2011 Progress Report: Prenatal Exposures, DNA Methylation & Childhood Leukemia

EPA Grant Number: R834511C003
Subproject: this is subproject number 003 , established and managed by the Center Director under grant R834511
(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 (CIRCLE)
Center Director: Buffler, Patricia
Title: Prenatal Exposures, DNA Methylation & Childhood Leukemia
Investigators: Buffler, Patricia , Wiemels, Joseph
Institution: University of California - Berkeley , University of California - San Francisco
EPA Project Officer: Louie, Nica
Project Period: September 24, 2009 through September 24, 2015
Project Period Covered by this Report: September 25, 2010 through September 24,2011
RFA: Children's Environmental Health and Disease Prevention Research Centers (with NIEHS) (2009) RFA Text |  Recipients Lists
Research Category: Children's Health , Health


The proposed new Children’'s Environmental Health Center based at the University of California, Berkeley is designed to examine the effects of in utero and early life exposure to potentially carcinogenic chemicals present in homes (i.e., pesticides, tobacco-related contaminants, polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs)), and genetic and epigenetic factors, and their interplay in the development of childhood leukemia. The proposed Center, referred to as Center for Interdisciplinary Research on Childhood Leukemia and the Environment (CIRCLE) includes three Research Projects and two Cores.
Project 3: Prenatal Exposures, DNA Methylation, & Childhood Leukemia. This project will provide a clearer understanding of the association between parental smoking, pesticides, PCBs, and PBDEs exposures and DNA methylation patterns in childhood leukemia, using neonatal bloods.

Progress Summary:

Aim 1: Characterize the DNA methylation pattern of normal B-cell differentiation as compared to their leukemic cell counterparts.
We have continued our research activities on characterizing the normal pattern of DNA methylation during B-cell differentiation. This activity is dependent upon two key activities: obtaining high quality primary normal bone marrow, and high quality cell sorting procedures for fine sorting of pre-B cell populations. In our progress report from last year, we identified sources for the normal B-cell populations and have performed pilot experiments to sort these populations. Bone marrow is obtained from fetal sources, from children who have recovered from leukemia (who are relatively age-matched to our population of interest), and young adults. Therefore, we are able to assess DNA methylation patterns in ontological stages and calendar ages. An example of our cell sorting was demonstrated in Figure 1 from last year’'s progress report, and a number of genes that were identified as being de-methylated and methylated are shown in Figure 1 in this year'’s report. The presence of CD19 as one of the loci that lost methylation is a testament to the success of this experiment. This involves the use of the Illumina 27,000 CpG site array, but our larger experiments currently underway use the Illumina 486,000 CpG site array, which will provide much more detailed and extensive data than we originally proposed.
We now have carefully assessed and chosen 253 case and 260 control samples with the most extensive data available regarding smoking, pesticides, and other exposure information with which to complete the aims of this proposal. These DNAs and their matched Guthrie cards will be analyzed during 2011 using Year 2 funds and Year 1 carry-forward funds. This DNA will be bisulfite-treated and processed by the UCSF Center for Human Genetics Core using the 486,000 CpG site array and analyzed in the mid to latter half of this year.
Aim 2: Characterize DNA methylation pattern in 250 neonatal DBS cards from leukemia cases (derived from the same case samples as Aim 1) and 250 controls. The laboratory component of this aim currently is underway.
Aim 3: Replicate and extend the findings of Aim 1 by characterizing DNA methylation in a set of disease- and exposure-relevant meta-stable CpG sites in DBS cards from select groups of DBS cards from California leukemia cases and controls. No activities are scheduled in Years 2 and 3. We have, however, completed and approved IRB protocols for this work at UC Berkeley and UCSF. We currently are submitting our IRB for approval at the State of California level.

Future Activities:

Specific Aim 1: We will complete the isolation of DNA and perform Illumina Infinium DNA methylation screens on 250 diagnostic bone marrow mononuclear cell preparations. We will complete the same Infinium panel on several stages of B-cell precursor populations among eight fetal B-cell preparations, to establish the DNA methylation pattern of B-cell development. In addition, we will perform gene expression arrays on the fetal bone marrows to detect which gene methylation changes are associated with functional changes in expression.
Specific Aim 2: We will complete the processing of 250 case and 250 matched control Guthrie cards for DNA methylation assessments by the Illumina Infinium method.
Specific Aim 3: We will commence the collection of Guthrie cards for this Aim by completing the IRB process first. Biological assays will be performed in future years.

Progress and Final Reports:

Original Abstract
  • 2010
  • 2012
  • 2013
  • 2014
  • Final

  • Main Center Abstract and Reports:

    R834511    Center for Integrative Research on Childhood Leukemia and the Environment (CIRCLE)

    Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R834511C001 Childhood Leukemia International Consortium Studies
    R834511C002 Exposure Assessment for Childhood Leukemia
    R834511C003 Prenatal Exposures, DNA Methylation & Childhood Leukemia