2017 Progress Report: Prenatal Exposures, Constitutive Genetics, DNA Methylation & Childhood Leukemia

EPA Grant Number: R836159C003
Subproject: this is subproject number 003 , established and managed by the Center Director under grant R836159
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).

Center: Center for Integrative Research on Childhood Leukemia and the Environment - 2015
Center Director: Metayer, Catherine
Title: Prenatal Exposures, Constitutive Genetics, DNA Methylation & Childhood Leukemia
Investigators: Wiemels, Joseph , Metayer, Catherine , Segal, Mark , Whitehead, Todd , de Smith, Adam
Institution: University of California - San Francisco , University of California - Berkeley
EPA Project Officer: Louie, Nica
Project Period: September 1, 2015 through August 31, 2019
Project Period Covered by this Report: September 1, 2016 through August 31,2017
RFA: Children's Environmental Health and Disease Prevention Research Centers (2014) RFA Text |  Recipients Lists
Research Category: Health , Children's Health


The overarching research theme of CIRCLE is to identify additional in utero chemical risk factors for childhood acute lymphoblastic leukemia (ALL) in an ethnically diverse population, and to understand how chemicals increase risk via immunological, genetic, and epigenetic mechanisms. In this project, researchers will construct a constitutive genetic framework for DNA methylation profiles at birth; evaluate the perturbation of DNA methylation by chemical, immune, and dietary factors; and assess the impact of these factors on childhood ALL risk. Researchers will leverage existing resources from two NIH-funded studies, the California Childhood Leukemia Study (CCLS, a population-based case-control study), and the California Mother-Child Birth Cohort (CA Birth Cohort, a cohort of children diagnosed with leukemia, healthy children without leukemia, and their mothers). Additionally, researchers will test the effect of in utero chemical exposures on DNA methylation in pre-B cells (our target cell population), as well as on leukemogenesis, using an engineered mouse model for the first time. 

Aim 1: Construct a constitutive genetic framework for DNA methylation profiles at birth in 200 childhood ALL cases and 400 controls in the CA Birth Cohort.

Aim 2:  Determine the perturbation of DNA methylation by in utero chemical, dietary, and immune factors, incorporating constitutive genetics, and the subsequent effect on childhood ALL risk, using resources from the California Childhood Leukemia Study (CCLS).

Aim 3: Assess the impact of in utero chemical exposures on pre-B cell development, pre-B cell DNA methylation, and leukemogenesis in the offspring of exposed mice.

Progress Summary:

Aims 1 and 2: The Center received from the California State biobank the archived blood spots for neonatal DNA methylation studies, as well as blood clots from maternal pregnancy screening. The initial linkage between the maternal and child biobanks yielded less sample than expected mother/child cases. In order to maintain sufficient statistical power, researchers increased the case:control ratio from 1:2 to 1:3. Researchers have isolated DNA from the blood spots and have commenced DNA isolation from the maternal clots. These specimens will be utilized for Project 1 cytokine testing (neonatal bloods and maternal pregnancy bloods) and for Project 2 (exposure measurements) and the current project (DNA methylation and genotyping).

Researchers continued to work with our previously collected HM450K data to address several aspects of the aims. Researchers assessed the genomic contribution both genome-wide and locally to known epigenetic markers of maternal smoking, which was published this year. Researchers noted that the top CpG loci recently replicated in PACE consortium studies also were the top hits in our data. This allowed us the potential to use CpG methylation at specific sites as an “epigenetic biomarker” of maternal smoking. Interestingly, epidemiologic case-control studies have long shown a consistent risk estimate for paternal smoking and childhood leukemia, but no relationship with maternal smoking. There are potential biases that could affect this – maternal smoking may be underreported or the risk may occur via sidestream smoke from other housing members for instance. Researchers therefore used DNA methylation at the most sensitive locus for maternal smoking, cg05575921, and found that DNA methylation at this locus was lower (which is the direction indicating increased smoking) at birth in our leukemia cases compared to controls (Gonseth, et al., 2016). Researchers also assessed maternal smoking and tumor genetic features of leukemia cells, finding that self-reported smoking was associated with numbers of deletions in leukemia cells in a dose-dependent fashion (de Smith, et al., 2017). This result also was corroborated by using DNA methylation of cg05575921 as a biomarker of maternal smoking.

In addition, researchers have worked with our colleagues at the International Agency for Research on Cancer (Zdenko Herceg and Akram Ghantous) and the University of Melbourne (Richard Saffery) to discover and validate new DNA methylation marks at birth that predict future risk of leukemia. Researchers have discovered two new loci that seem to validate in all three datasets, and researchers will report on these in the coming year as well as analyze the role of environmental and genetic determinants that affect their DNA methylation status.

Our research group also is heavily involved in a new field called “immunomethylomics,” which is the analysis of blood cell types by their DNA methylation patterns and how this influences biology and disease incidence and progression. Our goal for neonates is to identify the presence of myeloid-derived suppressor cells and determine their role in response to environmental chemicals and leukemogenesis. This represents a connection between Projects 3 and 1. As new blood cell reference sets have become available, researchers also found that certain CpG loci are capable of identifying fetal versus postnatal developed stem cells. This stem cell profile is highly variable among our leukemia case population and researchers now are working to determine the relationship of the fetal stem cell profile with demographic and exposure variables.

Aim 3: Researchers have continued work on optimizing our mouse model for leukemia and preparing relevant chemical dosing strategies. This work was completed for PCBs as an exposure (see Core C Progress Report), and researchers now have on hand DNA samples to begin DNA methylation profiling of exposed mice. Researchers have chosen to perform enhanced reduced representation bisulfite sequencing of the mouse DNA specimens as a service provided by Weill College epigenetic profiling services (Cornell University).

Future Activities:

In the next year for Aims 1 and 2, researchers plan to complete the physical genotyping and DNA methylation profiling (HM450K EPIC array) of our DNA samples for Project 3. Also, researchers will complete our collaborative (with IARC and U. Melbourne) analysis of leukemia case-control differences at birth, which will create a catalog of DNA methylation events at birth that predict future risk of leukemia. This catalog will be useful in our plans for later this year to replicate and extend our investigation of the effects of environmental agents on DNA methylation profiles at birth with the influence of genetic variation.

In the next year for Aim 3, researchers will continue to refine our animal model and continue chemical dosing on mouse experiments. These experiments require extended periods of observation, which will extend into Year 4. Researchers also will continue to work on ERRBS methodology (for mouse cell DNA methylation) and data analysis.

Journal Articles on this Report : 2 Displayed | Download in RIS Format

Other subproject views: All 3 publications 3 publications in selected types All 3 journal articles
Other center views: All 25 publications 23 publications in selected types All 23 journal articles
Type Citation Sub Project Document Sources
Journal Article de Smith AJ, Kaur M, Gonseth S, Endicott A, Selvin S, Zhang L, Roy R, Shao X, Hansen HM, Kang AY, Walsh KM, Dahl GV, McKean-Cowdin R, Metayer C, Wiemels JL. Correlates of prenatal and early-life tobacco smoke exposure and frequency of common gene deletions in childhood acute lymphoblastic leukemia. Cancer Research 2017;77(7):1674-1683. R836159 (2017)
R836159 (2018)
R836159C003 (2017)
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  • Journal Article Gonseth S, de Smith AJ, Roy R, Zhou M, Lee S-T, Shao X, Ohja J, Wrensch MR, Walsh KM, Metayer C, Wiemels JL. Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates. Epigenetics 2016;11(9):664-673. R836159 (2017)
    R836159 (2018)
    R836159C003 (2017)
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    Progress and Final Reports:

    Original Abstract
  • 2016 Progress Report
  • 2018

  • Main Center Abstract and Reports:

    R836159    Center for Integrative Research on Childhood Leukemia and the Environment - 2015

    Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R836159C001 In Utero Chemical Exposures, Immune Status, and Childhood Leukemia
    R836159C002 Identifying In Utero Exposures that are Risk Factors for Childhood Leukemia
    R836159C003 Prenatal Exposures, Constitutive Genetics, DNA Methylation & Childhood Leukemia