Neonatal Genome-Wide Methylation Patterns in Relation to Birth Weight in the Norwegian Mother and Child Cohort

Stephanie M. Engel 0 Bonnie R. Joubert 0 Michael C. Wu 0 Andrew F. Olshan 0 Siri E. Hberg 0 Per Magne Ueland 0 Wenche Nystad 0 Roy M. Nilsen 0 Stein Emil Vollset 0 Shyamal D. Peddada 0 Stephanie J. London ) 0 0 of North Carolina at Chapel Hill , Chapel Hill, NC, 27599-7435 ( American Journal of Epidemiology Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US. Although epigenetic regulation plays a critical role in embryonic development, few studies have examined the relationship of epigenome-wide methylation with fetal growth. Using the Infinium HumanMethylation450 BeadChip (Illumina, Inc., San Diego, California) in a substudy of 1,046 infants from the Norwegian Mother and Child Cohort Study (MoBa) enrolled between 1999 and 2008, we examined epigenome-wide cord blood DNA methylation in relation to birth weight. In multivariable-adjusted robust linear regression models, we identified differential methylation at 19 cytosine-guanine dinucleotides (CpGs) associated with either decreased (AT-rich interactive domain 5B (MRF1-like) (ARID5B), 2 CpGs) or increased (x-ray repair complementing defective repair in Chinese hamster cells 3 (XRCC3), 4 CpGs) birth weight. ARID5B knockout mice have less adipose tissue and significantly lower weight in the postnatal period. XRCC3 plays a key role in the maintenance of chromosome stability and the repair of DNA damage. Although there are fewer data on the other implicated genes, many of these genes have been shown to have roles in developmental processes. This constitutes the largest and most robust study of birth weight using an epigenome-wide methylation platform and offers potential insights into epigenetic mechanisms of fetal growth. birth weight; cord blood; epigenetics; methylation; MoBa; Norwegian Mother and Child Cohort Study Abbreviations: CpG, cytosine-guanine dinucleotide; MoBa, Norwegian Mother and Child Cohort Study. - Epigenetic pathways regulate fetal development by controlling the expression of genes (1), facilitating both precisely timed and highly coordinated developmental processes (2). The most well-characterized of these epigenetic pathways is DNA methylation, the addition of a methyl group usually to cytosines in cytosine-guanine dinucleotide (CpG) sites (3). The relationship between CpG methylation and gene expression is complex and incompletely understood. Recent studies indicate that methylation at promoter and island regions tends to result in gene silencing; however, methylation in gene bodies tends to enhance gene expression (46). Loss of methylation at specific imprinted regions leads to serious growthrelated congenital anomalies, such as Beckwith-Wiedemann and Silver-Russell syndromes (7, 8). However, there are limited data in humans on the role of more modest variability in DNA methylation status in the growth and development of the fetus. Although some portion of epigenetic lability is under genetic control (9), epigenomic consequences of exposures experienced in utero (1012) have been documented in humans. For example, maternal depression (13) and smoking during pregnancy (11), both of which are predictors of reduced birth weight, have been associated with altered methylation profiles in either gene-specific (13) or epigenomescale (11) investigations. In particular, Joubert et al. (11) identified significant associations between maternal smoking in pregnancy and differential methylation in genes involved in fundamental developmental processes. Together, these results support the hypothesis that birth weight, and/or pathways leading to birth weight, may be affected by differences in methylation. A few studies have begun to examine the associations of gene-specific methylation with birth weight. Targeted investigations have involved genes hypothesized to play key roles in growth (e.g., insulinlike growth factor 2), and/or that may be sensitive to famine exposure in pregnancy (GNAS antisense RNA 1 (GNASAS), INS-IGF2 readthrough (INS-IGF2), and leptin (LEP)). However, studies have thus far not provided consistent evidence of an association with birth weight in humans (1416). Recently, 2 epigenome-scale investigations of methylation in relation to birth weight have been published, although both had relatively small study populations and lacked adjustment for potentially important confounders. None of the principal findings in these studies overlap (17, 18). We undertook an investigation of the relationship between CpG-specific cord blood DNA methylation and birth weight using the Infinium HumanMethylation450 BeadChip (Illumina, Inc., San Diego, California) among 1,046 newborns from the Norwegian Mother and Child Cohort Study (MoBa). Study population MoBa enrolled more than 100,000 women between 1999 and 2008. Study design and selection characteristics have been described in detail elsewhere (19, 20). Women were invited by mail to participate prior to their routine ultrasonography examinations at their local hospitals, usually scheduled at approximately 18 weeks gestation. Participation rates varied by study year (20) but averaged 38.5%. Exposure-related information was collected by questionnaire at the first enrollment visit and then again at approximately 30 weeks gestation. Information on dietary folate intake was collected using a semiquantitative food frequency questionnaire returned by the mothers at approximately 1822 gestational weeks. The food frequency questionnaire consisted of 263 questions about 255 food items and was designed to capture dietary habits and intakes of dietary supplements during the first 45 months of pregnancy (21, 22). Methods regarding calculation of nutrient and energy intakes have been previously described (21, 22). Briefly, nutrient and energy intakes were calculated using FoodCalc (http://www.ibt.ku.dk/jesper/ FoodCalc/Default.htm) and the Norwegian Food Composition Table (23). We adjusted for folate intake from foods. Measurement of plasma folate status was obtained from maternal blood samples collected at the enrollment visit (at approximately 18 weeks gestation). Plasma folate was measured using a microbiological assay with a chloramphenicol-resistant strain of Lactobacillus casei (24). The assay determines biologically active folate species, predominantly 5-methyltetrahydrofolate, and has a coefficient of variation of 4% within day and 5% between days at population median concentration (24). The Medical Birth Registry of Norway receives mandatory information on all deliveries at hospitals using a standardized birth notification form (25). This form includes demographic information about the mother and father, information about the mothers health before and during pregnancy, including chronic diseases and pregnancy complications, and information on delivery characteristics. Within MoBa, a nested case-cohort subset was (...truncated)