Goodrich Jaclyn M, Sánchez Brisa N, Dolinoy Dana C, Zhang Zhenzhen, Hernández-Ávila Mauricio, Hu Howard, Peterson Karen E, Téllez-Rojo Martha M
a Department of Environmental Health Sciences ; University of Michigan School of Public Health ; Ann Arbor , MI USA.
Epigenetics. 2015;10(1):19-30. doi: 10.4161/15592294.2014.989077. Epub 2015 Jan 27.
DNA methylation data assayed using pyrosequencing techniques are increasingly being used in human cohort studies to investigate associations between epigenetic modifications at candidate genes and exposures to environmental toxicants and to examine environmentally-induced epigenetic alterations as a mechanism underlying observed toxicant-health outcome associations. For instance, in utero lead (Pb) exposure is a neurodevelopmental toxicant of global concern that has also been linked to altered growth in human epidemiological cohorts; a potential mechanism of this association is through alteration of DNA methylation (e.g., at growth-related genes). However, because the associations between toxicants and DNA methylation might be weak, using appropriate quality control and statistical methods is important to increase reliability and power of such studies. Using a simulation study, we compared potential approaches to estimate toxicant-DNA methylation associations that varied by how methylation data were analyzed (repeated measures vs. averaging all CpG sites) and by method to adjust for batch effects (batch controls vs. random effects). We demonstrate that correcting for batch effects using plate controls yields unbiased associations, and that explicitly modeling the CpG site-specific variances and correlations among CpG sites increases statistical power. Using the recommended approaches, we examined the association between DNA methylation (in LINE-1 and growth related genes IGF2, H19 and HSD11B2) and 3 biomarkers of Pb exposure (Pb concentrations in umbilical cord blood, maternal tibia, and maternal patella), among mother-infant pairs of the Early Life Exposures in Mexico to Environmental Toxicants (ELEMENT) cohort (n = 247). Those with 10 μg/g higher patella Pb had, on average, 0.61% higher IGF2 methylation (P = 0.05). Sex-specific trends between Pb and DNA methylation (P < 0.1) were observed among girls including a 0.23% increase in HSD11B2 methylation with 10 μg/g higher patella Pb.
使用焦磷酸测序技术测定的DNA甲基化数据越来越多地用于人类队列研究，以调查候选基因的表观遗传修饰与环境毒物暴露之间的关联，并检查环境诱导的表观遗传改变，作为观察到的毒物-健康结果关联的潜在机制。例如，子宫内铅（Pb）暴露是一种全球关注的神经发育毒物，也与人类流行病学队列中的生长改变有关；这种关联的一个潜在机制是通过DNA甲基化的改变（例如，在与生长相关的基因处）。然而，由于毒物与DNA甲基化之间的关联可能很弱，因此使用适当的质量控制和统计方法对于提高此类研究的可靠性和效力很重要。通过模拟研究，我们比较了估计毒物-DNA甲基化关联的潜在方法，这些方法因甲基化数据分析方式（重复测量与平均所有CpG位点）和调整批次效应的方法（批次对照与随机效应）而异。我们证明，使用平板对照校正批次效应可产生无偏关联，并且明确建模CpG位点特异性方差和CpG位点之间的相关性可提高统计效力。使用推荐的方法，我们在墨西哥环境毒物早期生活暴露（ELEMENT）队列（n = 247）的母婴对中，研究了DNA甲基化（在LINE-1以及与生长相关的基因IGF2、H19和HSD11B2中）与3种铅暴露生物标志物（脐带血、母亲胫骨和母亲髌骨中的铅浓度）之间的关联。髌骨铅含量每高10μg/g的人群，IGF2甲基化平均高0.61%（P = 0.05）。在女孩中观察到铅与DNA甲基化之间的性别特异性趋势（P < 0.1），包括髌骨铅含量每高10μg/g，HSD11B2甲基化增加0.23%。
