A current aim of nutrigenetics is to personalize nutritional practices according to genetic variations that influence the way of digestion and metabolism of nutrients introduced with the diet. Nutritional epigenetics concerns knowledge about the effects of nutrients on gene expression. Nutrition in early life or in critical periods of development, may have a role in modulating gene expression, and, therefore, have later effects on health. Human breast milk is well-known for its ability in preventing several acute and chronic diseases. Indeed, breastfed children may have lower risk of neonatal necrotizing enterocolitis, infectious diseases, and also of non-communicable diseases, such as obesity and related-disorders. Beneficial effects of human breast milk on health may be associated in part with its peculiar components, possible also via epigenetic processes. This paper discusses about presumed epigenetic effects of human breast milk and components. While evidence suggests that a direct relationship may exist of some components of human breast milk with epigenetic changes, the mechanisms involved are still unclear. Studies have to be conducted to clarify the actual role of human breast milk on genetic expression, in particular when linked to the risk of non-communicable diseases, to potentially benefit the infant’s health and his later life.

1. Introduction

1.1. Beneficial Effects of Human Breast Milk Breastfeeding and human milk are the normative standards for infant feeding and nutrition. Short-and long-term benefits of breastfeeding on health are documented [1,2]. Breastfeeding has been associated with a reduction in the incidence of gastrointestinal tract infections, respiratory tract infections, and otitis media [1,2]. The relationship of human milk feeding with a significant reduction in the incidence of necrotizing enterocolitis (NEC) has been suggested in preterm infants [3]. Protective effects are shown also in autoimmune disorders (celiac disease, type-1 diabetes) and inflammatory bowel disease [1,2]. Additionally there is extensive evidence that individuals who had been breast-fed or received human milk show lower risk of some non-communicable diseases in later life [1,2]. Indeed breastfeeding has been associated with lower risk of obesity, lower levels of arterial blood pressure, lower total-and LDL-blood cholesterol levels in adulthood, and lower risk of developing type-2 diabetes [1,2]. Furthermore consistent differences in neurodevelopmental outcome between breastfed and formula fed infants have been reported [1,2]. Evidence about the association between neurodevelopment and exclusive breastfeeding was provided by the cluster-randomized Promotion of Breastfeeding Intervention Trial (PROBIT) study [4]. Adjusted outcomes of intelligence scores were significantly greater in exclusively breastfed for three months or longer. Human milk consists not only of nutrients, but also of biologically active compounds, which may play an important role in the health benefits associated with breast-feeding [1]. For example nutrition is one of many factors that affect brain development not only morphologically, but also for neurochemistry and neurophysiology. The NUTRIMENTHE (The Effect of Diet on the Mental Performance of Children) is a large collaborative European Project assessing the short- and long-term effects of specific nutrients and food components in early-post-natal diet on neurodevelopment through well-designed large-scale epidemiological studies [5]. The fatty acids provided in breast milk are thought to play a crucial role in this respect. Indeed, a recent review indicated that neurodevelopment and cognitive abilities may be enhanced by early provision of n-3 long-chain polyunsaturated fatty acids (LCPUFAs) through breast milk or docosahexaenoic acid (DHA)-fortified foods may improve neurodevelopment and cognitive abilities [6]. However nutrients should not be considered only as an energy source or as factors involved in the development of the organism. More recently molecular biology studies have shown that nutrients, either directly or by hormonal activity, are able to significantly influence the expression of genes [7]. Through the nutrigenomics it may be possible to identify mechanisms that underline individual variations in dietary requirements, as well as in the capacity to respond to food-based interventions [7]. In this way nutrigenomics may be able to provide personalized nutrition recommendations in order to improve the prevention and therapy of pathologies in which each would be predisposed [8]. The research, aimed to analyzing the influence of nutrients on health through nutrigenomics, find their basis on two observations: The diet changes the gene expression (nutritional epigenetics). The metabolic processes of nutrients may vary and affect the state of health depending on the individual genotype (nutrigenetics). Nutrigenetics, a fundamental branch of nutrigenomics, has the purpose to identify the genetic variations influencing the way of digestion and metabolism of molecules introduced in the diet [9]. The analysis of the Single Nucleotide Polymorphisms (SNPs) has identified genetic variations linked to the risk of each individual. SNPs, single base-pair differences in DNA sequence, represent a primary form of human genetic variation. The presence of differences in genetic material due to a single nucleotide may explain not only the onset of certain pathological conditions, but also the different responses to nutrients/foods in the diet [10]. An example of application of the concepts of nutrigenetics concerns the relationship between the apolipoprotein E gene polymorphism and the diet. The subjects with the apoE gene promoter (−219G/T) polymorphism show higher levels of LDL cholesterol and apoB plasma concentrations after consuming a saturated fatty acids rich diet [11]. Therefore, the 219G/T polymorphism may partly explain the individual differences in response to the diet introducing the possibility of prevention of hypercholesterolemia and its complications consuming a saturated fatty acids poor diet in individuals with this particular genotype [11]. Current nutrition recommendations are based on estimated average nutrient requirements for a target population and aim to meet the needs of most individuals within a population but also to prevent non-communicable diseases [12]. In the case of specific genetic polymorphisms, personalized nutrition recommendations may be needed [13]. Nutrigenetics is a promising tool that may be important to refine current nutrition recommendations and to provide personalized recommendations in population subgroups.

1.2. Nutritional Epigenetics If evidence suggests that genome may be able to influence the nutrition [9], nutrients may be able to regulate gene expression [14]. Genes and nutrition seem, therefore, to be in mutual relationship. The term epigenetics literally means on top of genetics and refers to processes that induce heritable changes in gene expression without altering the gene sequence [10]. Epigenetic processes are integral in determining when and where specific genes are expressed. Alterations in the epigenetic regulation of genes may lead to profound changes in phenotype. The major epigenetic processes are DNA methylation, histone modification, chromatin remodeling and microRNAs, although it is still debated if miRNA may be considered as an epigenetic phenomenon. To date, most studies on the effect of early-life nutrition on the epigenetic regulation of genes have focused on DNA methylation [15,16,17,18]. Methylation of the 5′ position of a cytosine within the genome occurs by the enzymatic family of DNA methyltransferases forming 5-methylcytosine (5-mC), that is present in an estimated 4%–6% of the cytosine bases within a human genome. Most of DNA methylation occurs within CpG dinucleotides, although methylation outside of the CpG context has been reported in human DNA in recent years [18]. The human genome contains about 30 million CpG dinucleotides that exist in a methylated or unmethylated state. Dense repeats of CpG nucleotides are called CpG islands and occur throughout the genome. Methylation of CpG islands located in the promoter region of a gene is usually inversely associated with transcription of that gene due to binding of methyl-CpG binding proteins, which recruit proteins to the promoter of the gene, thereby blocking transcription. Therefore, epigenetics, that is the inter-individual variation in DNA methylation patterns and chromatin remodeling, provide a potential explanation for how environmental factors (e.g., bioactive food components, nutrients, specific diets) can modify the risk for development of many common diseases [16,17]. Age, genetics, and environment may together interact to affect epigenetic regulation. The epigenetics determinants may interfere at any time during the life of the individual [18]. Several studies have shown that the environment and nutrition, at an early stage or at critical periods of development, may influence the expression of genes with short- and long-term effects on the organism [15,16,17]. Data obtained from animal models suggest that maternal malnutrition during pregnancy results in a retardation of growth but also in a modification of the expression of biochemical mechanisms related to the endocrinological and metabolic control [15]. Indeed, it has been showed that offspring of mothers in a protein-restricted diet, from conception throughout pregnancy, present an altered metabolic phenotype showing a number of features of human cardio-metabolic disease, including hypertension, increased fat deposition, impaired glucose homeostasis, dyslipidaemia and vascular dysfunction [16]. In rats, maternal protein-restriction seems to epigenetically program metabolism in the offspring. In pups whose mothers were fed a diet low in protein was observed a reduced methylation and increased expression of peroxisome proliferator-activated receptor a (PPARα) in the liver [18]. Similar results were seen for the glucocorticoid receptor gene [18]. More recently, a low protein maternal diets in pigs was shown to effect global DNA methylation in the newborn offspring through changes in DNA methyltransferase (Dnmt1, Dnmt2 and Dnmt3) expression in both the liver and skeletal muscle [18]. These findings may demonstrate the influence of the maternal diet on the pup’s fat and carbohydrate metabolism. Human studies found that adult disease risk may be associated with adverse environmental conditions early in development. In particular, the risk of obesity and its associated conditions may be related to the timing of nutrient constraint during pregnancy [19]. Several studies, focused on individuals exposed to famine in utero which occurred in the Netherlands during the winter of 1944, presented evidences that individuals whose mothers were exposed to famine periconceptually and in the first trimester of pregnancy showed low birth weight compared with unexposed individuals and, as adults, exhibited increased risk of obesity and cardiovascular disease [20]. In addition, nutrition in early postnatal life may affect susceptibility to future obesity [21]. Early catch up growth in infants born preterm, who also have a reduced fat mass at birth, and who were formula fed show increased risk of cardio-metabolic disease in later life, including obesity [21]. The exact mechanisms underlying how early nutrition may cause programming of risk of non-communicable diseases are unknown, but are thought to be associated with altered development of organ structure or persistent alteration at cellular level [22]. Among proposed mechanisms, acute or persistently altered gene expression through a variety of epigenetic pathways may be included [22]. During in utero or early postnatal development, short-term changes through environmental influences could permanently change organ development at a time of extreme vulnerability or “plasticity” [22]. A recent study is the first example of an association between periconceptional exposure to environmental factors and DNA methylation in humans [20]. Individuals who were prenatally exposed to famine during the Dutch Hunger Winter had, six decades later, showed less DNA methylation of the imprinted Insulin Growth Factor (IGF) 2 gene compared with unexposed, same-sex siblings. The association was specific for periconceptional exposure, reinforcing that very early mammalian development is a crucial period for establishing and maintaining epigenetic marks [20]. Changes in epigenetic marks as differences in methylation of the IGF2 DMR (differentially methylated region) could affect the phenotypic expression and be associated with an increased risk of adult disease considering that IGF2 is a key factor in human growth and development [20]. These findings demonstrate that the prenatal and early postnatal periods have a critical role in the individual outcome, as Barker affirms: “Much of human development is completed during the first 1000 days after conception” [21]. At least epigenetics might partially explain the mechanism that delucidates the fetal “programming” [16,17].