Epigenetic DNA Methylation, Nutrition, and Growth

Epigenetic DNA Methylation, Nutrition, and Growth

Introduction

Epigenetics comprises different heritable biochemical DNA modifications that can alter gene transcription into RNA, and hence the degree of formation of the respective gene product, while the sequence of DNA is preserved. Key mechanisms of epigenetic DNA changes are histone modifications and DNA methylation, with the latter being the most widely studied epigenetic mechanism in human populations. DNA methylation occurs at DNA regions where cytosine is followed by guanine, which are referred to as CpG sites. Early life periods including embryonic, fetal, and infant development represent time windows when the human epigenome shows a high degree of plasticity and is particularly susceptible to external exposures. Accumulating evidence points to marked effects of environmental and nutritional cues in modulating epigenetic processes, which may induce long-lasting effects of later cell function, health, and disease risks. Considerable efforts are therefore invested into exploration of epigenetic mechanisms, susceptible time windows, as well as populations or patient groups, relevant exposures, effects and effect sizes, and their fluidity or persistence over time.

For this chapter, a search was performed in the US National Library of Medicine (PubMed) with the search terms “(epigenetic*) AND ((nutrit*) OR (growth))” and filter “humans” for the time period from June 30, 2022, to July 1, 2023. The first 1,000 hits were hand searched by the author, and the publications included here (shown below) were subjectively selected based on interest and a relation to human nutrition and growth.

Gestational weight gain in pregnant women with obesity is associated with cord blood DNA methylation, which partially mediates offspring anthropometrics

Comments: Gestational weight gain (GWG) has been associated with the risk of the offspring for
obesity, adiposity, and a variety of noncommunicable diseases in numerous studies. However, genome-wide studies on cord blood DNA methylation (DNAm) found no association with GWG in pregnant women with normal body weight. In contrast, this study with more than 200 pregnant women with obesity and a very wide variation of GWG found that GWG has been associated with cord blood DNAm. DNAm at 21 sites was associated with neonatal birthweight, and DNAm at 62 sites with neonatal body mass. Pathway analyses suggested the DNAm mediated 15–23% of the GWG effect on birthweight, and 14–27% of the GWG effect on lean body mass. Methylation quantitative trait loci, i.e., genetic variants that may affect the DNAm patterns of CpG sites, associated with GWG suggest associations to birthweight and to disease traits such as asthma, body mass index, and waist-to-hip ratio adjusted for body mass index. Overall, this study suggests that DNAm in the offspring may be differentially impacted by GWG in mothers with normal body weight and obesity, respectively. DNAm appears to have a mediating effect on neonatal birthweight and lean body mass, and interventions effectively lowering GWG in obese pregnant women have the potential to improve longterm health outcomes of the offspring.

An examination of mediation by DNA methylation on birthweight differences induced by assisted reproductive technologies

Comments: Previous studies reported the effects of assisted reproduction on birthweight, with
lower birthweight compared to natural conception in infants born after fresh embryo transfer and a slightly higher birthweight in infants born after frozen embryo transfer, respectively. It is unclear whether the assisted reproductive technologies and/or the hormonal treatment used to induce ovulation may underly these alterations of fetal growth. Since the application of assisted reproductive technologies occurs at the periconceptional time period when the early embryo undergoes extensive epigenetic reprogramming, this study examined whether cord blood DNA methylation (DNAm) mediated birthweight differences in infants born after fresh embryo transfer or natural conception in a large group of 764 newborns conceived by fresh embryo transfer, 126 newborns conceived by frozen embryo transfer, and 983 newborns conceived naturally form the Norwegian Mother and Child Cohort Study. The results show cord blood DNAm at 4 CpG sites to explain 44% of the birthweight difference between newborns conceived with fresh embryo transfer and/or conceived naturally and DNAm at 2 CpG sites to explain 22% of the birthweight difference between newborns conceived with fresh or frozen embryo transfer. One of the differentially methylated CpGs mediating the birthweight difference was located near LOXL1, the expression of which has previously been associated with premature rupture of membranes. Therefore, the authors speculate that assisted reproduction with fresh embryo transfer may increase the risk of premature rupture of membranes through methylation of this gene, resulting in lower gestational age and thereby lower birthweight, which however was not to be measured in this cohort.

Altered epigenetic profiles in the placenta of preeclamptic and intrauterine growth restriction patients

Comments: This pilot study examined DNA methylation in 6 frozen samples each of placentas from normal pregnancies and pregnancies complicated by intrauterine growth restriction (IUGR) or preeclampsia (PE), respectively, which were obtained from the Research Center for Women’s and Infants’ Health BioBank, Ontario, Canada. The study found three differentially methylated regions (DMR) in IUGR and six DMR in PE, compared to healthy pregnancies. Eight of the identified regions could be located on gene promoters or exons, but only two of these were common to both PE and IUGR pathologies. The data suggest hypomethylation at several gene promoters in placental DNA, including FAN-1 and HLA-L pseudogene, to be associated with IUGR and PE.

Prenatal social support in low-risk pregnancy shapes placental epigenome

Comments: The degree of prenatal social support has previously been associated with adiposity during infancy and health in later life, as well as DNA methylation (DNAm) in maternal blood. In a subgroup of participants of the Eunice Kennedy Shriver National Institute of Child Health and Human Development Fetal Growth Studies cohort in whom placental tissue had been collected at the time of childbirth, self-reported social support was assessed with the Enhancing Recovery in Coronary Heart Disease Social Support Questionnaire, and Instrument, and perceived stress with the self-report ten-item Cohen’s Perceived Stress Scale. Higher maternal social support during the first trimester of pregnancy was associated with higher methylation at 7 CpGs located within/near genes HAUS3, ARHGEF7, VGF, FAM210B, SBF1, ILVBL, and EIF3F. The social support-associated epigenetic signatures in placenta are independent of prenatal stress. There was a marked infant sex effect: in males, maternal social support was significantly associated with higher methylation at 9 CpGs and in females with higher methylation at 32 CpGs and lower methylation at 3 CpGs. The higher methylation at specific CPG sites was correlated with lower expression of VGF, a protein-coding gene highly expressed in parts of the brain and neuroendocrine cells and related to brain development, behavior, and regulation of energy metabolism, and with lower expression of ILVBL involved in fatty acid alpha-oxidation in the endoplasmic reticulum and the biosynthesis of isoleucine and valine. The genes annotated to the DNA methylation loci were found to be enriched for pathways involved in the immune system, placental growth and maturation, brain development, and energy metabolism. Continued research on molecular mechanisms of social support effects on offspring health could support in developing specific interventions targeting child neurodevelopment and other outcomes.

Cord blood epigenome-wide meta-analysis in six European-based child cohorts
identifies signatures linked to rapid weight growth

Comments: A large number of studies have associated the trajectories of weight or body mass index gain in early childhood, particularly an upward centile crossing of weight with
a change greater than 0.67 standard deviation scores during the first two years of life,
with an increased risk of later overweight, obesity, and other health outcomes. This study analyzed the link between cord blood DNA methylation (DNAm) and weight gain up to age 1 year in more than 2,000 children from six European child cohort studies. Rapid weight gain between birth and age 1 year was associated with 16 differentially methylated regions, even though only 3 CpGs reached genome-wide significance at the single CpG level. Children with greater gestational age acceleration had a lower risk of rapid weight gain. Adding DNAm to conventional risk factors resulted in a slight improvement in predicting rapid weight gain. A mediation analysis suggested that some DNAm signatures mediated the effect of gestational age on rapid weight gain.

Umbilical cord DNA methylation is associated with body mass index trajectories from birth to adolescence.

Comments: This study of 831 mother-child pairs from the prospective Boston Birth Cohort related child body mass index trajectories from birth up to age 18 years to cord blood DNA
methylation (DNAm). The four distinct body mass index trajectory patterns identified in this multiethnic cohort were associated with specific cord DNAm CpG sites. Interestingly, a higher number of significant findings was found in girls than in boys, with a decrease of the number of significant sex interactions at the age of 6 years. The results suggest that DNAm might be one underlying mechanism to explain the relationship between early weight gain and later overweight and obesity, which could offer novel opportunities for early risk prediction and targeted preventive approaches.

Association of the DNA methylation of obesity-related genes with the dietary nutrient intake in children

Comments: In a small group of 113 children aged 6–10 years from Alabama (60 normal body
weight, 53 overweight or obese), dietary intake was assessed by a parental 24-h recall
record, and DNA methylation in saliva samples was assessed for three genes, NRF1, FTO, and LEPR. Significant associations between the estimated intake of different nutrients and the methylation of NRF1, FTO, and LEPR genes in various subgroups of children based on body weight and ethnicity were found. The authors suggest that intervention studies should be conducted to characterize the role of nutrient intake, specifically of dietary methyl donors, in DNA methylation and that possibly related risk of childhood obesity.

Racial disparities in methylation of NRF1, FTO, and LEPR gene in childhood obesity

Comments: In the same study as reported in the publication cited above, children with over-
weight and obesity had significantly higher DNA methylation of NRF1 and FTO and lesser methylation of LEPR than children with normal body weight. African American children showed higher methylation of LEPR than European American children. Only European American children had significantly higher levels of methylation in the NRF1 and FTO genes than normal weight children. African American children with normal weight had higher methylation of the LEPR gene than the children with overweight of obesity. The reported ethic differences in the association between DNA methylation of the NRF1, FTO, and LEPR genes with childhood obesity should be considered in future studies.

Environment- and epigenome-wide association study of obesity in ‘Children of 1997’ birth cohort

Comments: This large cohort study including Chinese children in Hong Kong found DNA methylation at RPS6KA2 associated with both body mass index and waist-hip ratio, which is consistent with findings in previous studies on obesity in different populations. Associations with several other genes including ZNF827, MIR7641-2, RAPTOR, KSR1, GT-F3C3, and NFIC previously associated with obesity or obesity-related disorders were also found. The cross-sectional design of the study does not allow to draw conclusions on the direction of causality.

Is adiposity related to repeat measures of blood leukocyte DNA methylation across
childhood and adolescence?

Comments: Previous studies have suggested that altered DNA methylation (DNAm) might be a consequence rather than a cause of childhood obesity, which however remains somewhat controversial. This pilot study in 113 children in Mexico evaluated measures of DNAm at birth and early and late teenage and related it to childhood body mass index and adiposity measures at different ages. The observed inverse association between measures of childhood BMI and repeat measures of H19 DNAm provides preliminary indications for an association between early-life adiposity and DNA methylation at H19. Potential interactions between age and early teen adiposity on H19 and HSD11B2 methylation are also suggested.

Differential methylation pattern in pubertal girls associated with biochemical premature adrenarche

Comments: In 86 girls from the longitudinal Growth and Obesity Cohort Study in Chile, the dehydroepiandrosterone sulfate (DHEAS) concentration was measured in the fasting morning blood sample at ∼7 years of age and during pubertal progression at Tanner breast stages T2 and T4. At the same time points, DNA methylation was assessed from buffy coat. The results show 69 differentially methylated positions that discriminate girls with high or low DHEAS at both Tanner stages. DNA methylation at four CpG sites also showed a significant association with measures of glucose metabolism. While the authors propose that DHEAS concentration may induce a consistent blood methylation signature and be a causal link between premature adrenarche and insulin resistance, the study design does not allow firm conclusions on the direction of causality.

Long-term impact of paediatric critical illness on the difference between epigenetic
and chronological age in relation to physical growth

Comments: This impressive study builds on a previous study involving some of the same authors who demonstrated an association between critical illness and early administration of parenteral nutrition with altered leucocyte DNA methylation (DNAm), which was related to long-term developmental sequelae. “Epigenetic clocks” have been developed based on data indicating that chronological age can be predicted from certain DNAm patterns. In a sizeable subgroup of the original multicenter randomized trial on nutritional management in the pediatric intensive care unit, the authors tested whether critical illness in childhood and its nutritional management affect the epigenetic age, and whether there is a relationship to child growth. The results show that critically ill children later were epigenetically younger, based on DNAm at 94 CpG sites, than their chronological age, particularly if the critical illness occurred at an age of 6 years or later. Critical illness also resulted in reduced length but not weight, again particularly in children with critical illness at age 6 years or later. The potential longterm consequences and underlying mechanisms deserve further investigation.

Changes in DNA methylation of clock genes in obese adolescents after a short-term body weight reduction program: a possible metabolic and endocrine chrono-resynchronization

Comments: In this study, a 3-week body weight reduction program with a restricted calorie diet and enhanced physical activity in adolescents induced a significant body mass index
reduction from 2.94 to 2.82 standard deviation score, along with hypermethylation of clock and cry2 genes, hypomethylation of the per2 gene, and no changes in methylation of arntl, cry1, per1, and per3 genes in leucocytes. Appreciable gender-related differences were observed. It is tempting to speculate whether the methylation changes caused the observed cardiometabolic improvements or were the results thereof. The observed epigenetic remodeling of specific clock genes might be interpreted as partly correcting chronodisruption associated with obesity.

Conflict of Interest Statement

No conflict of interest is declared with respect to the contents of this manuscript, with no circumstances involving the risk that the professional judgment or acts of primary interest may be unduly influenced by a secondary interest.

Funding Sources
This work has been financially supported in part by the European Joint Programming Initiative
Projects NutriPROGRAM and BiomarKids and by the German Federal Ministry of Education and Research – 01EA1904 and 01EA2203A. Further support was provided by B.K., who is Else Kröner-Senior professor of Paediatrics at the Ludwig-Maximilians-Universität München (LMU), University of Munich, financially supported by Else Kröner-Fresenius Foundation, LMU Medical Faculty, and LMU University Hospitals.