Developmental programming: Differing impact of prenatal testosterone and prenatal bisphenol-A -treatment on hepatic methylome in female sheep
Steroid hormones are integral to pregnancy and fetal development, regulating processes such as metabolism, inflammation, and immune responses. Excessive prenatal steroid exposure, through lifestyle choices or environmental chemicals, can lead to metabolic dysfunctions in offspring. The research focuses on how exposure to testosterone (T) and bisphenol A (BPA) affects the liver’s DNA methylome, a key component of the epigenome influencing long-term health. Using Suffolk sheep, the study involved two cohorts: one exposed to prenatal-T and the other to prenatal-BPA. Whole genome bisulfite sequencing was employed to map DNA methylation across over 22 million CpG sites. Regions with p-value<10−4 and a magnitude of difference of at least 5 % methylation between groups were considered differentially methylated. Results demonstrated substantial differential methylation in the liver tissues due to both treatments, with prenatal-T causing unique epigenetic modifications distinct from those induced by prenatal-BPA. Specifically, prenatal-T treatment resulted in 53 differentially methylated regions (DMRs), of which 31 were located in gene regions, including exons. Prenatal-BPA exposure led to 32 DMRs, with 22 associated with gene regions. These modifications were associated with genes governing lipid and glucose metabolism, potentially underlying the observed metabolic disruptions such as insulin resistance and dyslipidemia. Pathway analysis revealed that genes differentially methylated due to prenatal-T were involved in cellular organization, while those affected by prenatal-BPA were enriched in signal regulation pathways. The findings underscore how prenatal exposure to steroid excess and steroid-mimics influence epigenetic landscapes, contributing to metabolic disease programming.
- Research Article
131
- 10.1289/ehp.1104175
- Feb 14, 2012
- Environmental Health Perspectives
Background: Bisphenol A (BPA), an endocrine-disrupting chemical that is routinely detected in > 90% of Americans, promotes experimental asthma in mice. The association of prenatal BPA exposure and wheeze has not been evaluated in humans.Objective: We examined the relationship between prenatal BPA exposure and wheeze in early childhood.Methods: We measured BPA concentrations in serial maternal urine samples from a prospective birth cohort of 398 mother–infant pairs and assessed parent-reported child wheeze every 6 months for 3 years. We used generalized estimating equations with a logit link to evaluate the association of prenatal urinary BPA concentration with the dichotomous outcome wheeze (wheeze over the previous 6 months).Results: Data were available for 365 children; BPA was detected in 99% of maternal urine samples during pregnancy. In multivariable analysis, a one-unit increase in log-transformed creatinine-standardized mean prenatal urinary BPA concentration was not significantly associated with child wheeze from birth to 3 years of age, but there was an interaction of BPA concentration with time (p = 0.003). Mean prenatal BPA above versus below the median was positively associated with wheeze at 6 months of age [adjusted odds ratio (AOR) = 2.3; 95% confidence interval (CI): 1.3, 4.1] but not at 3 years (AOR = 0.6; 95% CI: 0.3, 1.1). In secondary analyses evaluating associations of each prenatal BPA concentration separately, urinary BPA concentrations measured at 16 weeks gestation were associated with wheeze (AOR = 1.2; 95% CI: 1.0, 1.5), but BPA concentrations at 26 weeks of gestation or at birth were not.Conclusions: Mean prenatal BPA was associated with increased odds of wheeze in early life, and the effect diminished over time. Evaluating exposure at each prenatal time point demonstrated an association between wheeze from 6 months to 3 years and log-transformed BPA concentration at 16 weeks gestation only.
- Research Article
2
- 10.2174/0115748936245495230925112419
- Jun 1, 2024
- Current Bioinformatics
Introduction:: Differentially methylated regions (DMRs), including tissue-specific DMRs and disease-specific DMRs, can be used in revealing the mechanisms of gene regulation and screening diseases. Up until now, many methods have been proposed to detect DMRs from bisulfite sequencing data. In these methods, differentially methylated CpG sites and DMRs are usually identified based on statistical tests or distribution models, which neglect the joint methylation statuses provided in each read and result in inaccurate boundaries of DMRs. Methods:: In this paper, a method, named DMR_Kmeans, is proposed to detect DMRs based on kmeans clustering and read methylation haplotype filtering. In DMR_Kmeans, for each CpG site, the k-means algorithm is used to cluster the methylation levels from two groups, and the methylation difference of the CpG is measured based on the different distributions in clusters. Methylation haplotypes of reads are employed to extract the methylation patterns in a candidate region. Finally, DMRs are identified based on the methylation differences and the methylation patterns in candidate regions. Result:: Comparing the performance of DMR_Kmeans and eight DMR detection methods on the whole genome bisulfite sequencing data of six pairs of tissues, the results show that DMR_Kmeans achieves higher Qn and Ql, and more overlapped promoters than other methods when given a certain threshold of methylation difference greater than 0.4, which indicates that the DMRs predicted by DMR_Kmeans with accurate boundaries contain less CpGs with small methylation differences than those by other methods. Conclusion:: Furthermore, it suggests that DMR_Kmeans can provide a DMR set with high quality for downstream analysis since the total length of DMRs predicted by DMR_Kmeans is longer and the total number of CpG sites in the DMRs is greater than those of other methods.
- Research Article
- 10.1289/isesisee.2018.p02.2630
- Sep 24, 2018
- ISEE Conference Abstracts
Background: Exposure to bisphenol A (BPA) may impact obesity development, either in the exposed subjects or offspring.Objective: To investigate the association between prenatal and postnatal exposure to BPA and children&#8217;s body mass index (BMI) as well as its trajectories, in a cohort study.Methods: We recruited pregnant women in their second trimester, between 2008 and 2011; their creatinine-adjusted urinary BPA levels were measured. In 2012-2016, we measured their children&#8217;s BPA levels, at ages 2, 4, and 6 years, and assessed the BMI values, z-scores, and prevalence of overweight (n &#61; 202). Adiposity trajectories were determined in latent class mixed models. We assessed the association between prenatal mid-term exposure to BPA and postnatal exposure, at each age, and anthropometric measurements, at a single time point, at ages 2, 4, and 6 years. The relationship between prenatal exposure to BPA and adiposity trajectory, over multiple ages, was investigated through linear regression.Results: The association of prenatal and postnatal BPA concentrations with the anthropometric measurements, at a single time point, at 2, 4, and 6 years of age, were not statistically significant after controlling for covariates. However, the adiposity trajectories, over ages 2 to 6 years, were related with prenatal BPA concentrations. A 2-fold increase in prenatal BPA level was significantly associated with increasing adiposity trajectories, in early childhood, by 39.6% (95% confidence intervals: 2.2%, 90.7%).Conclusion: Adiposity trajectory, in early childhood, was affected by prenatal BPA exposure levels. The study provides supporting evidence on the transgenerational effects of BPA on children&#8217;s growth.
- Research Article
50
- 10.1093/humrep/dey234
- Jul 4, 2018
- Human Reproduction
Are maternal and paternal preconception urinary bisphenol A (BPA) or bisphenol S (BPS) concentrations associated with offspring birth size? Maternal-but not paternal-preconception urinary BPA concentrations were associated with lower birth size among couples seeking fertility evaluation. Prenatal BPA exposure has been previously associated with reduced birth size in some but not all epidemiologic studies. However, the potential effect of BPA exposure before conception in either parent is unknown. Data on BPS is practically absent. Ongoing prospective preconception cohort of women and men seeking fertility evaluation between 2005 and 2016 in a large fertility center in an academic hospital in Boston, MA, USA. We examined the association between maternal and paternal preconception, as well as maternal prenatal urinary BPA and BPS concentrations, and size at birth among 346 singletons from couples recruited in the Environment and Reproductive Health (EARTH) Study using multivariable linear regression. Infant birth weight and head circumference were abstracted from delivery records. Mean preconception and prenatal exposures were estimated by averaging urinary ln-BPA and ln-BPS concentrations in multiple maternal and paternal urine samples collected before pregnancy, and maternal pregnancy samples collected in each trimester. Maternal preconception urinary BPA concentrations were inversely associated with birth weight and head circumference in adjusted models: each ln-unit increase was associated with a decrease in birth weight of 119 g (95% CI: -212, -27), and a head circumference decrease of 0.72 cm (95% CI: -1.3, -0.1). Additional adjustment by gestational age or prenatal BPA exposure modestly attenuated results. Women with higher prenatal BPA concentrations had infants with lower mean birth weight (-75 g, 95% CI: -153, 2) although this did not achieve statistical significance. Paternal preconception urinary BPA concentrations were not associated with either birth weight or head circumference. No consistent patterns emerged for BPS concentrations measured in either parent. We observed a strong negative association between maternal-but not paternal-preconception BPA concentrations and offspring birth size among a subfertile population. Although these results are overall consistent with prior studies on prenatal BPA exposure, these findings may not be generalizable to women without fertility concerns. This study suggests that the unexplored maternal preconception period may be a sensitive window for BPA effects on birth outcomes. Work supported by Grants (ES R01 009718, ES 022955 and ES 000002) from the National Institute of Environmental Health Sciences (NIEHS). C.M. was supported by a post-doctoral fellowship award from the Canadian Institutes of Health Research. There are no competing interests to declare.
- Abstract
- 10.1210/jendso/bvab048.992
- May 3, 2021
- Journal of the Endocrine Society
Developmental exposure to endocrine disruptor bisphenol A (BPA) is associated \\with metabolic defects during adulthood in the female sheep. These are characterized by peripheral insulin resistance and increase in negative mediators of insulin sensitivity such as oxidative stress in metabolic tissues, lipotoxicity in liver and muscle and adipocyte hypertrophy in visceral (VAT) and subcutaneous (SAT) adipose tissue. Conceivably, developmental impact of BPA on regulators of insulin sensitivity involves changes in epigenetic machinery and mediated via changes in expression of enzymes that induce covalent modifications of DNA and histone. To determine the impact of prenatal BPA exposure on epigenetic enzymes [DNA methyltransferases (DNMT), histone deacetylases (HDAC), histone acetyl transferase EP300, histone methylases (SUV39H1, SMYD3 and EZH2) and histone demethylase KDM1A], metabolic tissues (liver, muscle, VAT and SAT) were collected from 21-month-old female offspring born to mothers treated with 0, 0.05, 0.5, or 5 mg/kg/day of BPA from days 30-90 of gestation. Data were analyzed by Cohen’s effect size analysis and large magnitude differences (Cohens d>0.8) discussed. In liver, prenatal BPA induced: 1) a decrease in DNMT1 and 3B at all doses and DNMT3A at the highest dose, 2) a decrease in histone deacetylase HDAC3 as opposed to increase in acetylase EP300 at the highest dose, 3) a decrease in SUV39H1 at the two higher doses, and 4) an increase in EZH2 only with 0.5 mg dose. The prenatal BPA-induced changes in muscle include: 1) increases in expression of DNMTs and EP300 at all doses, 2) an increase in SUV39H1 at 0.5 mg dose and EZH2 at 0.05 and 0.5 mg doses, and 3) decreases in SMYD3 at the lowest dose and KDM1A with 0.05 and 5 mg doses. Prenatal BPA treatment also induced depot-specific changes at the adipose tissue level. In the VAT prenatal BPA induced: 1) increases in expression of all DNMTs examined 2) increases in HDAC2 at all doses except HDAC3 only at 0.05 and 0.5mg dose and 3) increases in histone acetylase EP300 at all doses. In SAT BPA induced: 1) decrease in DNMT3A at 0.5mg and increase at 5 mg, 2) decreases in HDAC1 and HDAC2 at the lowest dose, 3) an increase in HDAC3 at the medium dose, and 4) a decrease in EP300 at the lowest dose. Contrasting changes in histone methylation modifying enzymes were also evident between VAT and SAT manifested as increases in SUV39H1 at the two higher doses and SMYD3 at all three doses in the VAT as opposed to decrease in SUV39H1 and SMYD3 at 0.05 and 0.5 mg doses and EZH2 and KDM1A at the lowest dose in the SAT. These findings indicating developmental exposure to BPA induces non-monotonic dose responses in epigenetic modifying enzymes are consistent with the premise that changes in epigenetic machinery underlie the metabolic disruptions induced by prenatal BPA treatment likely accounting for the tissue specific changes in insulin sensitivity. (support by R01-ES-016541)
- Research Article
139
- 10.1016/j.envres.2016.07.028
- Aug 3, 2016
- Environmental Research
Bisphenol A exposure and symptoms of anxiety and depression among inner city children at 10–12 years of age
- Research Article
34
- 10.1186/s12940-017-0259-8
- May 19, 2017
- Environmental Health
BackgroundAnimal models show that prenatal bisphenol A (BPA) exposure leads to sexually dimorphic disruption of the neuroendocrine system in offspring, including the hypothalamic-pituitary-adrenal (HPA) neuroendocrine system, but human data are lacking. In humans, prenatal BPA exposure is associated with sex-specific behavioural problems in children, and HPA axis dysregulation may be a biological mechanism. The objective of the current study was to examine sex differences in associations between prenatal maternal urinary BPA concentration and HPA axis function in 3 month old infants.MethodsMother-infant pairs (n = 132) were part of the Alberta Pregnancy Outcomes and Nutrition study, a longitudinal birth cohort recruited (2010–2012) during pregnancy. Maternal spot urine samples collected during the 2nd trimester were analyzed for total BPA and creatinine. Infant saliva samples collected prior to and after a blood draw were analyzed for cortisol. Linear growth curve models were used to characterize changes in infant cortisol as a function of prenatal BPA exposure.ResultsHigher maternal BPA was associated with increases in baseline cortisol among females (β = 0.13 log μg/dL; 95% CI: 0.01, 0.26), but decreases among males (β = −0.22 log μg/dL; 95% CI: -0.39, −0.05). In contrast, higher BPA was associated with increased reactivity in males (β = .30 log μg/dL; 95% CI: 0.04, 0.56) but decreased reactivity in females (β = −0.15 log μg/dL; 95% CI: -0.35, 0.05). Models adjusting for creatinine yielded similar results.ConclusionsPrenatal BPA exposure is associated with sex-specific changes in infant HPA axis function. The biological plausibility of these findings is supported by their consistency with evidence in rodent models. Furthermore, these data support the hypotheses that sexually dimorphic changes in children’s behaviour following prenatal BPA exposure are mediated by sexually dimorphic changes in HPA axis function.
- Research Article
3
- 10.1016/j.neuro.2022.05.018
- Jun 2, 2022
- NeuroToxicology
Prenatal bisphenol A exposure in relation to behavioral outcomes in girls aged 4–5 and modification by socio-demographic factors in The Infant Development and Environment Study (TIDES)
- Research Article
- 10.1289/isee.2020.virtual.o-os-111
- Oct 26, 2020
- ISEE Conference Abstracts
BACKGROUND: Epigenetic mechanisms have been suggested to play a role in the link between in utero exposure to bisphenol A (BPA) and pediatric obesity; however, there is little evidence regarding this in humans. OBJECTIVES: We identified differentially methylated CpG sites among 594-targeted obesity-related CpG sites (reported from previous epigenome-wide association studies) in children aged 2 and 6 years, depending on prenatal BPA exposure at second trimester. We then evaluated the relationship between the CpG methylation status and body mass index (BMI) in a prospective children’s cohort at ages 2, 4, 6, and 8 years. METHODS: Longitudinal blood samples of 59 children, aged 2 and 6 years, from the Environment and Development in Children cohort were used for methylation analysis using the Infinium Human Methylation BeadChip 450K, and compared between low and high prenatal BPA exposure groups based on the 80th percentile of maternal BPA levels. RESULTS: The unimodal CpG site, cg19196862(IGF2R), and bimodal CpG sites, cg09196346 and cg27596172, at the age of 2 years were significantly different depending on prenatal BPA exposure. There was significant increase in the methylation levels of cg19196862(IGF2R) in the high BPA group at age 2 years (p = 0.00030, false discovery rate corrected p < 0.05) but not at 6 years. With one standard deviation increase of methylation at cg19196862(IGF2R) at age 2 years, the BMI Z-score at ages 2, 4, 6, and 8 years increased significantly by 0.25 (95% confidence interval (CI); 0.05, 0.46), 0.240 (95% CI; 0.03, 0.45), 0.23 (95% CI; 0.02, 0.44), and 0.31 (95% CI; 0.02, 0.60), respectively. When stratified by sex, this positive association was significant in girls, but not in boys. CONCLUSION: Prenatal exposure to BPA may influence differential methylation of IGF2R at age 2 years, which could persistently affect the BMI Z-scores in early childhood.
- Research Article
10
- 10.1159/000516881
- Apr 29, 2021
- Neuroendocrinology
Introduction: Biomonitoring of bisphenol A (BPA) in human blood is still scarce, although already noticeable. We aimed to examine the associations between prenatal serum BPA concentrations and behavior and cognitive function in preschool children. Methods: A total of 1,782 mother-child pairs with complete demographic information, blood samples, and psychological measurements were included from the China-Anhui Birth Cohort (C-ABCS). We detected serum BPA concentrations and assessed children’s neurodevelopment using a set of psychometric scales. Results: The median prenatal maternal serum BPA concentration was 0.23 (P25, P75: 0.07, 0.52) ng/mL, with a detection frequency of 85.19%. Compared with the girls with the lowest concentrations, those with highest BPA concentrations had increased risks of inhibitory self-control impairment [relative risk (RR) = 3.66, 95% confidence interval (CI): 1.53, 7.58], emergent metacognition impairment (RR = 1.70, 95% CI: 1.07, 2.78), conduct problem (RR = 1.68, 95% CI: 1.12, 2.39), peer relationship problem (RR = 2.57, 95% CI: 1.33, 4.47), higher total difficulties score (RR = 1.76, 95% CI: 1.12, 2.67), and higher impact factor score (RR = 1.52, 95% CI: 1.11, 2.05), while the boys with the highest prenatal BPA concentrations had an increased risk of conduct problem compared with those with the lowest concentrations (RR = 1.59, 95% CI: 1.09, 2.24) (P-interaction = 0.011). After stratification by age, high prenatal BPA concentrations were associated with increased ADHD (RR = 4.44, 95% CI: 1.54, 10.85) among children aged 3 years, not among children aged 4 years. Conclusion: Our study revealed the sex-specific and age-specific impacts of prenatal BPA exposure on preschool children’s cognitive and behavioral development.
- Abstract
- 10.1210/jendso/bvac150.932
- Nov 1, 2022
- Journal of the Endocrine Society
Prenatal exposure to bisphenol-A (BPA), an ubiquitously present endocrine-disrupting chemicals, induces peripheral insulin resistance as well as lipotoxicity and oxidative stress in the liver and muscle along with tissue-specific transcriptional changes in female sheep. To gain a mechanistic understanding of contributors to these liver and muscle-specific transcriptional changes, we hypothesized that prenatal BPA exposure impacts non-coding RNA (ncRNA), regulators of transcriptional and post-transcriptional control of coding RNAs. We sequenced ncRNA (including lncRNA, microRNA, snoRNA, and snRNA) in the liver and muscle obtained during the late follicular phase from 21-month-old control and prenatal BPA-treated (0.5mg/kg/day from days 30 to 90 of gestation; Term: 147days) female sheep (n=4 control and 4 prenatal BPA treated). The sequence data were subjected to differential expression analysis and multivariate modeling to identify specific ncRNA signatures. In the liver, 77 lncRNA (49 down, 28 up), 14 microRNAs (6 down, 8 up), 127 snoRNAs (63 down, 64 up) and 55 snRNAs (15 down, 40 up) were dysregulated (FDR<0.1, absolute log2FC>0.5) with BPA exposure. In the muscle 6 lncRNA were upregulated and 65 snoRNAs (47 down, 18 up) were dysregulated (FDR<0.1, absolute log2FC>0.5). Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) plots identified microRNAs MIR200B, MIR409, MIR30B, and MIR154A in the liver and miRNAs MIR26B, MIR29A, MIR125B, and MIR127 in muscle and several uncharacterized ncRNAs as signatures of prenatal BPA exposure. Multiple ncRNA signatures correlated with coding genes including LCORL, MED17, and ZNF41 in the liver, but none were correlated in the muscle. Among the coding genes which correlated with ncRNA, LCORL is reported to be related to steatosis of the liver in geese, a feature also observed in livers from prenatal BPA-treated female sheep. Since lipid accumulation in the liver may result from increased fatty acid biosynthesis, MED17 which is involved in transcriptional activation of lipogenic genes that correlated with multiple ncRNA in the liver may be a contributor to the steatosis observed in this model. In addition, MIR200B and MIR30B in the liver and MIR26B and MIR29A in the muscle are linked to lipid dysfunction, endoplasmic reticulum stress, and fibrosis. These findings provide mechanistic clues into the role of ncRNA in the prenatal BPA-induced lipid accumulation and oxidative stress in the liver and muscle, contributors to metabolic dysfunction observed in this female sheep model of gestational BPA exposure. In addition, findings from this precocial model of human translational relevance is a step towards gaining mechanistic insights in the programming of metabolic dysfunctions from environmental exposure to BPA, an endocrine disruptor of public health relevance.Presentation: Sunday, June 12, 2022 1:06 p.m. - 1:11 p.m., Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.
- Research Article
43
- 10.1016/j.envint.2020.105929
- Jul 6, 2020
- Environment International
ObjectivesEpigenetic mechanisms have been suggested to play a role in the link between in utero exposure to bisphenol A (BPA) and pediatric obesity; however, there is little evidence regarding this mechanism in humans. We obtained data on obesity-associated CpG sites from a previous epigenome-wide association study, and then examined whether methylation at those CpG sites was influenced by prenatal BPA exposure. We then evaluated the relationship between CpG methylation status and body mass index (BMI) in a prospective children’s cohort at ages 2, 4, 6, and 8 years. MethodsMethylation profiles of 59 children were longitudinally analyzed at ages 2 and 6 years using the Infinium Human Methylation BeadChip. A total of 594 CpG sites known to be BMI or obesity-associated sites were tested for an association with prenatal BPA levels, categorized into low and high exposure groups based on the 80th percentile of maternal BPA levels (2.68 μg/g creatinine), followed by an analysis of the association between DNA methylation and BMI from ages 2–8. ResultsThere was a significant increase in the methylation levels of cg19196862 (IGF2R) in the high BPA group at age 2 years (p = 0.00030, false discovery rate corrected p < 0.10) but not at age 6. With one standard deviation increase of methylation at cg19196862 (IGF2R) at age 2 years, the linear mixed model analysis revealed that BMI during ages 2–8 years significantly increased by 0.49 (95% confidence interval; 0.08, 0.90) in girls, but not in boys. The indirect effect of prenatal BPA exposure on early childhood BMI through methylation at cg19196862 (IGF2R) at age 2 years was marginally significant. ConclusionsPrenatal exposure to BPA may influence differential methylation of IGF2R at age 2. This result indicates that a possible sensitive period of DNA methylation occurs earlier during development, which may affect BMI until later childhood in a sex-specific manner.
- Research Article
50
- 10.1152/ajpendo.00425.2015
- Dec 8, 2015
- American Journal of Physiology-Endocrinology and Metabolism
Among potential contributors for the increased incidence of metabolic diseases is the developmental exposure to endocrine-disrupting chemicals such as bisphenol A (BPA). BPA is an estrogenic chemical used in a variety of consumer products. Evidence points to interactions of BPA with the prevailing environment. The aim of this study was to assess the effects of prenatal exposure to BPA on postnatal metabolic outcomes, including insulin resistance, adipose tissue distribution, adipocyte morphometry, and expression of inflammatory markers in adipose tissue as well as to assess whether postnatal overfeeding would exacerbate these effects. Findings indicate that prenatal BPA exposure leads to insulin resistance in adulthood in the first breeder cohort (study 1), but not in the second cohort (study 2), which is suggestive of potential differences in genetic susceptibility. BPA exposure induced adipocyte hypertrophy in the visceral fat depot without an accompanying increase in visceral fat mass or increased CD68, a marker of macrophage infiltration, in the subcutaneous fat depot. Cohens effect size analysis found the ratio of visceral to subcutaneous fat depot in the prenatal BPA-treated overfed group to be higher compared with the control-overfed group. Altogether, these results suggest that exposure to BPA during fetal life at levels found in humans can program metabolic outcomes that lead to insulin resistance, a forerunner of type 2 diabetes, with postnatal obesity failing to manifest any interaction with prenatal BPA relative to insulin resistance and adipocyte hypertrophy.
- Research Article
1
- 10.3389/fgene.2024.1346150
- Feb 20, 2024
- Frontiers in Genetics
DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS). Bismark (0.22.3) were used for mapping the WGBS reads and R Bioconductor package DSS was used for differential methylation analysis. Cold exposure induced 3,163 differentially methylated cytosines (DMCs) with methylation difference ≥10% and a q-value < 0.05. We identified 438 differentially methylated regions (DMRs) with q-value < 0.05, which overlapped with 186 unique genes. We also identified eight unique differentially methylated genes (DMGs) (Pax6, Macf1, Mest, Ubqln1, Smg9, Ctnnb1, Lsm4, and Peg10) involved in embryonic development, and nine unique DMGs (Prmt6, Nipal1, C21h15orf40, Slc37a3, Fam210a, Raly, Rgs3, Lmbr1, and Gan) involved in osteogenesis. Peg10 and Mest, two paternally expressed imprinted genes, exhibited >50% higher methylation. The differential methylation patterns of six distinct DMRs: Peg10, Smg9 and Mest related to embryonic development and Lmbr1, C21h15orf40 and Prtm6 related to osteogenesis, were assessed by methylation-specific PCR (MS-PCR), which confirmed the existence of variable methylation patterns in those locations across the two seasons. In summary, cold exposure induces differential DNA methylation patterns in genes that appear to affect embryonic development and osteogenesis in the offspring. Our findings suggest the importance of replicating the results of the current study with a larger sample size and exploring the potential of these changes in affecting offspring development.
- Research Article
1
- 10.1158/1538-7755.disp15-a04
- Mar 1, 2016
- Cancer Epidemiology, Biomarkers & Prevention
African Americans (AAs) have more severe breast cancer, and higher death rate from breast cancer, than that of Caucasian Americans (CAs) even after socioeconomic status are accounted for. Various studies have been done to understand the biological mechanism of this health disparity. In this study, we performed a genome-wide differential DNA methylation analysis between AA and CA breast cancer patients. We analyzed differentially methylated positions (DMPs) and differentially methylated regions (DMRs) using data from 143 AA and 554 CA breast tumor tissues available at the Cancer Genome Atlas (TCGA). We found that there were 1232 DMPs and 661 DMRs between AA and CA breast cancer patients. Both DMP and DMR showed that PACS2 and ATP1A4 were highly differentially methylated among other genes. Network analysis showed that differential methylation occurred significantly in p53, EGFR, and ERS1 subnetwork, which is consistent from an early study on differentially expressed transcripts. We also conducted a correlation analysis between gene expression by RNA sequencing and DNA methylation, which showed that expressions of 129 genes with either DMP or DMR were highly negatively correlated with the corresponding DNA methylations, suggesting that these DNA methylation may play important roles in the breast cancer health disparity observed in AA women. Our discoveries may help researchers to better understand the biological factors for breast cancer health disparity and the biology of breast cancer in general. The genes or DMPs/DMRs identified may serve as the starting points for further experimental validations towards discovering biomarkers for cancer diagnosis and prognosis, and drug targets for personalized treatments. Citation Format: Kaixian Yu, Albert Steppi, Yun Xu, Ke Tang, Jinfeng Zhang. Differential DNA methylation and network analysis in African American breast cancer. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr A04.
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