Nutriepigenomics

Epigenetics relates to heritable changes in gene function that occur independently of alterations in primary DNA sequence. Two major epigenetic mechanisms implicated in nutriepigenomics are DNA methylation and histone modification. DNA methylation in gene promoter regions usually results in gene silencing and influences gene expression. While this form of gene silencing is extremely important in development and cellular differentiation, aberrant DNA methylation can be detrimental and has been linked to various disease processes, such as cancer.[2] The methyl groups used in DNA methylation are often derived from dietary sources, such as folate and choline, and explains why diet can have a significant impact on methylation patterns and gene expression.[3] Gene silencing can also be reinforced through the recruitment of histone deacetylases to decrease transcriptional activation. Conversely, histone acetylation induces transcriptional activation to increase gene expression. Dietary components can influence these epigenetic events, thereby altering gene expression and disturbing functions such as appetite control, metabolic balance and fuel utilization.[1]

Various genetic sequences can be targeted for epigenetic modification. A transcriptome-wide analysis in mice found that a protein-restricted (PR) diet during gestation resulted in differential gene expression in approximately 1% of the fetal genes analyzed (235/22,690). Specifically, increased expression was seen in genes involved in the p53 pathway, apoptosis, negative regulators of cell metabolism, and genes related to epigenetic control.[4] Additional studies have investigated the effect of a PR-diet in rats and found changes in promoter methylation of both the glucocorticoid receptor and peroxisome proliferator-activated receptor (PPAR).[5][6] Altered expression of these receptors can result in elevated blood glucose levels and affect lipid and carbohydrate metabolism.[3] Feeding a PR-diet to pregnant and/or lactating mice also increased expression of glucokinase, acetyl-CoA carboxylase, PPARα, and acyl-CoA oxidase.[7] Changes in expression were reportedly due to epigenetic regulation of either the gene promoter itself, or promoters of transcription factors that regulate gene expression. Additional genes that have been shown, either by in vitro or in vivo studies, to be regulated by epigenetic mechanisms include leptin, SOCS3, glucose transporter (GLUT)-4, POMC, 11-β-hydroxysteroid dehydrogenase type 2 and corticotrophin releasing hormone. Epigenetic modification of these genes may lead to “metabolic programming” of the fetus and result in long-term changes in metabolism and energy homeostasis.[8]

The period of development in which the nutritional imbalance occurs is very important in determining which disease-related genes will be affected. Different organs have critical developmental stages, and the time point at which they are compromised will predispose individuals to specific diseases.[9] Epigenetic modifications that occur during development may not be expressed until later in life depending on the function of the gene.[3] While the majority of studies implicate prenatal and perinatal periods as critical time windows, some research has shown that nutritional intake during adulthood can also affect the epigenome.

Low birth weight

Fetal exposure to calcium, folate, magnesium, high or low protein, and zinc have all been associated with birth weight.[9] Numerous studies have investigated the link between birth weight and risk of disease and have found that low birth weight is significantly associated with coronary heart disease, stroke and type-2 diabetes. Most importantly, these associations occurred after adjusting for lifestyle factors, implying a genetic basis for onset of disease.[10] Impaired insulin secretion is associated with low birth weight and can lead to insulin resistance as babies accumulate body fat.[11] Studies using intrauterine growth retarded (IUGR) rats have found that growth inhibition can lead to decreased expression of Pdx1 transcription factor, which is essential for differentiation and function of pancreatic beta cells.[12] Decreased histone acetylation at the proximal promoter of Pdx1 is responsible for reduced Pdx1 expression and subsequently results in a cascade of histone deacetylation and methylation events that can result in type-2 diabetes.

Development of type 2 diabetes following intrauterine growth retardation in rats is associated with progressive epigenetic silencing of Pdx1

Transgenerational effects of maternal protein restriction

Many believe epigenetic regulation is cleared during the fertilization process, yet more evidence for transgenerational effects (TGEs) are being revealed.[1] These TGEs take place when the epigenetic regulatory patterns are not sufficiently erased during fertilization, possibly due to nutrition levels in previous generations. Later generations may be affected from caloric and protein restriction, high-fat interventions and endocrine disruption in earlier generations.[1] Differences within the nutritional behavior of the maternal rat are believed to cause malprogramming in the F1 generation and may then be passed to subsequent generations.[1] Maternal rats fed a PR-diet during the entire length of pregnancy led to metabolic-related problems in the F1 and F2 generations, even with normal nutrition during the F1 pregnancy.[27][28] These effects have also been seen in the F3 generation depending on the length of protein restriction.[29][30] If protein restriction occurred solely during pregnancy, the F1 and F2 offspring had higher systolic blood pressure and lower nephron numbers, possibly predisposing them to hypertension.[30] Altered glucose utilization was detected in the grand-offspring of maternal rats fed a PR-diet during pregnancy and lactation, potentially resulting in diabetes later on in life [29]

Protein-restriction in the F0 generation led to hypomethylation of promoters involved in metabolism in the F1 and F2 generations, even though the F1 pregnant rat was given a normal diet.[31] The exact mechanism of this situation has yet to be elucidated; however, direct transmission is a distinct possibility, meaning the epigenetic marks were preserved during spermatogenesis and oogenesis, when they are normally erased.

Most research to date use common rodent models to investigate the role of nutrition on phenotype.[10] Popular areas to investigate include IUGR studies, whereby rodents, and sometimes sheep, are subjected to a variety of nutritional conditions. A model for studying IUGR in rodent was developed by Simmons et al. (2010) and is used to investigate type II diabetes.[32] The maternal rats have their uterine arteries ligated, causing altered use of glucose and insulin in the fetus and can therefore serve as a model for diabetes. These growth-retarded rats were found to be highly similar to human fetuses, as they both display symptoms such as lowered glucose and insulin levels. Gestational diabetes may also be studied through chemical induction using streptozotocin treatment of the pregnant rats.[33] Streptozotocin can cause destruction of the beta cells within the pancreas depending on the concentration given.

The predominant means of investigating nutriepigenetics involves varying the nutritional conditions to which a subject is exposed to and monitoring the effects thereafter. Restricting caloric and protein intake are the two most common methods.[33] A pregnant rodent may have their caloric intake reduced up to 30-50% of normal intake. Protein restricted rodents are given 8-9% casein, as opposed to control rats that are fed 20% casein. Micronutrients, such as zinc and iron, may also be restricted to investigate the effects on offspring. Additionally, rats fed diets lacking or including methyl donors are often used to study the effects of diet on epigenomics, as variations within the methylation of DNA are common means of silencing or expressing genes.[34] Supplementing maternal mice with folic acid, vitamin B12, choline and betaine leads to increased levels of DNA methylation at CpG sites and causes a coat color change.[35] This is an example of epigenetically modifiable loci called a “metastable epiallele”, of which only a few have been identified. The above is an example of the “agouti” gene locus, whereby the insertion of a transposable element upstream to the Agouti gene is hypermethylated from the supplementation and causes a change in the mice's coat color. Diets containing higher carbohydrate and fat content attempt to mimic typical Western-style diets may also be used in nutriepigenetic studies.[10][33] Another method used is “catch-up”, where offspring of rats born to mothers subjected to various diets are subsequently cross-fostered to mothers fed normal diets.[33]

The nutriepigenetic pathway of maternal choline-deficient diets helps to elucidate the development of fetal alcohol syndrome

The possibilities of utilizing nutriepigenomics for intervention are quite expansive. This can include preventative therapies, such as providing an optimal regime for nutrition during pregnancy and lactation.[33] It is already common place for pregnant mothers to supplement their diets with choline and folate to prevent the development of neurological disabilities in the fetus.

A highly specific diet, termed an "EpiG diet," may be employed for an individual believed to be at higher risk of developing a metabolic disorder.[1] These diets may include supplementation with methyl donors, such as folate. There are also many other natural compounds, such as resveratrol, curcumin and green tea that have been termed “epigenetic modifiers”, as they have anti-cancer capabilities in addition to being used as treatments for metabolic diseases.[36] However, the functions of these compounds still require long-term studies to evaluate their effect over time.

There also exists potential for therapeutic treatments that may correct metabolic disorders, such as type II diabetes.[33] Components of garlic and cruciferous vegetables are known to possess HDAC inhibitors that modify the acetylation of histone proteins and may contain a protection against cancer.[26] These same compounds have also been implicated in irritable bowel syndrome (IBS) and colon cancer, as they may modify the histones normally implicated in these diseases.[37]

Elucidation of disease pathways is another future direction for nutriepigenomic studies. For example, choline-deficient diets and alcohol metabolism during pregnancy may have very similar metabolic pathways.[38] Therefore, animal studies using choline-restricted diets may assist in investigations of fetal alcohol spectrum disorders.

When compared to studies of maternal transmission, investigations into the role of paternal diets are lacking. A review demonstrated the nutrition of both parents do in fact play a role in determining the health of their offspring.[39] A germ-line study reported paternal rats fed a high-fat diet led to insulin dysfunction in the F1 offspring.[40] While this likely occurs via epigenetic modifications similar to those postulated in the maternal diets, the exact mechanism remains to be defined. Assessing the role of epigenetic mechanisms may be easier using paternal inheritance, as sperm transmits epigenetic and genetic information, whereas the female cells also transmit mitochondrial DNA.[39]