Nutrigenomics

Nutrition vs. diseases

Margarita Pertseva, "Biomolecule"

Let food be your medicine 
Hippocrates

More and more people in the world are dying from chronic non-communicable diseases (diabetes, cancer and cardiovascular diseases). What can stop such an epidemic? The answer will be given by nutrigenomics, a new direction in science that studies how food affects gene expression. The article will reveal the molecular mechanisms of the effect of food on genes; tell you which foods should be consumed more often, and which should be abandoned in order to live longer and healthier; and describe the prospects of dietetics in the future. The second part of the series is "Nutrigerontology: Nutrition vs. aging" will focus in detail on the mechanisms of aging and how food can slow down these processes.

Since the time of ancient Greece, it has been known that food affects the state of the body and spirit and is able to get rid of diseases. However, fundamental discoveries in the science of nutrition were made only in the 18th and 20th centuries: the chemical composition of food and the main pathways of metabolism were studied [1]. Until the middle of the 20th century, due to an unbalanced diet, ailments associated with a deficiency of vitamins and minerals were common, so their functions were studied especially actively. Today, developed countries are faced with other consequences of irrational nutrition – obesity and type II diabetes [2] (Fig. 1).

Figure 1. Consequences of unbalanced nutrition in developed countries: the spread of obesity and type II diabetes. Overweight and the "Western" type of diet (an abundance of fried foods, red meat, sugary carbonated drinks, fatty dairy products) contribute to the development of cardiovascular and oncological diseases, type II diabetes. Drawing from the website uhc.com , adapted.

Moreover, it was found that the life expectancy and development of the "killer three" – cardiovascular, neurodegenerative and cancer diseases - depends on the human diet [3]. It became obvious to doctors and scientists that for the effective treatment and prevention of the above-mentioned diseases, it is necessary to understand the mechanisms of the effect of food on the body at the cellular and molecular levels. At the beginning of the 21st century, international genomic projects were completed [4], providing a lot of genetic information for analysis; productive molecular methods for studying the "inner life" of the cell began to develop [5]. All these factors led to the birth of a new science – nutrigenomics [6].

Nutrigenomics studies the effect of various food components and dietary supplements on gene expression [7]. It is expected that the determination of biochemical ways of interaction of food and genes will effectively treat non-communicable diseases (for example, diabetes, cancer, pathologies of the cardiovascular system), as well as prevent their development by identifying early markers of metabolic disorders and drawing up an individual nutrition plan [6].

How does food regulate the work of genes?

Nutrigenomics: from food to genes

Gene expression is a process in which hereditary information from a gene is transformed into a functional product – RNA or protein. Gene expression is regulated at different stages, but the main "checkpoint" is the beginning of transcription (synthesis of RNA on a DNA matrix). The initiation of transcription depends both on the availability of the necessary proteins (transcription factors, enzymes, etc.) and on availability (affinity) DNA for these proteins (i.e. from epigenetic modifications). Food components can influence both processes [6, 7].

Epigenetic modifications

All cells of our body – from neurons to leukocytes – carry the same genetic material. But each cell expresses a specific set of genes – this determines the specialization of cells. The switching on/off of genes is regulated by epigenetic modifications (such modifications do not affect the DNA sequence, but change its "body kit"). In a cell, DNA is compacted, i.e. wound on "beads" – a complex of histone proteins, various chemical modifications of which turn the gene on or off. In addition, the genes are switched off when the DNA molecule itself is modified (methylation).

Some components of food affect these processes (Fig. 2):

1. Acetylation of histones (gene activation). Sulfaraphane (found in cabbage, broccoli, cauliflower) and diallyl disulfide (from garlic) – turn on genes by suppressing enzymes that repress the gene by removing the acetyl label from histones. Therefore, sulfaraphane is able to turn on the genes regulating normal division that are silent in cancer cells, which suppresses tumor growth. Butyric acid, which is formed by the human microflora when eating fiber, has a similar effect on the work of genes, and also activates the immune system, which suppresses the growth of cancer cells. The inhibitory effect of butyric acid on metastasis has been shown in rats on a model of rectal cancer [8].
2. DNA methylation (gene shutdown). Sources of methyl groups (choline, methionine, folic acid) are found in eggs, spinach, legumes and liver. In adult rats, chronic deficiency of methyl groups leads to spontaneous formation of tumors [9], and also leads to activation of mobile elements of the genome [10]. The experiment conducted by Girtle and Waterland with transgenic rodents agouti (Avy agouti), which have a yellow color and a predisposition to obesity, diabetes and cancer, is widely known. When choline, methionine and folic acid were added to the feed of pregnant agouti females, they had normal offspring with brown coat color and without health abnormalities [11]. The fact is that the presence of sources of methyl groups in the mother's food contributed to the methylation (and, accordingly, the shutdown) of the agouti gene, which caused a painful phenotype in embryos*.

* – Read more about how epigenetic modifications affect development in "Development and Epigenetics, or the story of the Minotaur", "Epigenetics: the invisible commander of the genome" [12, 13].

Figure 2. The mechanism of food influence on epigenetic modifications. Drawing from the website epigeek.com .

For the normal development of the fetus and the course of pregnancy in women, sources of methyl groups, in particular, folic acid, are necessary. With its deficiency, the risk of premature birth, miscarriages increases, as well as pathologies in the fetal nervous system and low newborn weight are possible [14]. The exact mechanisms of folic acid action are still unclear, it is only known that methylation of the IGF2 gene (insulin-like growth factor 2) involved in fetal growth and development is enhanced [15].

Transcription factors

Figure 3. The mechanism of action of nutrients on gene expression through transcription factors. Figure from [6], adapted.

The second mechanism by which food changes gene expression is illustrated by the following diagram: "food component → receptor → signaling pathway → transcription factor → gene inclusion" [6, 16] (Fig. 3). Receptors recognize a strictly defined structure of substances, therefore similar components of food affect the body differently (for example, saturated and unsaturated fats). 

Small variations are possible in this scheme, for example, nuclear receptors combine the functions of a receptor and a transcription factor: they recognize various hydrophobic components of food or their derivatives (fatty acids, vitamin D, retinoic acid, bile salts, etc.), and then change the activity of the genes regulated by them [17-19].

Food consists of proteins, carbohydrates and fats. Food components are broken down during digestion to simpler substances (amino acids, monosaccharides, fatty acids), which are then transported to cells and bound by receptors. 

The signal from the receptor spreads through the cell, reaches the nucleus and gene expression changes. Long-term changes in gene expression ultimately affect health and life expectancy. But about everything in more detail.

Proteins in the digestive tract break down to amino acids, which are then transported inside the cells. In the cellular cytoplasm floats the molecule mTOR (mammalian target of rapamycin), which is activated by a high concentration of amino acids and regulates numerous aspects of metabolism in the cell. It is noteworthy that the mTOR signaling pathway is a conservative biochemical pathway that regulates aging in animals. Genetic mutations that weaken the signal of the mTOR pathway prolong the life of worms, flies and mice [20]. Since mTOR is activated by amino acids, it can be expected that a diet with a limited protein content will have a beneficial effect on health and longevity. Indeed, the consumption of a small amount of proteins or methionine (an essential amino acid) increases life expectancy in model animals [21]. In humans, a diet with a low protein-carbohydrate ratio reduces the risk of cancer, obesity and neurodegenerative diseases [22]. According to research, elderly people (50-65 years old) who receive more than 20% of daily calories from proteins four times (!) They are more likely to die from cancer, and their overall mortality rate is 75% higher compared to people who follow a low-protein diet (i.e. less than 10% of daily calories) [23]. Interestingly, there is no correlation between the consumption of plant proteins and the mortality rate. It is believed that this is due to the amino acid composition of plant proteins, which contain less methionine and cysteine [23].

Carbohydrates are broken down to monosaccharides during digestion; the most famous representative of this class is glucose. An increase in blood glucose levels causes the production of the hormone insulin. Insulin is captured by receptors on the cell surface, which leads to the activation of the IIS (Insulin/Insulin-like grow factor Signaling) signaling pathway, which triggers the absorption of glucose by cells, and also stimulates cell growth and division. The IIS signaling pathway is closely intertwined with the mTOR pathway, respectively, the level of its activation has consequences for health and life expectancy. Mice heterozygous for the IGF-1 receptor (Insulin-like grow factor) (Igf1r+/−), on average, lived 26% longer than their homozygous brothers (Igf1r+/+). As for humans, genetic polymorphisms that reduce the level of the IIS pathway signal are associated with longevity [23]. Numerous studies demonstrate that calorie restriction in animals reduces the level of IGF in the blood; along with IGF, the risk of developing atherosclerosis, cancer and other diseases also decreases [22]. In humans, fasting several days a week (consumption of less than 25% of the daily calorie intake) improves markers of cardiovascular diseases such as blood cholesterol (LDL) and insulin sensitivity* [23].

* – Details about the mechanisms of action of a low-protein diet and the signaling pathways of mTOR and IIS are discussed in the article "Nutrigerontology: Nutrition vs. aging" [24].

Polyunsaturated fatty acids (PUFA). PUFAs are found in olive oil, sunflower seeds, tuna, salmon. PUFAs are necessary for the normal functioning of the body, their use has a beneficial effect on the functioning of the cardiovascular and nervous systems [25]. Inside the cell, PUFAs are recognized by nuclear PPAR receptors (peroxisome proliferator–activated receptors), which also function as transcription factors and regulate metabolic genes. Activation of PPARa in the liver promotes the catabolism of fats in the body (i.e. their utilization). PUFA also reduces the expression of genes involved in the synthesis of cholesterol and fatty acids. Omega-3 fatty acids, which are rich in fish oil, linseed oil and walnuts, are especially useful for the body. Fish oil reduces cholesterol levels in the blood and liver [26]. Studies demonstrate that ω-3-fatty acids (but not ω-6-LC) inhibit the growth of colon cancer in vitro and in vivo [27]. In addition, ω-3 fatty acids have an anti-inflammatory effect, since they function as substrates for the synthesis of anti-inflammatory prostaglandin E3, protectins and resolvins involved in the resorption of inflammation and cell protection [28]. In addition, ω-3-fatty acids alter histone acetylation and thus inhibit the effect of transcription factor NF-kB on the immune response and apoptosis genes that it regulates [28].

Trans fats. Trans fats are formed in the food industry from unsaturated fatty acids in the production of margarine, which is used in the manufacture of pastries, crackers, chips, etc. Studies show that there is a direct relationship between the consumption of trans fats and the development of cardiovascular diseases, diabetes, obesity, allergies, breast cancer, as well as shortening the pregnancy period [29]. In experiments conducted on mice, scientists have determined that trans fats enhance the expression of PGC-1, a key regulator of lipid metabolism, in the liver. This contributes to the excretion of low-density lipoproteins into the blood and the deposition of cholesterol in the vessels [30]. Trans fats are also embedded in the cell membrane, cause inflammation and disrupt cell function (Fig. 4) [31].

Figure 4. Suggested mechanisms of action of trans fats. (a) Trans fats alter the production, secretion and catabolism of lipoproteins in liver cells, and also affect the transport of cholesterol esters to very low-density lipoproteins. (b) In endotheliocytes, the synthesis of circulating adhesion molecules increases and the function of NO-synthase decreases. (c) Under the influence of trans fats, the normal metabolism of fats in adipocytes changes and the inflammatory response increases. (d) The production of inflammatory mediators (interleukin-6, tumor necrosis factor) increases in macrophages. The listed effects of trans fats have been confirmed by human studies and contribute to atherosclerosis, diabetes, plaque detachment, sudden death from cardiac pathologies. The intracellular mechanisms of action of trans fats are not precisely established. Possible: changes in the membrane phospholipids of the cell, which affects the functions of membrane receptors (such as NO-synthase on endotheliocytes or TLR on macrophages); direct interaction of trans fatty acids with nuclear receptors regulating gene transcription (for example, the liver X receptor); indirect or direct effect on EPR, activation of kinase Jnk, which is usually activated in response to cellular stress and regulates apoptosis, cell division, cytokine production. The proposed mechanisms need further study. Drawing from the website ufrgs.br , adapted.

Saturated fatty acids (NLCs). The main sources of saturated fatty acids are butter, cheese, meat, egg yolks, coconut, palm kernel oil and cocoa butter. There is evidence that NLCs promote inflammation through direct activation of TLR4 (Toll-like receptor) receptors on macrophages [32]. The TLR4 receptor is a receptor of innate immunity that recognizes a certain component of the bacterial cell wall, which includes a lipid. The signal from TLR4 activates the key transcription factor of the immune response – NFkB. Despite the fact that the results of studies on the adverse effects of NLC on health are contradictory, the World Health Organization recommends reducing the proportion of saturated fatty acids in the diet to 5-10% (of the total number of calories).

It is known that the same factors (identical diet and degree of physical activity) can affect the metabolism of people in different ways. For example, it was recently revealed that in women, depending on the type of allele, consumption of PUFA can have opposite effects on the level of high-density lipoproteins (HDL) in the blood [33]. Accordingly, when conducting nutrigenomic studies, it is necessary to take into account individual genetic characteristics.

Nutrigenetics: from genes to food

Nutrigenetics studies how variations in genes affect the assimilation and metabolism of food and, accordingly, reveals genetic predispositions to diseases. Genetic diseases are divided into monogenic (determined by variation in one gene) and polygenic (determined by a combination of genes + environmental factors) [36].

Monogenic diseases include, for example, phenylketonuria, gluten disease, lactose intolerance. The cause of such diseases is clear, so it is easy to prevent external manifestations: it is enough to exclude an indigestible component of food from the diet.

For the prevention of polygenic diseases – obesity, type II diabetes, cancer, disorders of the cardiovascular system - it is necessary to monitor not only the diet, but also monitor the degree of physical activity, stress levels, etc. Nevertheless, accumulating knowledge from nutrigenetics and nutrigenomics allows you to individually (depending on the genotype) identify risk groups and determine which foods a given person should avoid, and which, on the contrary, supplement their daily menu to minimize the risks of diseases.

Cardiovascular diseases (CVD). The development of CVD is extremely complex, so scientists are still far from establishing all the risk factors and ways to eliminate them. However, in the genes of lipid metabolism (genes of apolipoproteins E, A1, A2, A54; PPARs; lipoxygenase-5, etc.), variations have been identified, the owners of which develop CVD faster from high-calorie nutrition [35]. It has also been shown that people with a slow caffeine metabolism have an increased risk of heart attacks when using it [36]. At the same time, the main risk of developing CVD has been proven – the presence of a metabolic syndrome, which is characterized by a "deadly four": increased blood pressure, blood sugar and lipids, obesity. Therefore, the main urgent task in this area is to establish the molecular mechanisms of the general pathological process that leads to such different metabolic disorders [34].

Cancer. Features of transport and metabolism of nutrients contribute to the development (or prevention) of cancer. For example, a mutation is common that reduces the effectiveness of an enzyme necessary for DNA methylation. With a lack of food sources of methyl groups (folate and choline), carriers of such a mutation are more likely to get colorectal cancer. For such people, alcohol consumption is an additional aggravating factor, since alcohol reduces the absorption of folate and increases its excretion from the body [34]. The consumption of red meat significantly increases the risk of colorectal cancer in both owners of fast N-acetyltransferase and carriers of a special combination of polymorphisms in the cytochrome P450 gene [33, 36]. It was also found that the probability of cancer increases with a mutation in the gene of one of the types of glutathione transferases (enzymes involved in detoxification), and the constant intake of toxins into the body (when smoking, etc.) is dangerous for people with such a mutation. And eating cabbage and other cruciferous plants, on the contrary, will be extremely useful, since they contain substances that increase the activity of glutathione transferases [34].

Fatness. A certain variant of the FTO (fat mass- and obesity-associated gene) gene is associated in people with obesity and diabetes. During the research, it turned out that with unlimited access to food, children with this variant of FTO tend to consume more high-calorie food. The effect of such a genetic variant is easily modulated by physical activity and a balanced diet.

Despite possible genetic predispositions to obesity, diabetes, cardiovascular diseases and cancer, it has been shown that environmental factors play a significant role in the development of the above pathologies [7]. Therefore, WHO has compiled basic recommendations for maintaining health: eating a variety of fruits and vegetables throughout the day, reducing the consumption of saturated and trans fats, smoked meats, salty foods; moderate alcohol consumption; an active lifestyle; maintaining a normal weight. Various studies have confirmed the inverse relationship between the consumption of vegetables and fruits and the incidence of cancer [37, 38]. In addition, accumulating data on the beneficial effects on health and longevity of a diet with a low content of animal proteins are already forcing nutritionists to build a new system of balanced nutrition. However, for a full understanding of the mechanisms of influence of food components (as well as their combinations) on the body, and the possible spread of such influence among the human population, there is still a lot of work to be done. There are a number of problems that need to be solved in order to obtain reliable information and introduce nutrigenomics/nutrigenetics into everyday life.

Problems

A single meal has a weak effect on the body, therefore, when conducting nutrigenomic studies, the duration of the use of nutrients is very important, which complicates the experiments. To analyze changes in gene expression and cell metabolism, the following methods are used: epigenetic analysis and analysis of cellular mRNAs (transcriptome), proteins (proteome) and metabolites (metabolome) (Fig. 5). Unfortunately, to date, methods for obtaining the proteome and metabolome are expensive and insufficiently developed, and the number of mRNAs is not always proportional the amount of protein in the cell and does not give information about the activity of the protein. In addition, a sufficiently large amount of biological material is required for research, therefore, blood is mainly analyzed, in particular, white blood cells (fat and muscle tissue are in second place), but it is still unknown how accurately they reflect early metabolic disorders [39].

Figure 5. Nutrigenomic research methods. Figure from [6], adapted.

Despite the fact that a sufficient amount of reliable information has not yet been accumulated to introduce nutrigenomics and nutrigenetics into everyday life, there are already companies offering nutrigenetic tests (the US government has issued a report on the dangers and unreliability of such tests). Such companies raise doubts among people about the scientific relevance of such fields as nutrigenomics and nutrigenetics, which prevents their spread and introduction into society.

The prospects

It is expected that the contribution of nutrigenomics and nutrigenetics to healthcare in the next decade will be very significant. The establishment of molecular mechanisms of the "food–genes" interaction and the identification of early markers of metabolic disorders will allow effective preventive treatment. It is planned to draw up an individual nutrition plan based on the characteristics of metabolism and genetic predispositions (Fig. 6). Food products will be tested not only for safety, but also for the effectiveness of their action on the body.

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