DNA methylation alterations in response to pesticide exposure in vitro

Although pesticides are subject to extensive carcinogenicity testing before regulatory approval, pesticide exposure has repeatedly been associated with various cancers. This suggests that pesticides may cause cancer via nonmutagenicity mechanisms. The present study provides evidence to support the hypothesis that pesticide‐induced cancer may be mediated in part by epigenetic mechanisms. We examined whether exposure to seven commonly used pesticides (i.e., fonofos, parathion, terbufos, chlorpyrifos, diazinon, malathion, and phorate) induces DNA methylation alterations in vitro. We conducted genome‐wide DNA methylation analyses on DNA samples obtained from the human hematopoietic K562 cell line exposed to ethanol (control) and several organophosphate pesticides (OPs) using the Illumina Infinium HumanMethylation27 BeadChip. Bayesian‐adjusted t‐tests were used to identify differentially methylated gene promoter CpG sites. In this report, we present our results on three pesticides (fonofos, parathion, and terbufos) that clustered together based on principle component analysis and hierarchical clustering. These three pesticides induced similar methylation changes in the promoter regions of 712 genes, while also exhibiting their own OP‐specific methylation alterations. Functional analysis of methylation changes specific to each OP, or common to all three OPs, revealed that differential methylation was associated with numerous genes that are involved in carcinogenesis‐related processes. Our results provide experimental evidence that pesticides may modify gene promoter DNA methylation levels, suggesting that epigenetic mechanisms may contribute to pesticide‐induced carcinogenesis. Further studies in other cell types and human samples are required, as well as determining the impact of these methylation changes on gene expression. Environ. Mol. Mutagen. 2012. © 2012 Wiley Periodicals, Inc.     

DNA甲基化和组蛋白乙酰化与胃癌的研究进展

胃癌是我国最常见的恶性肿瘤，但其具体发病机制还不是很清楚。表遗传学改变，如DNA甲基化和组蛋白修饰改变可以调节基因的表达，在肿瘤的发生和发展中可能起关键作用。近年来一些胃癌相关基因的DNA甲基化和组蛋白乙酰化改变已经得到证实，这些基因改变涉及细胞凋亡、细胞周期阻滞、分化和增殖等。     

Exercise training and DNA methylation in humans

The response to exercise training (trainability) has been shown to have a strong heritable component. There is growing evidence suggesting that traits such as trainability do not only depend on the genetic code, but also on epigenetic signals. Epigenetic signals play an important role in the modulation of gene expression, through mechanisms such as DNA methylation and histone modifications. There is an emerging evidence to show that physical activity influences DNA methylation in humans. The present review aims to summarize current knowledge on the link between DNA methylation and physical activity in humans. We have critically reviewed the literature and only papers focused on physical activity and its influence on DNA methylation status were included; a total of 25 papers were selected. We concluded that both acute and chronic exercises significantly impact DNA methylation, in a highly tissue‐ and gene‐specific manner. This review also provides insights into the molecular mechanisms of exercise‐induced DNA methylation changes, and recommendations for future research.     

Mercury biomarkers and DNA methylation among michigan dental professionals

Modification of the epigenome may be a mechanism underlying toxicity and disease following chemical exposure. Animal and human data suggest that mercury (Hg) impacts DNA methylation. We hypothesize that methylmercury and inorganic Hg exposures from fish consumption and dental amalgams, respectively, may be associated with altered DNA methylation at global repetitive elements (long interspersed elements, LINE‐1) and candidate genes related to epigenetic processes (DNMT1) and protection against Hg toxicity (SEPW1, SEPP1). Dental professionals were recruited at Michigan Dental Association (MDA) meetings in 2009 and 2010. Subjects (n = 131) provided survey data (e.g. exposure sources, demographics) and biological samples for Hg measurement and epigenetic analysis. Total Hg was quantified via atomic absorption spectrophotometry in hair and urine, indicative of methylmercury and inorganic Hg exposures, respectively. Global repetitive and candidate gene methylation was quantified via pyrosequencing of bisulfite converted DNA isolated from buccal mucosa. Hair Hg (geometric mean (95% CI): 0.37 (0.31–0.44) µg/g) and urine Hg (0.70 (0.60–0.83) µg/L) were associated with sources of exposure (fish consumption and dental amalgams, respectively). Multivariable linear regression revealed a trend of SEPP1 hypomethylation with increasing hair Hg levels, and this was significant (P < 0.05) among males. The trend remained when excluding non‐dentists. No significant relationships between urine Hg and DNA methylation were observed. Thus, in a limited cohort, we identified an association between methylmercury exposure and hypomethylation of a potentially labile region of the genome (SEPP1 promoter), and this relationship was gender specific. Environ. Mol. Mutagen. 54:195–203, 2013. © 2013 Wiley Periodicals, Inc.     

Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes

Transgenerational epigenetic inheritance has been defined by the study of relatively few loci. We examined a population of recombinant inbred lines with epigenetically mosaic chromosomes consisting of wild-type and CG methylation-depleted segments (epiRILs). Surprisingly, transposons that were immobile in the parental lines displayed stochastic movement in 28% of the epiRILs. Although analysis after eight generations of inbreeding, supported by genome-wide DNA methylation profiling, identified recombined parental chromosomal segments, these were interspersed with unexpectedly high frequencies of nonparental methylation polymorphism. Hence, epigenetic inheritance in hybrids derived from parents with divergent epigenomes permits long-lasting epi-allelic interactions that violate Mendelian expectations. Such persistently “unstable” epigenetic states complicate linkage-based epigenomic mapping. Thus, future epigenomic analyses should consider possible genetic instabilities and alternative mapping strategies.     

小鼠大脑亚硝酸盐暴露与DNA甲基化和组蛋白去乙酰化

目的 观察慢性亚硝酸盐暴露对小鼠大脑皮质炎症损伤的影响及其探讨DNA甲基化和组蛋白去乙酰化等相关机制。方法 选取8周龄健康雄性C57BL/6J小鼠,随机分为对照组（生理盐水）、低剂量亚硝酸盐组（3g/L）和高剂量亚硝酸盐组(6g/L),建立亚硝酸盐暴露模型,收集各组小鼠大脑皮质,利用免疫荧光染色法和Western blotting法分析大脑皮质炎症损伤,组蛋白去乙酰化酶和DNA甲基化相关酶的表达情况。结果 慢性亚硝酸盐暴露后小鼠大脑皮质炎症损伤因子环氧化酶2（COX2）、白细胞介素-1β（IL-1β）、离子钙接头蛋白分子1（Iba1）、c-Fos、IL-6表达量明显多于对照组（P<0.01）,同时高剂量暴露组DNA甲基化相关酶5-甲基胞嘧啶（5-mC）、DNA甲基转移酶1(DNMT1)、DNMT3a、和组蛋白去乙酰化酶1（HDAC1）表达明显低于对照组（P<0.01）且都呈亚硝酸盐剂量依赖性。结论 亚硝酸盐暴露可通过促进细胞免疫炎症对小鼠大脑皮质造成损伤,并且DNA甲基化和组蛋白去乙酰化可能参与了慢性亚硝酸盐暴露过程中的应答过程及其调控机制。     

The early-life social environment and DNA methylation

DNA methylation is a chemical modification of DNA that confers, upon identical sequences, different identities that are reflected in different gene expression programming. DNA methylation has a well-established role in cellular differentiation by providing a mechanism for one genome to express multiple phenotypes in a multicellular organism. Recent data point however to the possibility that in addition to the innate process of cellular differentiation, DNA methylation can serve as a genome adaptation mechanism, adapting genome function to changing environmental contexts including social environments. A critical time point for this process is early life when cues from the social and physical environments define lifelong trajectories of physical and mental health. DNA methylation and additional epigenetic modifications could therefore serve as molecular links between 'nurture' and 'nature'. Data that are consistent with this new role for DNA methylation as a mechanism for conferring an 'environment' specific identity to DNA will be discussed.     

Prenatal phthalate exposure,infant growth,and global DNA methylation of human placenta

Prenatal phthalate exposure has been shown to be associated with reduced fetal growth. Epigenetic changes such as DNA methylation might be a molecular mechanism through which phthalate exposure affects fetal growth. In this study, we examined associations between prenatal phthalate exposure, infant growth, and global DNA methylation in human placenta samples. We measured global DNA methylation of 119 subjects [55 fetal growth restriction (FGR) cases and 64 normal controls], as assessed by long interspersed nuclear element‐1 (LINE‐1) methylation, via quantitative polymerase chain reaction‐pyrosequencing. Prenatal phthalate exposure was assessed by measuring maternal urinary phthalate metabolites concentrations using high‐performance liquid chromatography‐tandem mass spectrometry. Concentrations of mono (2‐ethyl‐5‐hydroxyhexyl) phthalate (MEHHP), mono (2‐ethyl‐5‐oxohexyl) phthalate (MEOHP), and SumDEHP (molar sum of MEHP, MEHHP, and MEOHP) were significantly higher in FGR cases than those in normal controls (P = 0.002, 0.003, and 0.002, respectively). Placental LINE‐1 methylation were found to be positively associated with fetal birth weight standard deviation scores, and negatively associated with urinary phthalate metabolites concentrations (MEHHP and SumDEHP). Every natural‐log unit increase in urinary concentrations of MEHHP and SumDEHP was associated with 0.015 (β = ?0.015, P = 0.150) and 0.012 kg (β = ?0.012, P = 0.167) decrease in birth weight mediated through LINE‐1 methylation. These findings suggest that changes in placental LINE‐1 methylation might be part of the underlying biological pathway between prenatal phthalate exposure and adverse fetal growth. Environ. Mol. Mutagen. 56:286–292, 2015. © 2014 Wiley Periodicals, Inc.     

Prenatal phthalate exposure and altered patterns of DNA methylation in cord blood

Epigenetic changes such as DNA methylation may be a molecular mechanism through which environmental exposures affect health. Phthalates are known endocrine disruptors with ubiquitous exposures in the general population including pregnant women, and they have been linked with a number of adverse health outcomes. We examined the association between in utero phthalate exposure and altered patterns of cord blood DNA methylation in 336 Mexican‐American newborns. Concentrations of 11 phthalate metabolites were analyzed in maternal urine samples collected at 13 and 26 weeks gestation as a measure of fetal exposure. DNA methylation was assessed using the Infinium HumanMethylation 450K BeadChip adjusting for cord blood cell composition. To identify differentially methylated regions (DMRs) that may be more informative than individual CpG sites, we used two different approaches, DMRcate and comb‐p. Regional assessment by both methods identified 27 distinct DMRs, the majority of which were in relation to multiple phthalate metabolites. Most of the significant DMRs (67%) were observed for later pregnancy (26 weeks gestation). Further, 51% of the significant DMRs were associated with the di‐(2‐ethylhexyl) phthalate metabolites. Five individual CpG sites were associated with phthalate metabolite concentrations after multiple comparisons adjustment (FDR), all showing hypermethylation. Genes with DMRs were involved in inflammatory response (IRAK4 and ESM1), cancer (BRCA1 and LASP1), endocrine function (CNPY1), and male fertility (IFT140, TESC, and PRDM8). These results on differential DNA methylation in newborns with prenatal phthalate exposure provide new insights and targets to explore mechanism of adverse effects of phthalates on human health. Environ. Mol. Mutagen. 58:398–410, 2017. © 2017 Wiley Periodicals, Inc.     

DNA methylation changes in Mexican children exposed to arsenic from two historic mining areas in San Luis potosí

Arsenic is a carcinogen and epimutagen that threatens the health of exposed populations worldwide. In this study, we examined the methylation status of Alu and long interspersed nucleotide elements (LINE‐1) and their association with levels of urinary arsenic in 84 Mexican children between 6 and 12 years old from two historic mining areas in the State of San Luis Potosí, Mexico. Urinary arsenic levels were determined by atomic absorption spectrophotometry and DNA methylation analysis was performed in peripheral blood leukocytes by bisulfite‐pyrosequencing. The geometric mean of urinary arsenic was 26.44 µg/g Cr (range 1.93–139.35). No significant differences in urinary arsenic or methylation patterns due to gender were observed. A positive correlation was found between urinary arsenic and the mean percentage of methylated cytosines in Alu sequences (Spearman correlation coefficient r = 0.532, P < 0.001), and a trend of LINE‐1 hypomethylation was also observed (Spearman correlation coefficient r = ?0.232, P = 0.038) after adjustment for sex and age. A linear regression model showed an association with log‐normalized urinary arsenic for Alu (β = 1.05, 95% CI: 0.67; 1.43, P < 0.001) and LINE‐1 (β = ?0.703, 95% CI: ?1.36; ?0.38, P = 0.038). Despite the low‐level arsenic exposure, a subtle epigenetic imbalance measured as DNA methylation was detected in the leukocytes of Mexican children living in two historic mining areas. Environ. Mol. Mutagen. 57:717–723, 2016. © 2016 Wiley Periodicals, Inc.     

Perinatal lead (Pb) exposure results in sex and tissue‐dependent adult DNA methylation alterations in murine IAP transposons

Epidemiological and animal data suggest that adult chronic disease is influenced by early‐life exposure‐induced changes to the epigenome. Previously, we observed that perinatal lead (Pb) exposure results in persistent murine metabolic‐ and activity‐related effects. Using phylogenetic and DNA methylation analysis, we have also identified novel intracisternal A particle (IAP) retrotransposons exhibiting regions of variable methylation as candidate loci for environmental effects on the epigenome. Here, we now evaluate brain and kidney DNA methylation profiles of four representative IAPs in adult mice exposed to human physiologically relevant levels of Pb two weeks prior to mating through lactation. When IAPs across the genome were evaluated globally, average (sd) methylation levels were 92.84% (3.74) differing by tissue (P < 0.001), but not sex or dose. By contrast, the four individual IAPs displayed tissue‐specific Pb and sex effects. Medium Pb‐exposed mice had 3.86% less brain methylation at IAP 110 (P < 0.01), while high Pb‐exposed mice had 2.83% less brain methylation at IAP 236 (P = 0.01) and 1.77% less at IAP 506 (P = 0.05). Individual IAP DNA methylation differed by sex for IAP 110 in the brain and kidney, IAP 236 in the kidney, and IAP 1259 in the kidney. Using Tomtom, we identified three binding motifs that matched to each of our novel IAPs impacted by Pb, one of which (HMGA2) has been linked to metabolic‐related conditions in both mice and humans. Thus, these recently identified IAPs display tissue‐specific environmental lability as well as sex‐specific differences supporting an epigenetic link between early exposure to Pb and later‐in‐life health outcomes. Environ. Mol. Mutagen. 58:540–550, 2017. © 2017 Wiley Periodicals, Inc.     

Experiencing community and domestic violence is associated with epigenetic changes in DNA methylation of BDNF and CLPX in adolescents

Experiencing violence changes behavior, shapes personalities, and poses a risk factor for mental disorders. This association might be mediated through epigenetic modifications that affect gene expression, such as DNA methylation. The present study investigated the impact of community and domestic violence on DNA methylation measured in saliva collected from 375 individuals including three generations: grandmothers (n = 126), mothers (n = 125), and adolescents (n = 124, 53% female). Using the Infinium HumanMethylation450 BeadChip array, in adolescents, we detected two CpG sites that showed an association of DNA methylation and lifetime exposure to community and domestic violence even after FDR correction: BDNF_cg06260077 (logFC −0.454, p = 3.71E-07), and CLPX_cg01908660 (logFC = −0.372, p = 1.38E-07). Differential DNA methylation of the CpG BDNF_cg06260077 associated with exposure to violence was also observed in the maternal but not the grandmaternal generation. BDNF (brain-derived neurotrophic factor) and CLPX (caseinolytic mitochondrial matrix peptidase chaperone subunit) genes are involved in neural development. Our results thus reveal altered molecular mechanisms of developmental and intergenerational trajectories in survivors of repeated violent experiences.