Epigenetics, 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 the human population. 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. Environmental and nutritional cues appear to play a key role in regulating epigenetic processes, which may induce long-lasting effects of later tissue function, health, and disease risks. Therefore, exploration of epigenetic mechanisms, susceptible time windows and population or patient groups, relevant exposures, effects and effect sizes, and their fluidity or persistence are of great interest. For this chapter, 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 years 2021 and 2022. The hits were hand searched by the author, and the publications shown below were subjectively selected based on interest and relevance to human nutrition and growth.

Examining the association between adiposity and DNA methylation: a systematic review and meta-analysis

Comments: This is a very informative systematic review indicating significant associations of more than 50 methylated CpG sites in blood cells with body mass index (BMI), many of which have been linked to type 2 diabetes, cardiovascular disease, Crohn’s disease ,and depression. Since much of the data used are based on cross-sectional studies, no firm conclusions can be drawn on the direction of causality, i.e., whether methylation of specific CpG sites modulates BMI evolution or whether differences in BMI have an impact on DNA methylation, which was previously proposed based on longitudinal studies in cohorts of children.

Fat mass and obesity-associated (FTO) gene epigenetic modifications in gestational diabetes: new insights and possible pathophysiological connections

Comments: Gestational diabetes mellitus (GDM) is a very common complication of pregnancy, with a recent increase of its incidence observed along with an increasing prevalence of overweight and obesity in pregnant women. GDM is associated with adverse later health outcomes both in the mother, e.g. Diabetes mellitus type 2, metabolic and cardiovascular disease, and in the offspring, e.g., high birth weight, and increased later risk of obesity and noncommunicable diseases. Expression of the FTO gene has previously been reported to be associated with fetal weight and length, and with placental weight. This study in a relatively small sample of 60 pregnant women (33 with GDM and 27 without GDM) with a detailed characterization of clinical parameters, lifestyle, and diet analyzed DNA methylation of 4 CpGs within the promoter of the FTO gene from washed placental tissue samples. Interestingly, the results show that the 4CpGs were mainly unmethylated in both patient groups. Methylation was similar at the maternal and the fetal sides of the placenta. Differences in the methylation patterns occurred in women exposed to tobacco smoke during pregnancy, in line with previous studies reporting a marked effect of smoke exposure during pregnancy on DNA methylation. In contrast, GDM was not associated with placental DNA methylation in the FTO gene.

Genome-wide placental gene methylations in gestational diabetes mellitus, fetal growth, and metabolic health biomarkers in cord blood

Comments: In this study of 30 placentas of Chinese women with GDM paired with 30 placentas of women without GDM, GDM was associated with DNA methylation changes in a number of placental genes. However, these placental gene methylations were uncorrelated to the measured metabolic health biomarkers including fetal growth factor measures, and cord blood leptin and adiponectin.

Maternal glycemic dysregulation during pregnancy and neonatal blood DNA methylation: meta-analyses of epigenome-wide association studies

Comments: This meta-analysis combined data from 7 cohort studies with inclusion of a large number of pregnant women from Europe, North America, and Singapore with available data on cord blood DNA to explore associations with continuous maternal glucose measurements, insulin, and area under the curve of glucose measures after an oral glucose tolerance test conducted during pregnancy. No evidence of robust associations between maternal prenatal glucose and insulin levels and offspring DNA methylation in cord blood was revealed, which could be interpreted to refute the concept that maternal hyperglycemia during pregnancy would mediate childhood health phenotypes via changes in DNA methylation. But the meta-analysis of the area under the curve of glucose measures showed inverse associations with cord blood DNA methylation at 2 CpG sites in the thioredoxin interacting protein gene (TXNIP),which were only observed among women without GDM. Of interest, exposure to higher maternal fasting glucose, higher HbA1c, and maternal type 1 diabetes was also associated with a lower DNA methylation in TXNIP in cord blood. These observations should prompt further exploration of a potential pathway between prenatal exposure to hyperglycemia exposure, DNA methylation at TXNIP, and later offspring health.

Effect of an antenatal diet and lifestyle intervention and maternal BMI on cord blood DNA methylation in infants of overweight and obese women: the LIMIT randomised controlled trial

Comment: Most analyses associating DNA methylation with exposures in pregnancy are based on observational studies which cannot firmly establish cause-and-effect relationships. Therefore, DNA methylation studies in randomized controlled intervention trials addressing dietary or lifestyle exposures are of particular value. This publication reports on cord blood DNA methylation analyses in offspring of women who participated in the randomized controlled LIMIT trial which explored the effects of an antenatal diet and lifestyle intervention for women entering pregnancy with overweight. The intervention targeted the reduction of dietary sugar and saturated fat intake and enhanced physical activity. No probes were significantly differentially methylated between the Lifestyle Advice and Standard Care groups, and there was no evidence for effect modification by maternal BMI. The top 10 differentially methylated probes by p value were spread across the genome and showed small effect sizes. The top 10 differentially methylated probes by log-fold change did not overlap with the top 10 by p value, and again effect sizes were relatively small. Overall, an antenatal lifestyle intervention or maternal early pregnancy BMI did not affect DNA methylation in cord blood, which suggests that other causal pathways are primarily responsible for linking maternal and childhood obesity.

Placental multi-omics integration identifies candidate functional genes for birthweight

Comments: Tekola-Ayele et al. evaluated genome, DNA methylation, and gene expression from placenta samples of 2,802 women participating in a cohort study in the USA. Some 286 single-nucleotide polymorphisms (SNPs) were associated with birth weight, and 23 co-occurring SNPs were associated with both placental gene expression and DNA methylation. Causal inference analyses found evidence of a causal relationship between birthweight SNP altering DNA methylation in the placenta, which in turn causally influences gene expression in 88 of 197 triplets consisting of 15 SNPs, 17 protein coding genes, and 81 DNA methylation sites. The results obtained suggest that the effect of the genetic variants on birthweight is possibly mediated by their direct regulatory influence on epigenetic and transcriptomic changes in the placenta.

Epigenome-wide contributions to individual differences in childhood phenotypes: a GREML approach

Comments: In this impressive study combining data from the British ALSPAC and the Dutch Generation R studies, Neumann et al. aimed to assess the overall contribution of genome wide cord blood cell DNA methylation data towards gestational age, birthweight, and health outcomes in later childhood. Methylation data were found to explain a third of the variance for gestational age, and a much lesser degree of the variance of birthweight, while BMI, intelligence quotient, or attention-deficit hyperactivity symptoms at school age were not explained by cord blood DNA methylation.

DNA methylation mediates the association between breastfeeding and early-life growth trajectories

Comments: Breastfeeding is universally considered as the optimal way of infant feeding. It has been associated with numerous health effects, including mediation of growth in infancy and beyond. In a small number of previous studies, breastfeeding and its duration have been associated with DNA methylation changes, but the available information remains rather limited. In this study, Briollais et al. report on the analysis of DNA methylation data from blood cells of 1,018 mother-offspring pairs from the Avon Longitudinal Study of Parents and Children (ALSPAC) that were related to breastfeeding information reported by mothers, and growth measures. The duration of exclusive breastfeeding was associated with DNA methylation changes particularly during the first 3 years of life, and with lesser effect sizes at later ages up to 17 years. DNA methylation corresponding to 3–5 months of exclusive breastfeeding was associated with lower BMI growth the first 6 years of life, when compared to absence of exclusive breastfeeding, and in a dose-response manner with the duration of exclusive breastfeeding, but this mediation effect disappeared after 6 years of age. The CpG sites with highest levels of statistical significance were related to the AMP-activated protein kinase (AMPK) pathway, the insulin signaling pathway, and endocytosis in girls, and in boys to pathways related to cancer. The findings suggest that the mechanisms by which breastfeeding can reduce later overweight and obesity might be mediated through hypo- and hypermethylation of DNA early in life.

Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation

Comments: Several previous studies have suggested sex differences of DNA methylation in placenta, cord blood, and blood samples obtained in childhood. This large meta-analysis combined cord blood cell DNA methylation data of more than 8,000 neonates from as many as 40 birth cohort studies. Perhaps not surprisingly, 99.8% of the more than 9,600 CpG sites on the X chromosome were significantly differentially methylated between males and females. Also, almost 47,000 of the nearly 400,000 tested autosomal CpG sites showed significantly different DNA methylation, after adjusting for white blood cell proportions and batch, with about two thirds of the sites showing lower methylation levels in male neonates. Sex differences were enriched in genes involved in biological pathways important for development, and risk of cancer, psychiatric disorders, and cardiovascular phenotypes. It is tempting to speculate that early-life DNA methylation differences may represent a potential mechanism regulating differential disease risk by sex.

DNA methylation in newborns conceived by assisted reproductive technology

Comments: Assisted reproduction has markedly increased in use in recent years. It has been associated with different adverse pregnancy outcomes and adverse long-term health effects in the offspring affecting neurodevelopment, cardiovascular health, metabolism, growth, and risk of malignant diseases. It remains to be resolved to which extent such effects are due to the assisted reproduction interventions, or due to risk factors associated with reduced parental fertility. The authors used DNA samples obtained from large groups of couples from the Norwegian Mother, Father and Child Cohort study, either with children that were naturally conceived or conceived with assisted reproduction, as well as cord blood of the newborn infants. In neonates born after assisted reproduction, 74% of CpGs were hypomethylated, whereas no such shift was found in the parents. Differentially methylated CpGs in the 2 groups of neonates were annotated to 176 genes, where mutations in 14 of these cause Mendelian disorders, 9 of them with a neurological phenotype, suggesting potential implications for long-term development and health.

Epigenome-wide association study of bronchopulmonary dysplasia in preterm infants: results from the discovery-BPD program

Comments: Previous studies in animals and observational studies in humans reported an association of prenatal psychosocial stress with altered DNA methylation and behavioral outcomes in the offspring. In this small but rather interesting controlled intervention study, pregnant adolescents were randomized to either care as usual or to participate in a home-visit program by trained nurses from the first 16 weeks of pregnancy until the child’s age of 24 months. The program was designed to strengthen maternal competences for warm and responsive care, facilitate child-centered interactions and improve bonding with the infant, and improve parenting skills by modeling. The results suggest an effect of the prenatal intervention part on differential DNA methylation of cord blood cells, with causal mediation analyses suggesting a mediating effect on cognition at age 12 months. Further studies should be performed to replicate the apparent impact of maternal prenatal psychosocial intervention on neurodevelopmental outcomes mediated by epigenetic mechanisms.

Prenatal exposure to phthalates and peripheral blood and buccal epithelial DNA methylation in infants: an epigenome-wide association study

Comments: Phthalate esters are chemicals that have been widely used as plasticizers to increase the flexibility, transparency, and durability of plastic materials, and in many other products, e.g., liquid soaps, cosmetics, and medical devices and tubing. Concerns about apparent adverse health effects have been raised. This study in Canadian mother-infant pairs shows maternal high- and low-molecular-weight phthalate exposure in pregnancy associated with differential DNA methylation of infant blood and buccal epithelial cells at the age of 3 months after birth. Thus altered DNA methylation could be one mechanism by which prenatal phthalate exposure influences health and disease later in life. The results also support a precautionary approach, with measures to reduce the ubiquitous human exposure to phthalates as much as feasible.

Cumulative risks predict epigenetic age in adult survivors of extremely low birth weight

Comments: Chronological age and biological age are associated with changes in DNA methylation. In the second decade of the 21st century, Steven Horvath and coworkers developed the concept of an epigenetic clock based on a set of methylation markers. Several epigenetic clocks have since been developed and associated with age-related phenotypes. Mathewson et al. assessed epigenetic age based on DNA methylation at 353 CpG sites in 45 young adults born with extremely low birthweight (ELBW) and 47 born with normal birth weight. Epigenetic age was more than 2 years higher in ELBW subjects at the chronological age of 32 years, which may mediate the reported increased risk of adverse adult health outcomes in people born with ELBW.

Altered DNA methylation at age-associated CpG sites in children with growth disorders: impact on age estimation?

Comments: In forensic medicine, the age estimation based on the epigenetic clock approach applying DNA methylation analysis has become widely used. This observational study reports a significant impact of different childhood growth disorders on epigenetic DNA methylation. Age-related DNA methylation analysis appears to be feasible also in children; however, it tended to overestimate age in children with growth disorders. It appears desirable that future studies explore potential differences between various types of childhood growth disorders in greater detail.

Differentially methylated CpGs in response to growth hormone administration in children with idiopathic short stature

Comments: Considerable inter-individual differences exist between children receiving recombinant human growth hormone (rhGH) with respect to the response to treatment. This study explored whether rhGH produced epigenetic marks on the methylome of peripheral blood mononuclear cells, and their inter-individual variation, after a treatment duration ranging from 6 to 38.4 months. Comparing samples before and after treatment, 267 differentially methylated CpGs were identified in 265 genes which are enriched in pathways related to cell differentiation, system development, and growth-related pathways such as endoderm differentiation, adipocytokine signaling, PPAR alpha, and TGF-beta signaling pathways. However, significance was lost after correcting for multiple testing (false discovery rate). The authors also found marked intra-individual responses of DNA-methylation to long-term rhGH treatment. These results indicate the potential that effects of rhGH therapy might be partly mediated by epigenetic regulation, and that this might contribute to inter-individual variation in response to growth hormone.