Gestational Epigenetics and Risk of Childhood Leukemia
Authors: Pardeshi Anmol , Zhong Charlie , Li Shaobo , Metayer Catherine , Wiemels Joseph L. 
Published: December 2024

Chronological age is a risk factor for most cancers. Age is reflected in determinative changes in the epigenome, which can be described as epigenetic age. Accumulating changes to the epigenome over time, including acceleration by environmental stressors, plays a role in cancer onset in adults, but has not been comprehensively investigated in relation to risk of childhood cancer. Recent evidence suggests that discrepancy between biological age and chronological age (age-acceleration) may be associated with early onset cancer and this age acceleration is understudied in context of acute lymphoblastic leukemia (ALL) risk. In this analysis, we investigated the role of epigenetic gestational age (EGA) as a risk factor for ALL and assessed the association between epigenetic gestational age acceleration (EGAA) and age at diagnosis for ALL.
Subjects were a part of the California Childhood Leukemia Study (CCLS), a case-control study that recruited incident childhood leukemia cases matched to birth controls between 1995 and 2015. Each participants' dried blood spot (DBS), taken at birth, was retrieved from the California Biobank, and was assayed for DNA methylation array using either Illumina Infinium 450K or EPIC array after bisulfite conversion. For this analysis, we removed Down Syndrome cases (or unidentifiable Down Syndrome status) identified using either self-report or genetic analyses. Newborn DNA methylation measurements were used to calculate epigenetic gestational age (EGA) calculations, developed by Knight and Bohlin specifically for gestational age and developed from a pre-trained model. We used these available weights compute EGA, in weeks. Logistic regression models were used to evaluate the association between EGA and case-control status. EGAA were defined as the residuals from a linear regression model incorporating epigenetic and chronological gestational age. Multivariate linear regression models were implemented to estimate the association between EGAA and age at diagnosis in cases only. Both models were adjusted for smoking (based on DNA methylation of AHRR), sex, birth weight, race, ethnicity, income, and batch effects.
A total of 1306 participants (607 cases and 699 controls) were included in this analysis after meeting inclusion criteria. Bohlin clock was based on 96 CpG sites while the Knight clock was based on 148 CpG sites. Overall, there was no difference in distribution of sex (p=0.76) and race (p=0.70) comparing cases to controls. The mean chronological age in cases was 39.2 weeks while that in the controls was 39.3 (p=0.58). Gestational epigenetic age using the Bohlin clock was comparable across cases (mean=39.9 weeks) and controls (mean=39.9 weeks) (p=0.64). Similarly, means for Knight clock were also comparable across cases (mean=39.9 weeks) and controls (39.9 weeks) (p=0.56). A one-week increase in epigenetic age (Bohlin clock based) was associated with 4.95% decreased risk of ALL (Odds Ratio (OR)=0.95; p=0.29). Similarly, a one-week increase in epigenetic age (Knight clock based) was associated with 3.38% decreased risk of being diagnosed with ALL (OR=0.96; p=0.32). Next, in the case-only analyses, the median age at diagnosis for ALL was 4.3 years (223.86 weeks). A one week increase in age acceleration, calculated from the Bohlin clock was associated with an 17.82-week (p=0.008) increase in age at diagnosis and a 8.84-week (p=0.048) increase for the Knight clock. This increase seemed to be accounted for mostly by children diagnosed with ETV6-RUNX1 subtype (n=100 in our dataset) where a one week increase in epigenetic age acceleration was associated with 27.92-week (for Bohlin, P = 0.04) and 18.39-week (for Knight, P = 0.04) increase (or older) age at diagnoses.
This is the first analysis to investigate the role of EGA and EGAA on the risk of pediatric ALL. Overall, we did not observe a significant difference in epigenetic age between childhood ALL cases and matched controls. In this case-only analyses, we observed that accelerated EGAA was associated with later age at which the child is diagnosed with ALL. Further work is necessary to understand the mechanisms through which EGAA may influence leukemogenesis.