing conditions at baseline (P = 0·03) but not in women (P = 0·53). Fifty-two subjects (22 men, 30 women) who were negative for these CVD/predisposing conditions at baseline acquired one or more of these conditions by the time of their follow-up I interviews, which took place on average about 5·8 years post-enrollment. Global DNA methylation levels of the 22 incident cases in men were intermediate (AS, 177) relative to the 56 male subjects who remained free of CVD/predisposing conditions at follow-up (lowest AS, 132) and the 51 male subjects with a diagnosis of CVD or predisposing conditions reported at baseline (highest AS 184) (P for trend = 0.0008) No such association was observed in women (P = 0.91). Baseline body mass index was positively associated with AS in both men and women (P = 0·007).Conclusions/SignificanceOur findings indicate that elevated, not decreased, PBL DNA methylation is positively associated with prevalence of CVD/predisposing conditions and obesity in Singapore Chinese.

A Phase I Biological Study of Azacitidine (Vidaza) to Determine the Optimal Biological Dose and Route of Administration.

Abstract 1753Poster Board I-779 BackgroundAzacitidine (5-azacytidine, Vidaza) is a DNA methylation inhibitor with used to treat myelodysplastic syndrome (MDS). The studies which led to FDA approval based dosing and administration guidelines on clinical response. In vitro studies have demonstrated that azacitidine exerts its effect by inhibiting DNA methyltransferase in hypermethylated tumor suppressor genes in malignant cells. Research to date has not linked azacitidine dosing with biochemical and clinical response in vivo. The degree of DNA repetitive element sequence methylation (such as LINE-1) has been demonstrated to correlate with global DNA methylation and may be used to determine DNA methylation changes after treatment with azacitidine. We have conducted a phase I study to link clinical and biologic response to azacitidine. This study aims to determine the optimal dose and route of administration for azacitidine to inhibit global DNA methylation levels in the peripheral blood of patients with hematologic malignancies. MethodsPatients with hematologic malignancy who provided informed consent were eligible for study inclusion, with enrollment criteria based on the specific malignancy. Patients were enrolled into one of five dose level treatment groups (25mg, 50mg, 75mg, 100mg or 150mg IV per m2 per day for 5 days) for the first course of therapy. On day 28, all patients received a course of 75mg/m2/day IV for 5 days. Subcutaneous dosing of 75mg/m2/day for 5 days was used for course three. Patients received 75mg/m2/day either SQ or IV x 5 days every 4 weeks for course four and beyond. Peripheral blood was collected on days 1, 3, and 5 during each course, and global DNA methylation was measured using bisulfite-PCR Pyrosequencing of the 6 DNA repetitive elements (LINE1, AluYb8, AluSq, Sat-alpha, D4Z4, NBL-2). Additionally, gene promoter specific DNA methylation was assessed in a subset of patients using the Illumina GoldenGate Bead Array DNA Methylation Assay which measures DNA methylation of 1505 CpG sites (807 genes). ResultsSeventeen patients were treated (3 at 25mg, 4 at 50mg, 4 at 75mg, 3 at 100mg, and 3 at 150mg/m2). Diagnosis included 5 patients with MDS, 10 patients with AML (2 untreated older patients, 7 relapsed or refractory patients), 1 patient with CML (Imatinib refractory), and 1 patient with non-Hodgkin's lymphoma (relapsed disease). At the time of submission, 14 patients were evaluable for response with 4 CR (1 mCr, 1 CRp), 1 PR, 6 SD and 3 PD reported. The median number of cycles given was 3 (range 1-14+). LINE1 DNA methylation decreased by 1.4, 2.3, 4.8, 1.9 and 4.0% on day 5 for the 25mg, 50mg, 75mg, 100mg, and 150mg/m2 course one dose levels respectively. Mean decrease in LINE1 DNA methylation with 75mg/m2 IV was 3.7% and only 2.6% by 75mg/m2 of azacitidine SQ. There was a large amount of inter-patient variability but less intra-patient variability in DNA methylation response to azacitidine. ConclusionAzacitidine is effective at inhibiting DNA methylation at multiple dose levels for both IV and SQ routes of administration. There is a high degree of patient-to-patient variability in DNA methylation changes, although 75mg/m2 lead to the greatest mean decrease in DNA methylation by a 5 day IV regimen. Measurement of DNA methylation of LINE1 and AluYb8 repetitive elements were the best surrogate markers for measuring overall changes in gene specific promoter DNA methylation when compared with 807 genes assessed by the Illumina GoldenGate platform. High-throughput gene promoter DNA methylation analysis revealed subtle changes in DNA methylation, though gene specific changes could not be linked to therapeutic activity. DisclosuresOff Label Use: Azacitidine in hematologic malignancies other than MDS. Mohrbacher:Celgene: Honoraria, Speakers Bureau. Gorospe:Novartis: Honoraria, Speakers Bureau. Yang:Celgene: Honoraria, Research Funding, Speakers Bureau.

DNA Methylation Impacts on Cognitive Decline in a Cohort of Elderly Men

ISEE-0568 Background and Objective: Environmental exposures have been associated with both epigenetic mechanisms and decrements in cognitive function. Epigenetic phenomena regulate the normal function of cells, including neurons, while epigenetic dysregulation has been identified in cognitive function disorders. The role of DNA methylation on changes in cognitive function over time has not been investigated. The objective of the current study was to evaluate whether DNA methylation in repetitive elements widely represented across the human genome is associated with changes in cognitive function in normal aging individuals. Methods: A longitudinal cohort study was conducted in the context of the Normative Aging Study (Boston, USA) among 646 community-dwelling elderly men who underwent a battery of cognitive tests and who also had DNA methylation measurements. We used mixed effects models to assess the association between repeated measurements of scores on a battery of cognitive tests over time and DNA methylation in Alu and LINE-1 (long interspersed nucleotide element-1) repetitive elements. Cognitive testing was performed from 1993 through 2007 and a total of 1,659 observations were included in the final analysis. Results: The mean age of participants at baseline visit was 67.7 (SD = 7) years and the mean number of years of education was 14.4 (SD = 2.7). In multivariable models, a statistically significant greater decrease on a working memory test score (digit span backward test) over time with increasing LINE-1 DNA methylation (b = −0.019, P = 0.0397) was found. A decline in performance over time was observed on the majority of the tests as DNA methylation increased but the associations did not reach statistical significance. Conclusion: Higher levels of DNA methylation in LINE-1 repetitive elements may adversely affect cognitive function, particularly in the working memory domain.

Prolonged Exposure to Particulate Air Pollution and Decreased DNA Methylation

ISEE-0332 Background and Objective: Acute and chronic exposure to particulate air pollution is associated with increased cardiovascular morbidity and mortality. Epigenetic mechanisms are a potential pathway linking environmental exposures to disease. Lower blood DNA methylation, an epigenetic mechanism, has been found in processes related to cardiovascular disease. Recently, acute air pollution exposure has been associated with changes in DNA methylation in heavily methylated sequences with high representation throughout the human genome. We hypothesized that prolonged exposure to particulate pollution might also modify DNA methylation and be a potential mechanism by which chronic air pollution exposure adversely affects health. Methods: We measured DNA methylation of LINE-1 and Alu repetitive elements by quantitative PCR-Pyrosequencing of 985 blood samples from 680 elderly participants in the Boston Normative Aging Study. We used covariate-adjusted mixed models to account for repeated measures. We estimated effects on DNA methylation of ambient pollutants (black carbon, PM2.5, and sulfate) in multiple exposure windows (ranging from 1 month to 1 year) prior to the examination. Results: We found that a 1μg/m3 increase in black carbon over a 60-day period was associated with a 0.8% (95% CI: 0.004%, 1.6%) decrease in methylation of LINE-1 repetitive elements. A 1 μg/m3 increase in black carbon over a 90-day period was associated with a 0.6% (0.001%, 1.1%) decrease in Alu repetitive elements. A 1 μg/m3 increase in sulfate over a 90-day period was associated with 0.3% (0.02%, 0.6%) decrease in LINE-1 repetitive elements. The association with longer exposure windows persisted when we fit models simultaneously adjusting for 1-week moving averages of pollutant exposure. There was no association with PM2.5. Conclusion: Exposure to particulates over 2 to 3 months is associated with decreased repetitive element methylation. This may be a mechanism by which chronic exposure to air pollution increases risk of morbidity and mortality.

Changes in DNA methylation of tandem DNA repeats are different from interspersed repeats in cancer

Hypomethylation of DNA repetitive elements is a common finding in cancer, but very little is known about the DNA methylation changes of different types of DNA repetitive elements, such as interspersed repeats (LINE1 and Alu Yb8) and tandem repeats (Sat-alpha, NBL-2 and D4Z4). We used bisulfite-PCR Pyrosequencing to quantitatively measure the DNA methylation of five different DNA repetitive elements in normal tissue and cancer. In all we studied 10 different tissues from four individuals undergoing autopsy, 34 paired normal and tumor tissues from patients with bladder cancer, 58 patients with chronic myelogenous leukemia and 23 patients with acute promyelocytic leukemia. We found that the DNA methylation of interspersed repeats (LINE1 and Alu Yb8) was very consistent from person to person and tissue to tissue while tandem DNA repeats appeared more variable in normal tissues. In bladder cancer we found clear hypomethylation of LINE1, Alu Yb8, Sat-alpha and NBL-2. Conversely, we found an increase in the DNA methylation levels of D4Z4 from normal to cancer. In contrast leukemia showed no significant changes in the DNA methylation of LINE1 and Alu Yb8, but DNA methylation increases in NBL-2 and D4Z4 tandem repeats. Our findings show that the changes in DNA methylation levels of individual DNA repetitive elements are unique for each repetitive element, which may reflect distinct epigenetic factors and may have important implications in the use of DNA methylation of repetitive elements as global DNA methylation biomarkers.

Rapid DNA Methylation Changes after Exposure to Traffic Particles

Exposure to particulate air pollution has been related to increased hospitalization and death, particularly from cardiovascular disease. Lower blood DNA methylation content is found in processes related to cardiovascular outcomes, such as oxidative stress, aging, and atherosclerosis. We evaluated whether particulate pollution modifies DNA methylation in heavily methylated sequences with high representation throughout the human genome. We measured DNA methylation of long interspersed nucleotide element (LINE)-1 and Alu repetitive elements by quantitative polymerase chain reaction-pyrosequencing of 1,097 blood samples from 718 elderly participants in the Boston area Normative Aging Study. We used covariate-adjusted mixed models to account for within-subject correlation in repeated measures. We estimated the effects on DNA methylation of ambient particulate pollutants (black carbon, particulate matter with aerodynamic diameter < or = 2.5 microm [PM2.5], or sulfate) in multiple time windows (4 h to 7 d) before the examination. We estimated standardized regression coefficients (beta) expressing the fraction of a standard deviation change in DNA methylation associated with a standard deviation increase in exposure. Repetitive element DNA methylation varied in association with time-related variables, such as day of the week and season. LINE-1 methylation decreased after recent exposure to higher black carbon (beta = -0.11; 95% confidence interval [CI], -0.18 to -0.04; P = 0.002) and PM2.5 (beta = -0.13; 95% CI, -0.19 to -0.06; P < 0.001 for the 7-d moving average). In two-pollutant models, only black carbon, a tracer of traffic particles, was significantly associated with LINE-1 methylation (beta = -0.09; 95% CI, -0.17 to -0.01; P = 0.03). No association was found with Alu methylation (P > 0.12). We found decreased repeated-element methylation after exposure to traffic particles. Whether decreased methylation mediates exposure-related health effects remains to be determined.