Ancestry Dependent DNA Methylation and Influence of Maternal Nutrition

March Ancestry Dependent DNA Methylation and Influence of Maternal Nutrition Khyobeni Mozhui 0 1 2 3 Alicia K. Smith 0 1 2 3 Frances A. Tylavsky 0 1 2 3 0 Funding: Supported by the Grants HD055462 and HD060713 from the US National Institute of Child Health and Human Development; 1R01HL109977 US National Institute of the Heart, Lung and Blood and R01MD009064 from the US National Institute on Minority Health and Health Disparities; Children's Foundation Research Center of Memphis, University of Tennessee Health Science Center's Clinical Translational Science Institute; by the grant from the Urban Child Institute, Memphis, TN; and by the Grant M01-RR00211 from the US National Center for 1 Data Availability Statement: Data are available from the NCBI GEO repository: accession number GSE64940 2 Academic Editor: Huiping Zhang, Yale University , UNITED STATES 3 1 Department of Preventive Medicine, University of Tennessee Health Science Center , Memphis, TN , United States of America, 2 Department of Psychiatry and Behavioral Science, Emory University , Atlanta, GA , United States of America There is extensive variation in DNA methylation between individuals and ethnic groups. These differences arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we compare genome-wide DNA methylation in neonatal cord blood from African American (AA; N = 112) and European American (EA; N = 91) participants of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood). Our goal is to determine if there are replicable ancestry-specific methylation patterns that may implicate risk factors for diseases that have differential prevalence between populations. To identify the most robust ancestry-specific CpG sites, we replicate our results in lymphoblastoid cell lines from Yoruba African and CEPH European panels of HapMap. We also evaluate the influence of maternal nutrition-specifically, plasma levels of vitamin D and folate during pregnancy-on methylation in newborns. We define stable ancestry-dependent methylation of genes that include tumor suppressors and cell cycle regulators (e.g., APC, BRCA1, MCC). Overall, there is lower global methylation in African ancestral groups. Plasma levels of 25-hydroxy vitamin D are also considerably lower among AA mothers and about 60% of AA and 40% of EA mothers have concentrations below 20 ng/ml. Using a weighted correlation analysis, we define a network of CpG sites that is jointly modulated by ancestry and maternal vitamin D. Our results show that differences in DNA methylation patterns are remarkably stable and maternal micronutrients can exert an influence on the child epigenome. - Introduction Epigenetics refer to a host of molecular mechanisms that can influence phenotypes by regulating gene expression. In humans, much of the research on the epigenome has focused on DNA methylation, partly because methylation is far more amenable to high-throughput and semiquantitative genome-wide assessments using microarrays. The epigenome-wide surveys have characterized significant inter-individual variability that likely results from a combination of Research. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. influences that include environmental stimuli [1, 2], diet and medication use [36], psychosocial factors [79], and physiological changes [10, 11]. While both DNA methylation and gene expression have partially stochastic kinetics [1214], changes in the methylome may be comparatively stable and serve as reliable indicators of environmental and developmental conditions [15, 16]. There is extensive population and ancestry dependent variation in DNA methylation. According to recent studies, African populations have generally lower global methylation than Caucasians [17, 18]. Additionally, Lam et al. [19] reported that the methylation measured in peripheral blood correlates with leukocyte composition and is associated with ethnicity, psychosocial stress, and early-life socioeconomic status. Studies that have explored genetic regulation of DNA methylation show that variation in the methylome has ancestry-dependent heritability patterns that are modulated by underlying quantitative trait loci or meQTLs [18, 2024]. The variability in methylation is extensive and it is difficult to disentangle the relative contribution of genetics vs. environment, and to estimate the health implications of individual or ethnic variation. In the United States, African Americans suffer from disproportionately higher rates of chronic diseases (e.g., diabetes, hypertension, heart diseases) and African American infants also show poorer birth outcomes compared to Caucasian counterparts [5, 25, 26]. The reasons for these persistent health disparities are not entirely clear but are, without doubt, multifactorial and arise from a combination of social, environmental, nutritional, and biological factors. The risk conditions start early in life, as early as the prenatal stage, and epigenetic pathways offer a potential mechanism for perpetuating the effects of early life exposures and setting the stage for future outcomes [25]. Among the many factors, maternal diet and nutritional state are tractable modifiers of the infant epigenome that have impact on offspring health [3, 4, 27, 28]. For instance, folate is a methyl group donor and maternal deficiency is correlated with altered DNA methylation in neonate [2931]. Similarly, maternal vitamin D is the largest predictor of circulating vitamin D in the neonate, and vitamin D levels are also reported to influence DNA methylation [3235]. Notably, plasma levels of vitamin D are known to be considerably lower among AAs and this has been attributed to differences in skin pigmentation, availability of vitamin D-binding proteins, and genetic polymorphism [36]. In this study, we systematically compare DNA methylation in neonatal cord blood from African American (AA) and European American (EA) participants of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood; http:// candlestudy.com) [18, 3739]. Our goal is to determine if there are replicable ancestry-specific methylation patterns that may implicate risks for diseases that disproportionately affect one group over another. To identify the most robust ancestry-specific CpG sites, we replicate our results in HapMap samples [21]. We then evaluate if maternal micronutrients during pregnancy, specifically maternal vitamin D and folate levels, explain some of the population differences. Finally, we apply a network level analysis to examine if population and nutritional differences influence global patterns in DNA methylation in newborns. The pre (...truncated)