Investigating the Role of Dietary Patterns and Methyl-Donor Nutrients During Critical Developmental Windows on DNA Methylation in Adolescents

Abstract

Dietary intake during critical developmental stages, including in utero and adolescence, can influence the epigenome, potentially leading to long-term cardiometabolic consequences. Specifically, methyl-donor nutrients, due to their role in the one-carbon metabolism pathway, could modulate DNA methylation. The role of dietary patterns in relation to DNA methylation is less understood, and studies in adolescents are limited. This dissertation investigated how dietary patterns and methyl-donor nutrient intakes during gestation and adolescence relate to DNA methylation in adolescents. We investigated DNA methylation in two ways. First, DNA methylation across multiple loci can be used to estimate epigenetic age, a marker of biological aging with potential implications for future disease. Additionally, locus-specific DNA methylation can yield insights into important genes and biological pathways. Of particular interest is DNA methylation within circadian genes that control biological rhythms; these could regulate the metabolic processes, providing a better understanding of potential circadian pathways linking diet and cardiometabolic health, an emerging area of research. This study included 526 adolescents from the Mexico City-based ELEMENT cohort, with prenatal data from 392 mothers. Usual dietary intake was assessed using semi-quantitative food frequency questionnaires, and dietary patterns were derived through principal component analysis of energy-adjusted food groups. Intake of methyl-donor nutrients (folate, methionine, riboflavin, and vitamins B6 and B12) were energy-adjusted. Blood leukocyte DNA methylation was analyzed using the Illumina Infinium MethylationEPIC BeadChip. Epigenetic age acceleration was calculated for Horvath, Skin-Blood, PhenoAge, GrimAge, PedBE, and Wu clocks. Of 745,797 CpG sites, DNA methylation at 707 sites annotated to 18 circadian genes was analyzed. RNA-seq data was used to analyze circadian gene expression. Linear regression assessed relationships between adolescent dietary patterns and methyl-donor nutrients with epigenetic age acceleration, and prospective associations between epigenetic age acceleration and cardiometabolic measures at two-year follow-up (Aim 1). The relationships between adolescent (Aim 2) and prenatal (Aim 3) trimester-specific dietary patterns and methyl-donor nutrients with circadian gene DNA methylation in adolescents were also examined, with False Discovery Rate correction for multiple comparisons. Cross-sectional analyses revealed no significant associations between adolescent dietary intake and epigenetic age acceleration. Prospective analyses showed positive associations between PhenoAge and GrimAge accelerations with waist circumference, BMI, fasting insulin, and HOMA-IR. In adolescents, the Breakfast pattern, vitamin B6, and riboflavin intakes were linked to DNA methylation of core clock genes, including RORA and PER3. Vitamin B6 and riboflavin intakes were associated with DNA methylation at MTNR1B, involved in melatonin signaling. While these significant CpG sites did not correlate with gene expression, inverse relationships were found between the Breakfast pattern with TIMELESS expression and between vitamin B12 intake and CRY1 expression in males. Gestational diet influenced offspring DNA methylation in adolescence with trimester-specific associations. In the first trimester, riboflavin intake was positively associated with DNA methylation at RORA and NR1D2, while vitamin B12 intake was negatively associated with RORA. Second-trimester Transitioning Mexican Diet was linked to DNA methylation at RORA. Third-trimester High Meat & Fat Diet was negatively associated with DNA methylation at CLOCK, and methionine intake with DNA methylation at RORA and PER1. In sex-stratified analysis, more associations were noted among males than females. Overall, this dissertation provides evidence that both prenatal and adolescent dietary intake could impact DNA methylation of circadian genes and circadian gene regulation. Conversely, concurrent diet was not linked to epigenetic markers of biological aging in adolescence.