2012 Progress Report: Epigenetics Project

EPA Grant Number: R834513C003
Subproject: this is subproject number 003 , established and managed by the Center Director under grant R834513
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).

Center: Center for the Health Assessment of Mothers and Children of Salinas - UC Berkeley School of Public Health: CHAMACOS Office, Berkeley, CA
Center Director: Eskenazi, Brenda
Title: Epigenetics Project
Investigators: Eskenazi, Brenda , Barcellos, Lisa , Bradman, Asa , Harley, Kim , Holland, Nina T. , Lustig, Robert
Current Investigators: Eskenazi, Brenda , Barcellos, Lisa , Bradman, Asa , Harley, Kim , Holland, Nina T. , Hubbard, Alan , Lustig, Robert
Institution: University of California - Berkeley
Current Institution: University of California - Berkeley , University of California - San Francisco
EPA Project Officer: Louie, Nica
Project Period: August 1, 2009 through July 31, 2014 (Extended to July 31, 2016)
Project Period Covered by this Report: June 1, 2011 through May 31,2012
RFA: Children's Environmental Health and Disease Prevention Research Centers (with NIEHS) (2009) RFA Text |  Recipients Lists
Research Category: Children's Health , Health

Objective:

In Project C (R834513C003), we are investigating the effects of exposure to environmental chemicals on the epigenome and its relationship with pubertal onset.

Progress Summary:

1. To analyze global DNA methylation in newborn children by three different assays.
Our preliminary analysis of global methylation as measured by pyrosequencing of LINE-1 and Alu repeats revealed systematic differences due to batch variability. To address this issue, all samples were reanalyzed in triplicate as one single batch performed on the same day to minimize technical variability. All sample plates were designed to ensure that genders and ages were distributed similarly on each plate. Mean LINE-1 global methylation was significantly higher in boys compared to girls in both newborns (p = 0.033) and 9-year-olds (p < 0.005). Higher Alu global methylation was also observed in boys, but this difference was not statistically significant (p = 0.063).
 
We also completed analysis of global and site-specific methylation in 485,577 CpG sites using the Illumina Infinium Methylation 450K Assay in an additional 96 samples. Overall, the assay showed good reproducibility. DNA methylation levels measured for duplicate samples were highly correlated with each other. However, we determined that the current normalization methodologies recommended by the manufacturer (normalization of green and red channel signals for all samples in the project by the control signals measured for the first sample in the first project plate) were inadequate for reducing technical variability and risked biasing results. We are currently developing a multiple step normalization process that can adequately adjust for plate variability, and a manuscript describing our novel approach is in preparation for submission to Epigenomics.
 
2. To determine ontogenetic changes in global DNA methylation in blood of children between birth and 12 years.
Global methylation via pyrosequencing of Alu and LINE-1 repeats has been performed in > 600 blood samples collected from CHAMACOS children at delivery, 2, 5, 7, and 9 years of age. We used generalized estimating equations (GEE) to assess differences in LINE-1 and Alu methylation by age while accounting for within-subject correlations. LINE-1 global DNA methylation was found to decrease 0.3% per month increase in child age (95% CI: 0.2 – 0.6%). A similar decreasing trend was found for Alu methylation as well, but this association was not statistically significant (p = 0.18).
 
3. To investigate the relationship of in utero and 9-year-old blood concentrations of DDT/E and PBDEs with global DNA methylation.
Small but consistent decreases in global methylation measured by both LINE-1 and Alu assays were observed in response to OC and PBDE exposures. However, none of these effects reached statistical significance, likely due to low power to detect small effect sizes.
 
4. To determine whether global methylation is associated with onset of puberty and hormonal changes.
Assessment of pubertal onset at age 9 has been completed in all children (n = 314). These data are still in the process of being entered and cleaned. Analysis of the association between global methylation and age of pubertal onset will begin later this year.
 
5. To examine site-specific methylation in relation to age, sex, exposure to DDT/E and PBDEs and puberty onset.
We analyzed genome-wide and site-specific DNA methylation in 142 CHAMACOS children for subjects that had matched data both at birth and 9 years of age using the Illumina 450K platform and found meaningful variation in methylome by sex and age. We found that 78,599 CpG sites in 15,411 genes were differentially methylated between newborns and 9-year-olds after Bonferroni adjustment for multiple testing. Among boys and girls, 8,741 CpG sites in 1,329 genes were differentially methylated by sex in newborns after Bonferroni adjustment for multiple testing. Furthermore, multiple genes and CpG sites that were differentially methylated in restricted analyses for age and sex were also found to overlap across both of these factors. For exposure, we identified over 100 CpG sites that were differentially methylated by at least one organochlorine congener after adjusting for multiple testing using the false discovery rate (FDR) in 9-year-old children. Pathway enrichment analysis for the 101 genes differentially methylated by o,p'’-DDT exposure identified 10 pathways as significantly overrepresented in our sample, including Neurotropin signaling, spliceosome, and the p53 tumor suppression pathways. Additionally, gene ontology enrichment analysis identified cell-cycle and signaling pathways as significantly overrepresented. In contrast to organochlorines, we observed very few CpG sites that were differentially methylated by PBDE exposure.

Future Activities:

Later this year, we will begin analysis of the relationship between DNA methylation (global and site-specific) and pubertal onset. We will also confirm our preliminary findings for Alu, LINE-1 and Illumina for a larger sample size.


Journal Articles on this Report : 5 Displayed | Download in RIS Format

Other subproject views: All 60 publications 22 publications in selected types All 22 journal articles
Other center views: All 666 publications 138 publications in selected types All 137 journal articles
Type Citation Sub Project Document Sources
Journal Article Bradman A, Castorina R, Sjodin A, Fenster L, Jones RS, Harley KG, Chevrier J, Holland NT, Eskenazi B. Factors associated with serum polybrominated diphenyl ether (PBDE) levels among school-age children in the CHAMACOS cohort. Environmental Science & Technology 2012;46(13):7373-7381. R834513 (2012)
R834513 (2013)
R834513 (Final)
R834513C002 (2012)
R834513C002 (2013)
R834513C003 (2012)
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  • Journal Article Castorina R, Bradman A, Sjodin A, Fenster L, Jones RS, Harley KG, Eisen EA, Eskenazi B. Determinants of serum polybrominated diphenyl ether (PBDE) levels among pregnant women in the CHAMACOS cohort. Environmental Science & Technology 2011;45(15):6553-6560. R834513 (2010)
    R834513 (2011)
    R834513 (2012)
    R834513 (2013)
    R834513 (2015)
    R834513 (Final)
    R834513C001 (2010)
    R834513C001 (2011)
    R834513C001 (2012)
    R834513C002 (2010)
    R834513C002 (2011)
    R834513C002 (2012)
    R834513C003 (2012)
    R831710 (Final)
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  • Journal Article Huen K, Bradman A, Harley K, Yousefi P, Boyd Barr D, Eskenazi B, Holland N. Organophosphate pesticide levels in blood and urine of women and newborns living in an agricultural community. Environmental Research 2012;117:8-16. R834513 (2010)
    R834513 (2011)
    R834513 (2012)
    R834513 (2013)
    R834513 (2015)
    R834513 (Final)
    R834513C001 (2010)
    R834513C001 (2011)
    R834513C002 (2010)
    R834513C002 (2012)
    R834513C002 (2013)
    R834513C003 (2010)
    R834513C003 (2011)
    R834513C003 (2012)
    R831710 (Final)
    R832734 (Final)
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  • Journal Article Huen K, Yousefi P, Bradman A, Yan L, Harley KG, Kogut K, Eskenazi B, Holland N. Effects of age, sex, and persistent organic pollutants on DNA methylation in children. Environmental and Molecular Mutagenesis 2014;55(3):209-222. R834513 (2012)
    R834513 (2013)
    R834513 (2014)
    R834513 (2015)
    R834513 (Final)
    R834513C001 (2015)
    R834513C003 (2010)
    R834513C003 (2012)
    R834513C003 (2014)
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  • Abstract: Wiley-Abstract
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  • Journal Article Yousefi P, Huen K, Schall RA, Decker A, Elboudwarej E, Quach H, Barcellos L, Holland N. Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies. Epigenetics 2013;8(11):1141-1152. R834513 (2012)
    R834513 (2013)
    R834513 (2014)
    R834513 (2015)
    R834513 (Final)
    R834513C003 (2012)
    R834513C003 (2013)
    R834513C003 (2014)
    R834513C003 (2015)
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  • Supplemental Keywords:

    DDE, DDT, epigenetics, flame retardants, maneb, manganese, methylation, PBDEs, puberty, RFA, Health, Scientific Discipline, INTERNATIONAL COOPERATION, Health Risk Assessment, Biochemistry, Children's Health, Environmental Policy, Biology, farmworkers, pesticide exposure, flame retardants, PBDE, children's vulnerablity, neurochemical effects, harmful environmental agents, biological markers, agricultural community

    Relevant Websites:

    http://cerch.org/ Exit

    Progress and Final Reports:

    Original Abstract
  • 2010 Progress Report
  • 2011 Progress Report
  • 2013 Progress Report
  • 2014 Progress Report
  • 2015 Progress Report
  • Final

  • Main Center Abstract and Reports:

    R834513    Center for the Health Assessment of Mothers and Children of Salinas - UC Berkeley School of Public Health: CHAMACOS Office, Berkeley, CA

    Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R834513C001 CHAMACOS Cohort Project: Pesticides and PBDE on Neurobehavior and Puberty
    R834513C002 Project B: Exposure Project: Mn, DDT/E and PBDE Exposure to Farmworker Children
    R834513C003 Epigenetics Project
    R834513C004 Community Outreach and Translation Core