DNA methylation profiles in the blood of newborn term infants born to mothers with obesity

Abstract

Maternal obesity is an important risk factor for childhood obesity and influences the prevalence of metabolic diseases in offspring. As childhood obesity is influenced by postnatal factors, it is critical to determine whether children born to women with obesity during pregnancy show alterations that are detectable at birth. Epigenetic mechanisms such as DNA methylation modifications have been proposed to mediate prenatal programming. We investigated DNA methylation signatures in male and female infants from mothers with a normal Body Mass Index (BMI 18.5-24.9 kg/m2) compared to mothers with obesity (BMI≥30 kg/m2). BMI was measured during the first prenatal visit from women recruited into the Ontario Birth Study (OBS) at Mount Sinai Hospital in Toronto, ON, Canada. DNA was extracted from neonatal dried blood spots collected from heel pricks obtained 24 hours after birth at term (total n = 40) from women with a normal BMI and women with obesity matched for parity, age, and neonatal sex. Reduced representation bisulfite sequencing was used to identify genomic loci associated with differentially methylated regions (DMRs) in CpG-dense regions most likely to influence gene regulation. DMRs were predominantly localized to intergenic regions and gene bodies, with only 9% of DMRs localized to promoter regions. Genes associated with DMRs were compared to those from a large publicly available cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC; total n = 859). Hypergeometric tests revealed a significant overlap in genes associated with DMRs in the OBS and ALSPAC cohorts. PTPRN2, a gene involved in insulin secretion, and MAD1L1, which plays a role in the cell cycle and tumor suppression, contained DMRs in males and females in both cohorts. In males, KEGG pathway analysis revealed significant overrepresentation of genes involved in endocytosis and pathways in cancer, including IGF1R, which was previously shown to respond to diet-induced metabolic stress in animal models and in lymphocytes in the context of childhood obesity. These preliminary findings are consistent with Developmental Origins of Health and Disease paradigm, which posits that adverse prenatal exposures set developmental health trajectories.

Fig 1. Hierarchical clustering of samples for males (A) and females (B) in the OBS discovery cohort.

C: neonates of non-obese control mothers (n = 10/sex), O: neonates of mothers with obesity (n = 10/sex).

Fig 2. Overview of differentially methylated regions in the OBS discovery cohort.

(A) Number of DMRs in relation to chromosomal locations that are either hypermethylated (red) or hypomethylated (blue) in male and female neonates born to mothers with obesity compared to controls. (B) Proportion of DMRs in relation to genetic regions. (C) Representative top DMR in male neonates on the ABCG1 gene showing methylation percentage in individual CpG sites within the DMR. (D) Representative top DMR in female neonates on the BCL9 gene showing methylation percentage in individual CpG sites within the DMR. The genomic track shows the gene location starting from the first exon and the DMR location. Hypermethylation refers to greater DNA methylation among neonates from mothers with obesity compared to neonates from mothers with a normal BMI. Hypomethylation refers to lesser DNA methylation among neonates from mothers with obesity compared to neonates from mothers with a normal BMI.

Fig 3. Annotation of differentially methylated regions for the OBS and ALSPAC cohorts.

The numbers of genes associated with DMRs for (A) male and (B) female neonates. (C) The number of genes for each sex for genes that replicated across both cohorts. The total number of genes associated with DMRs for each sex are shown in parentheses.