Gene-Environment Analyses Reveal Novel Genetic Candidates with Prenatal Tobacco Exposure in Relation to Risk for Childhood Acute Lymphoblastic Leukemia

Abstract

Background: Associations between maternal tobacco exposure during pregnancy and childhood acute lymphoblastic leukemia (ALL) have yielded mixed results. This may be due to biases in self-reported smoking or other differences in individual-level risk factors. We utilized a biological marker of maternal tobacco exposure to evaluate the association between maternal tobacco exposure during pregnancy, genetics, and subsequent childhood ALL risk in two large population-based studies of childhood ALL in California.

Methods: Maternal exposure to tobacco smoke was assessed with a validated methylation marker (cg05575921) of the aryl hydrocarbon receptor repressor (AHRR) gene in newborn dried blood spots. We adjusted for sex, birthweight, gestational age, mode of delivery, year of birth, AHRR quantitative trait locus (mQTL) rs77111113, and a polygenetic risk score for childhood ALL. We additionally adjusted for principal components in a gene-environment interaction testing method that incorporates gene-only and environment-only effects along with interactions.

Results: AHRR hypomethylation overall was not associated with childhood ALL. In gene-environment interaction testing, several genetic variants displayed significant interaction with AHRR hypomethylation and childhood ALL.

Conclusions: Our results suggest that novel candidates in PTPRK and DPP6 may play a role in tobacco-related leukemogenesis. Further research is necessary to better understand the effects of tobacco and these variants on childhood ALL risk.

Impact: Despite the lack of an overall "main effect," tobacco exposure during pregnancy affects childhood ALL risk depending on specific genetic variants.

Figure 1:

Density distribution of cases and controls (combined) by ethnicity based on percentage of AHRR hypomethylation: AHRR cg05575921 status (raw, without genetic correction) is shown among Hispanic and non-Hispanic White children.

Figure 2:

Complex relationships of AHRR DNA methylation status (a biomarker for maternal tobacco exposure during pregnancy), gestational age, birthweight, and ALL risk. Each line corresponds to the percentile (10^th, median, 90^th) of the variable indicated on the right side of the Y-axis. The X-axis variable is presented as a continuous measure, with relative ALL risk plotted on the Y-axis. A: Association between AHRR hypomethylation (increased tobacco exposure) and birthweight (z-score adjusted for sex at gestational age based on standards developed by the INTERGROWTH-21st Project) when gestational age is set to median. While higher birthweight is associated with risk (note the 0.9 quantile at the top of the figure), tobacco exposure is inversely related to risk for higher birthweight children compared to lower birthweight children. B: Association between AHHR hypomethylation and gestational age when birthweight is set to median. Accounting for birthweight, younger gestational age (0.1 quantile) has a relatively higher ALL risk. C: Association between birthweight and gestational age when AHRR hypomethylation set to median. The three lines correspond to early (0.1 quantile), mid, and late (0.9 quantile) gestational age at birth. Note that the relationships between birthweight and ALL risk are profoundly different depending on gestational age and controlling for tobacco exposures.

Figure 3:

Manhattan plot of 3-degree-of-freedom test of gene-environment interaction and ALL risk. This is a meta-analysis of four different analyses involving Hispanic subjects from CCRLP and CCLS, and non-Hispanic White subjects from CCRLP and CCLS. The top 10 gene “hits” are shown in the inset -- #1–6 being statistically significant based on the genome-wide significance cutoff of 5 X 10⁸ (the red line).

Figure 4:

The top 10 most significant regions in 3-degree-of-freedom gene-environmental association test (as seen in Figure 3). The bolded line corresponds to genome wide significance cutoff of the 3-degree of freedom test, with the top 6 genes reaching significance. Note that the overall 3-DF test incorporates significance of main effects along with the interaction. The shaded colors serve as a visual guide of genome wide significance level (5 × 10⁸). 3-DF: 3 degree of freedom test p-value; D-G: disease-gene test p-value; E-G: environment-gene test p-value; GxE: gene-environment interaction test p-value.