Abstract 831: In utero polycyclic aromatic hydrocarbons exposure and genome-wide DNA methylation modifications at birth in children who develop acute lymphoblastic leukemia
Authors: Gonseth Semira , Whitehead Todd P. , Roy Ritu , Houseman E. Andres , de Smith Adam J. , Zhou Mi , Lee Seung-Tae , Wrensch Margaret R. , Rappaport Stephen M. , Metayer Catherine , Wiemels Joseph L. 
Published: August 2015

Introduction

Previously, residential dust content of polycyclic aromatic hydrocarbons (PAHs) was associated with an increased risk of acute lymphoblastic childhood leukemia (ALL), and PAHs exposure levels have been associated with differentially methylated regions (DMRs) in candidate genes studies. Thus, we hypothesized that in utero exposure to residential PAHs may be associated with genome-wide DMRs in genes that may influence ALL development.

Methods

PAHs were measured in dust samples collected using a high-volume surface sampler or household vacuum cleaners from homes of California Childhood Leukemia Study participants who have lived in the same home since diagnosis. The different PAHs were summed according to their toxic equivalency. DNA was extracted from archived neonatal blood spots of participants, then treated with bisulfite and assayed on Illumina Infinium 450K genome-wide DNA methylation arrays. Following removal of cross-reacting probes, SNP-related and polymorphic CpGs, we analyzed the association of residential PAH levels with methylation intensity of 319,265 CpGs in two independent case-only datasets (model #1: set 1 cases n = 84, set 2 cases n = 51). We used a false discovery rate with random resampling to reduce the number of false-positive findings and cross-validated the results between sets. This first step of the analysis gave 11 significant and sign concordant CpGs. Then we assessed interactions between case/control status and PAHs levels with methylation intensities at those 11 CpGs in set 1 (model #2: total cases and controls n = 306). Models were adjusted for cell mixture, sex, gestational age, race and the first 2 principal components of the models’ residuals.

Results

In model #1, methylation levels at 11 CpGs were significantly associated with residential PAH levels and sign concordant in both sets with a corresponding q-value &lt; 10−08. In model #2, the interaction terms between PAH and case/control status were significant (p&lt;0.05) in 7 of these 11 CpGs, and the 3 most significant were: cg13484813 (p &lt;0.001) in LGR5 (chr12q21.1) which is differentially expressed in pre-B cell vs. leukemia cells; cg23196133 (p &lt;0.01) in ZBTB4 (chr17p13.1) which is a transcription factor linked to p53; and cg07617339 (p &lt;0.01) in ATF6B (chr6p21.3) which encodes a transcription factor.

Conclusions

For the first time, our genome-wide methylation investigation found that residential PAH levels were associated with 11 CpGs at birth among children who later developed ALL. Moreover, the future cases had significantly different DNA methylation responses to PAH exposures than the unaffected controls for 7 CpGs. This may suggest a case/control difference present at birth in the sensitivity to PAHs in particular cell-cycle and tumor-suppressor genes. These CpGs may be good candidates to further investigate with respect to leukemogenesis.

Citation Format: Semira Gonseth, Todd P. Whitehead, Ritu Roy, E. Andres Houseman, Adam J. de Smith, Mi Zhou, Seung-Tae Lee, Margaret R. Wrensch, Stephen M. Rappaport, Catherine Metayer, Joseph L. Wiemels. In utero polycyclic aromatic hydrocarbons exposure and genome-wide DNA methylation modifications at birth in children who develop acute lymphoblastic leukemia. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 831. doi:10.1158/1538-7445.AM2015-831