Nutrition and Genomics

1. Nutrition and Genomics BMB 505 – Advanced Nutrition and Nutritional Biochemistry Yearul Kabir (Handout # 1) Date: 09.11.2009

2. Nutrition and Genomics • Nutritional genomics, or nutrigenomics, is the study of how foods affect the expression of genetic information in an individual and how an individual’s genetic makeup metabolizes and responds to nutrients and bioactives. • Not all individuals respond similarly to food. • That food alters expression of genetic information and that genotypic differences result in different metabolic profiles are concepts central to nutritional genomics – and, indeed, provide the critical link between diet and health. • In other words, the need to understand nutritional influence on the genome and the genome’s influence on metabolism led to the concept of nutritional genomics. • The notation that interactions between dietary factors and genes (or their variants) can promote health or cause disease is perhaps best captured by the term “nutrigenomics” (a contraction of nutritional genomics).

3. Nutrigenomics • Nutrigenomics adhere to the following percepts: • Poor nutrition can be a risk factor for diseases; • Common dietary chemicals can act on the human genome, either directly or indirectly, to alter gene expression and/or gene structure; • The degree to which diet influences the balance between health and disease depends on an individual’s genetic makeup; • Some diet-regulated genes (and their common variants) play a role in the onset, incidence, progression, and/or severity of chronic diseases, and • Dietary intervention based on knowledge of nutritional requirement, nutritional status, and genotype can be used to prevent, mitigate, or cure chronic disease. • Genomic analysis reveals that humans are 99.9% identical at the DNA level. This implies that the remaining 0.1% of the human genome (or about 3 million single nucleotide polymorphisms (SNPs) is responsible for all the morphological, physiological, biochemical and molecular differences between any two individuals and susceptibility to disease.

4. Nutrigenomics ….. • Common genetic variation in the form of SNPs in enzyme-encoding genes (or their promoters) can affect reaction rates in metabolic pathways that in turn, can create individual differences in the way we absorb, metabolize, store, and utilize nutrients. • SNPs are the most common variation in the primary sequence of human DNA; more than 10 million SNPs are estimated to be present in the human genome. • SNPs are defined as nucleotide base pair differences in the primary sequence of DNA and can be single base pair insertions, deletions, or substitutions of one base pair for another. • SNPs contribute to susceptibility for common disease and developmental anomalies, and polymorphic alleles have been identified that increase the risk of common disorders including neural tube defects, cardiovascular disease, cancers, hypertension, and obesity.

5. Nutrigenomics ….. • The initial successes of nutrigenomics have revealed that indeed the natural variation in the human genome is responsible for significant variations in response to diets. • Therefore, the optimal diet for one individual in a population will not be the same for every individual in that population. • As we learn more about the health-promoting dietary chemicals we eat and how they interact with nutrient-regulated and disease-associated genes, we should be able to achieve optimal health and wellness earlier, maintain it longer, and at a lower cost. • Just as pharmacogenomics has led to the development of “personalized drugs,” so will nutrigenomics open the way for “personalized nutrition”.

6. Nutritional Regulation of Gene Expression • Nutrient regulation of gene expression is a well-recognized topics in contemporary nutritional science. • It is difficult to separate direct effects of individual nutrients on gene expression from those produced indirectly through physiologically controlled mediators and modulating molecules that are responsive to the diet. • The way in which the diet, in concert with hormones, cytokines, and growth factors, interacts to influence the differential expression of specific genes has reached such a high level of awareness that a new term, nutrigenomics has evolved to describe such phenomenon. • Nutrigenomics includes all genetic factors, including epigenetic events, as they modulate individual genes and gene networks.

7. Nutritional Regulation of Gene Expression ….. • From the stand-point of nutritional influences on gene expression, processes are envisioned in which dietary conditions, through either direct interaction of specific nutrients with transcription factors or mRNA binding proteins, or, more commonly, through indirect means (e.g., hormones or signaling systems), produce changes that define phenotypic expression. • Classic experiments demonstrated that polyribosome formation depended on the presence of essential amino acids in the diet. • In addition, inhibitors of mRNA synthesis (actinomycin D) and translation (cycloheximide) were used in animal experiments to study many nutrient-induced changes in gene expression. • Examples: iron-induced synthesis of ferritin, regulation of phosphoenolpyruvic-carboxykinase (PEPCK) by high carbohydrate intake and fasting.

8. Your Health – Genes or Environment? • You have no doubt grown accustomed to thinking about certain aspects of your physical body, its function and your health as immutable, given or cast in stone. For example, if you have brown eyes, you know you will never have blue ones. If you wear size 10 shoes, you will never wear size 6. • It is Heredity. You inherited your brown eyes. • However, if genes alone determine the size, shape and function of our bodies, how can we explain the fact that the average height of adult Japanese men and women has increased nearly six inches since WW II? • The genes have not changed. What has changed is the nutrition of Japanese children and adolescent. • Nutritional environment combined with genetic inheritance yields what is called the “phenotype” of the individual, his or her observable size, shape and function.

9. Disease – Inherited Risk, Not Inevitable Outcome • Phenotype: The entirephysical, biochemical and physiological makeup of an individual, as determined both genetically and environmentally, as opposed to genotype. • Most people assume that diseases like diabetes, heart disease, high blood pressure, stroke and cancer are results of genetic inheritance factors. • The Human Genome Project is providing that genes are only a part of the story. • More important than genetic inheritance is the phenotype – the result of gene expression and function. • In terms of your health or disease state as an adult, your phenotype is determined by the way you have treated your genes throughout your life.

10. Disease – Inherited Risk, Not Inevitable Outcome… • What you have eaten or drunk, inhaled, surrounded yourself with in your environment, endured as stresses, participated in as activities or suffered as injury, infection or inflammation – all of these factors alter the expression of your genes and contribute in a major way to your state of health or disease. • Expression means the way messages that are locked into your genetic inheritance factors are translated and ultimately influence your function. • These changes in function result from two important influences that modify how your genes are expressed. • The first is how the messages in your genes are transcribed, and the second is what happens to the cells of your body after the genes are translated. (Cell biologists call these “post-translation” effects of gene expression.)

11. Nutritional Modification of Genetic Expression • In early 1900s, Drs. Joseph and Mary Goldberger research led to the discovery that nutrition influences gene expression. • Pellagra: A clinical deficiency due to deficiency of niacin or failure to convert tryptophan to niacin. It is characterized by dermatitis, inflammation of mucous membranes, diarrhea and dementia – psychic disturbances (the 3 Ds of pellagra). • Each fall and winter in the Southeaster US filled with people with pellagra. Who contracted pellagra were immigrants from Eastern Europe; therefore believed to be of genetic origin. The seasonality of the illness suggested that, like the flu, it was caused by an infection contracted by genetically susceptible individuals. • The Goldbergers quickly became convinced from their observations that pellagra was neither genetic nor caused by the infection. Instead, they found it resulted from a nutritional deficiency.

12. Gene Expression • During the course of your life, many events alter the way your genetic characteristics are expressed in individuals cells, tissues or organs. • Changes in gene expression may reflect changes in phenotype that indicate disease or the loss of health and vitality. • An extreme example of this change in phenotype is the case of J.M. Barrie, the author of Peter Pan. When he died in his 60s, he was only 4 feet 10 inches tall and apparently had never gone through puberty. • This phenomenon occurred in the absence of any known disease or genetic abnormality. • In the medical literature of today, this appears to be a case of arrested maturation due to a psychological trauma so severe that it altered gene expression of the hormones required for development.

13. Gene Expression…. • Our environment and experiences can play a significant role in modifying our phenotype. This most remarkable case of stree-induced dwarfism in Barrie demonstrates the power of the environment to control the activity of our genes. • In most cases, however, the first manifestation of this type of gene expression is generally a loss of function that could be as simple as sleep disturbance, fatigue, chronic pain, changes in body temperature and weight or poor exercise tolerance. • These changes may be the early warning signs or what are called “biomarkers” of altered gene expression. If you do not pay attention to those early warnings, the result, after many years, could be the expression of disease. • Physical fitness improves your health. Exercise is good for you. • The complete explanation is that moderate regular exercise is one of the factors that improves gene expression and alters your phenotype.

14. Can Food Improve the Expression of Our Genes? • One meal does not make a difference in the expression of your genes, but over the course of many years your dietary choices can influence your gene expression in such a way as to modify your phenotype, enhancing or diminishing your cellular function. • This does not mean that food changes your genes in any way. The message you were born with remains intact, embedded in the nucleus of cells in every organ of your body. • What does change is the way the message from your genes is expressed. • The effect of the nutrients you ingest on the expression of messages within your genes is like the effect of hydroxyurea or butyrate on sickel cell anemia. • Both substance are capable of waking up the sleeping message in the genome for the production of fetal hemoglobin.

15. Figure: Red-Cell Sickling • Sickel cell anemia a “molecular disease” because just one molecule was damaged due to a genetic uniqueness (i.e., a genetic mutation).

16. Can Food Improve the Expression…. • When a fetus is in the womb, its hemoglobin is unique in its structure and ability to capture oxygen from the mother’s blood supply. • After birth, the genetic message for the production of this type of hemoglobin goes to sleep and is replaced by the message for the production of adult hemoglobin. • The fetal hemoglobin message is still on the genome; it is just not being expressed. • Administering hydroxyurea or butyrate to an individual who carries the genetic message for the production of sickle hemoglobin awakens the message to produce the normal fetal hemoglobin that dilutes the sickel hemoglobin, preventing it from crystallizing. • This nutritional intervention is a classic example of the genetic nutritioneering approach.

17. Can Food Improve the Expression…. • By using a substance that modifies genetic expression, it is possible to alter the course of a genetically determined illness. • Genetic messages can either be put to sleep or awakened as a consequence of alterations in your diet. Putting to sleep the messages that result in increased risk of disease and awakening those messages enhance health.

18. How diet Influences Genetic Expression • The understanding that diet can modify gene expression achieved a new level of acceptance due to the pioneering work of Michael Brown & Joseph Goldstein on cholesterol and its relationship to heart disease. • They found that there is a basic defect (genetic trail) in families whose members have high incidence of heart disease, which is associated with very high blood cholesterol levels. That genetic trail occurs in about 1 in 500 individuals worldwide. • Affected individuals have elevated blood levels of the “bad” LDL cholesterol. Over time, cholesterol is deposited in arteries, resulting in plaque and a narrowing of the arteries which leads to heart disease, particularly in males with this genetic condition who are between the ages 35 and 50.

19. How diet Influences Genetic Expression…. • In these individuals the difficulty is not necessarily that they are consuming too much cholesterol in their diet. Instead, their bodies produce too much cholesterol as a consequence of a defect in the thermostat that regulates the manufacture of choleterol in the liver. • Through their pioneering work, statin drugs were found that could turn off the thermostat that controls cholesterol synthesis. • The result was a reduction in cholesterol and in heart disease incidence among these individuals. • Significant side effects, including a potential increased risk of cancer, have subsequently been associated with these cholesterol-lowering drugs in some individuals. • A number of recently discovered dietary substances can also help regulate the cholesterol thermostat. One such substance is tocotrienol, a nutrient found in high levels in rice, barely and palm oils.

20. How diet Influences Genetic Expression…. • This is one example of a specific food that is enriched in a certain nutrient that can have an impact on physiological function in individuals with specific genetic risk. • Research has also been conducted into the management of high blood pressure with nutritional modulation of gene expression and function. Increased intake of fresh juices of fruits and vegetables rich in potassium and magnesium, along with calcium supplementation, has been found helpful in lowering blood pressure in individuals with essential hypertension who have not responded to sodium restriction.

21. Phytochemicals and Gene Expression • Phytochemicals are plant-derived substances that can modify gene expression or physiological functions in individuals who consume them. • One example of the power of phytochemicals is the recent report that the flavonoid naringenin, which is found in grapefruit but not in orange, lemon or lime, can assist the costly prescription drug cyclosporin in preventing organ transplant rejection after surgery. • Naringenin suppresses the gene expression for a detoxifying enzymes in the liver that eliminates the drug cyclosporin from the body. By inhibiting the expression of this enzyme, naringenin helps patients get more benefit from cyclosporin by preventing its detoxification, thereby slowing its elimination from the body. • A number of biologically active substances in foods help regulate gene expression.

22. Phytochemicals and Gene Expression…. • Limonene, a monoterpene nutrient found in grapefruit and orange juice, inhibits tumor formation by stimulating the gene expression for a detoxifying enzyme called glutathione S-transferase. Glutathione S-transferase is an important enzyme that promotes the detoxification of cancer-producing chemicals and their elimination from the body as nontoxic derivatives. • Garlic is another food that contains a number of phytochemicals that can help modulate gene expression. The sulfur compounds in garlic help protect against carcinogenic chemicals, lower blood pressure and blood cholesterol levels and help boost immunity.

23. Vitamins, Minerals and Gene Expression • Vitamin B6 (pyridoxine), vitamin B12 (cobalamin) and folic acid play important roles in modulating gene activity through their ability to mask certain portions of the gene that should not be expressed in adults. Through this masking effect, messages related to the risk of both heart disease and cancer can be put to sleep. • The essential trace mineral zinc is important in modulating gene expression as well. • Zinc is a pivotal nutrient in supporting immune system function and it helps regulate the way that the genetic message is translated into protein synthesis in the cell. • One of the first signs of zinc inadequacy is the loss of taste or smell. • Individuals whose gene expression is modified as a consequence of zinc insufficiency frequently have a poor sense of taste or smell.

24. Foods and Gene Expression • Scientists have learned during the past decade that the nutrients found in foods engage in complex interactions with our genetic machinery. • Your food and beverage selections play a significant role in determining aspects of your gene expression. • Each of us carries different genetic sensitivities to nutrients, and therefore, a diet that may be optimal for someone else may not even be adequate for you. • Over the course of the lifetime of an individual food substances may be much more important in determining health and disease patterns than the drugs he or she may take for a short period of time.

25. Foods and Gene Expression • Genes affect our response to the food we eat on several levels. They influence the way we absorb, metabolize, and excrete nutrients. • They partially control other factors, such as taste and smell, and how quickly or slowly we feel full after eating a meal. • For example, phenylthiocarbamide (PTC) crystals taste bitter to some people and not to others because genes control the ability to taste this substance. Those who can taste PTC show a greater sensitivity to bitterness in other substances, such as saccharin and caffeine, and to the sweetness of sugar. • They also can detect the sharp taste of cruciferous vegetables and dislike cabbage, brussels sprouts, and broccoli. • This indicates once more how important individual reactions are.

26. How Our Diet Communicates with Our Genes • The exposure of your genotype to specific foods, stress, and environmental and lifestyle factors, such as smoking and alcohol consumption, result in altered function of your genotype as expressed in your phenotype. • Certain genetic characteristics can be induced by exposure to specific foods and nutrients, and other genetic characteristics may be suppressed. • The communication between the food you eat and your genotype contributes to your health by modifying your phenotype or function. • For example, oat bran or wheat bran will or will not help to lower a person’s blood cholesterol level depends on that person’s genes. • The individuals whose cholesterol goes down in response to increased dietary fiber are those who are carriers of two particular gene variants. One is the E2 allele; the second is a change in the base pair at a specific site of the low-density lipoprotein receptor (LDLR). • A genetic test can therefore determine who will lower his or her blood cholesterol by eating more fiber, and who will not. It is clear that future nutritional advice will be based on each individual’s genotype.

27. How Our Diet Communicates with Our Genes…. • Sugar Sensitivity • Researcher has found that many individuals have experience serious digestive problems or disorder, including colitis, irritable bowel syndrome (IBS) and Crohn’s disease due to carbohydre diet. • How could the carbohydrate in foods lead to serious digestive inflammation and ulceration? • One answer that is emerging from research is that individuals with specific genetic inheritance factors are more sensitive to fructose. • There are a variety of genetic uniquenesses in the way that individuals metabolize sugar and absorb it from their intestinal tract. • Fructose sensitivity, which results from the altered absorption and metabolism of fructose, can result in inflammation of the intestinal tract.

28. How Our Diet Communicates with Our Genes…. • Another sugar that produces digestive difficulty in individuals with specific genetic inheritance factors is the milk sugar lactose. • Individuals who complain of diarrhea, gas and intestinal pain after drinking milk may suffer from the genetic inheritance of lactose intolerance. • Some people have a genetic sensitivity not to milk sugar but to the milk protein casein. • Some genetic characteristics are “constitutional,” which means the expression of the genes that encode for these characteristics is not easily modified by changes in diet, lifestyle or environment. • Other genetic characteristics, however, are inducible: their expression can be activated or suppressed by dietary, environmental or lifestyle exposures. Inducible genetic characteristics, which are sensitive to what you eat, form the basis of the genetic nutritioneering approach.

29. Detoxification, Genotypes and the Risk of Disease • Alcohol consumption provide an illustration of the inducible nature of the genes. At the modest levels of intake, alcohol is metabolized in the liver by action of the enzyme alcohol dehydrogenase. • At high levels of intake the genes are induced to express a different detoxification enzyme (i.e., cytochrome P450 1e2), which, in its alcohol-metabolizing activity, releases oxidants that can damage the liver. • Liver damage that is observed as a result of excessive alcohol intake is caused in part by this inducible factor from altered gene expression. • A person can defend him/herself against the damaging effects of oxidants released after alcohol consumption by increasing his or her dietary intake of antioxidants like vitamin E, thereby providing protection against this inducible process.

30. Detoxification, Genotypes and the Risk of Disease…. • Scientists have identified specific genotypes that have a higher risk of certain diseases as a consequence of reduced detoxification ability. • Cigarette smokers who carry in their genes poor detoxification may have a more toxic response and a greater cancer risk from smoking than those who got the genetic luck of the draw and have better detoxification ability. • A study of breast cancer in women found a much higher incidence of breast cancer in smokers who had very poor detoxification ability as a consequence of the poor genetic expression of a detoxification enzyme called N-acetyltransferase (NAT). • Similarly, lung cancer risk in smokers is increased in individuals who have a genetically sluggish detoxifacation enzyme called glutathione transferase.

31. Detoxification, Genotypes and the Risk of Disease…. • A single exposure or a single substance may not overburden the body and induce damage. It is the total exposure to toxic substances and how effectively they can be detoxified that determines relative health risk. • A man who lives in a very polluted environment, pursues an occupation that exposes him to toxic substances, smoke cigarettes, drinks excessive alcohol, has a poor-quality diet and eats foods like charbroiled meats that are high in toxic substances adds constantly to the total load on his detoxification machinery. Eventually, it can be overwhelmed. • If he has a sluggish detoxification system as a consequence of specific genetic uniqueness, he definitely becomes a potential candidate for heart disease, cancer, arthritis or neurological disease.

32. Detoxification, Genotypes and the Risk of Disease…. • The medical and scientific communities now recognize that diet plays an important role in modifying detoxification ability. • Poor-quality diets that are very high in toxic substances and low in nutrients that help support gene expression of detoxification enzymes result in increased risk of toxic reactions. • Diets that are low in toxic substances and high in the nutrients that support the expression of inducible genes associated with detoxification, on the other hand, can make individuals much more tolerant of exposure to various toxins. • One of the first studies that indicated the important role of dietary substances in modifying detoxification ability occurred in 1945, when investigators reported that detoxification of caffeine-like substances could be enhanced by specific dietary factors. • These dietary factors included increased levels of protein, adequate levels of the B vitamins, improved antioxidant intake and proper mineral nutrition.

33. The Genetic Impact • It is important to distinguish between the genetic and nongenetic forms of hyperlipidemia. • Individuals with the genetic form will experience severe high blood cholesterol, sometimes in the 400 to 600 mg/dl range, because of a genetic defect in the way the body handle, or metabolizes, cholesterol. Often this occurs because they do not have enough LDL receptors, allowing excessive amounts of LDL to circulate in the blood. • Their serum cholesterol will be high despite normal or low amounts of cholesterol and saturated fat in their diets. • Therefore, doctors must use drugs to treat this type of hyperlipidemia – because diet and other lifestyle changes are simply inadequate to reduce serum cholesterol levels. • The presumed nongenetic form of hyperlipidemia is much more common.

34. The Genetic Impact • It is important to distinguish between the genetic and nongenetic forms of hyperlipidemia. • Individuals with the genetic form will experience severe high blood cholesterol, sometimes in the 400 to 600 mg/dl range, because of a genetic defect in the way the body handle, or metabolizes, cholesterol. Often this occurs because they do not have enough LDL receptors, allowing excessive amounts of LDL to circulate in the blood. • Their serum cholesterol will be high despite normal or low amounts of cholesterol and saturated fat in their diets. • Therefore, doctors must use drugs to treat this type of hyperlipidemia – because diet and other lifestyle changes are simply inadequate to reduce serum cholesterol levels. • The presumed nongenetic form of hyperlipidemia is much more common.

35. The Genetic Impact…. • Here the individual’s genoptype is normal, but detrimental lifestyle factors – being obese, leading a sedentary lifestyle, and consuming a diet that is high in cholesterol and saturated fat for many years – raise blood cholesterol levels above the 200-240 range. • This diet induced high cholesterol is one situation where dietary changes, such as eating less fat and more fish, and other lifestyle changes, including regular exercise and weight loss, can make a difference. • Such dietary and behavioral modifications can lower the levels of total blood cholesterol, HDL, LDL, and triglycerides. • Recent research shows that more and more of the risk factors for coronary heart disease are caused by genes. In addition to abnormalities in LDL receptor activity, faulty genes may produce low HDL cholesterol levels and affect blood pressure, a person’s insulin level and his or her insulin response.

36. Familial Hypercholesterolemia (FH) • This disorder, which afflicts 15 percent of those with heart attacks, occurs because of a mutation in a single gene that leads to unusually high blood levels of cholesterol and premature development of atherosclerosis. • Individuals with only one mutant gene develop the condition because this is an autosomal-dominant trait in which the defective gene overpowers the normal gene of handling cholesterol. • Although they are not obese, people with FH experience two to three times the average level of blood cholesterol at birth, and the condition persists throughout life. • About 10% of those with one mutant FH gene have elevated triglyceride levels as well.

37. Familial Hypercholesterolemia (FH)…. • Since there are more than 100 different mutations, they collectively affect 1 in every 500 people in the USA, making familial hypercholesterolemia the most common disorder caused by a single abnormal gene. • The basic defect here is in the gene that is found on the cell surface of the LDL receptor, located on chromosome 19. • The cell produces only half the number of receptors that remove LDL cholesterol from the blood, causing a cascade of ill effects – high blood cholesterol levels, cholesterol deposits in the arteries, and the consequent arterial blockages that produce coronary heart disease early in life. • Men experience problems as young as their thirties or forties, with an average age of forty-three at the first heart attack; for women this occurs ten years later.

38. Familial Hypertriglyceridemia • This condition, responsible for 5% of heart attacks, is common in the US population. • 10% of men between the ages of 35 and 39 have triglyceride levels above 250 mg/dl. • It is also an autosomal-dominant disorder that shows up in early childhood or at puberty. • The underlying defect here is a single faulty gene that increases the production of triglycerides in very low density lipoproteins (VLDLs), decreases their breakdown, and produces an accumulation of triglycerides in the blood. • Typical levels are in the 200 to 500 mg/dl range, particularly in people who eat high carbohydrate diets. • These patients are usually obese, have high blood pressure, and have high levels of sugar, insulin, and uric acid in their blood.

39. Genes, Diet, and Cardiovascular Disease • Dyslipidemia is commonly associated with the development of atherosclerosis and can be caused by improper function of a variety of proteins that control lipid homeostasis, such as nuclear factors, binding proteins, apolipoproteins, enzymes, lipoprotein receptors, and hormones. • Polymorphisms have been identified in most of these components and many of the underlying genes have been explored in terms of diet–gene interactions. • Amongst these, the apolipoprotein E gene (apoE) is the most intensively studied with regard to its effects on low-density lipoprotein (LDL)-cholesterol levels in response to dietary interventions. • Genetic variation at the apoE locus results from three common alleles in the population, E4, E3, and E2. However, other genetic variants at the apoE locus have been described as well.

40. Genes, Diet, and Cardiovascular Disease ….. • Besides the fact that LDL-cholesterol levels were highest in subjects carrying the apoE4 isoform, this association was especially prominent in populations consuming diets rich in saturated fats and cholesterol. • These epidemiology data, therefore, indicate that high LDL-cholesterol levels are manifested primarily in the presence of an atherogenic diet but that an individual’s response to dietary saturated fat and cholesterol may differ depending on the individual apoE alleles. • However, it needs to be stressed that especially for apoE, investigations of diet–gene interactions have yielded quite diverse outcomes.

41. Genes, Diet, and Cardiovascular Disease ….. • Significant diet–apoE interactions occurred in studies focusing on males, suggesting a significant gene–gender interaction. • Baseline lipid levels seem to affect the outcome and significant associations were frequently found only in subjects who were moderately hypercholesterolemic. • More consistent effects were reported on the impact of alcohol intake on LDL-cholesterol depending on the apoE genotype in men. • A negative association between alcohol consumption and LDL-cholesterol was found for carriers of apoE2, whereas subjects with apoE4 displayed a positive correlation. • Within these genotype studies apoA1 has emerged as a primary candidate for genetic variability in high-density lipoprotein (HDL) levels and its gene product plays a crucial role in lipid metabolism and for cardiovascular disease risk.

42. Genes, Diet, and Cardiovascular Disease ….. • In women it has been found that a G to A transition in the apoA1 gene is associated with an increase in HDL-cholesterol levels depending on the dietary intake of polyunsaturated fatty acids. • Similar to this G/A single-nucleotide polymorphism in apoA1, increased HDL levels were found to be associated with a homozygous 514(CC) polymorphism in the hepatic lipase gene in response to higher fat contents in the diet. • This increase in the level of protective HDL particles was interpreted as a defense mechanism that was not found in subjects carrying the TT genotype. • Interestingly the TT genotype is common in certain ethnic groups, such as African-Americans, and might help to explain their limited ability to adapt rapidly to new nutritional environments.

43. Gene Regulation by Nutrients • Regulation of gene expression by nutrients. • A ‘direct’ effect of some nutrients (vitamin A, D, and E; zinc; n-3 fatty acids; and sterols) on gene transcription is shown in which, subsequent to ligand binding to a specific transcription factor, cytoplasmic to nuclear translocation of the complex occur, and interaction through a specific domain of the factor with a response element sequence (specific nucleotide sequence) of the regulatory region produces a change in transcription rate of the gene. • Some nutrients activate transmembrane receptors, which use intracellular signaling pathways to initiate or modify gene expression.

44. Gene Regulation by Nutrients • Regulation of gene expression by nutrients. • A ‘direct’ effect of some nutrients (vitamin A, D, and E; zinc; n-3 fatty acids; and sterols) on gene transcription is shown in which, subsequent to ligand binding to a specific transcription factor, cytoplasmic to nuclear translocation of the complex occur, and interaction through a specific domain of the factor with a response element sequence (specific nucleotide sequence) of the regulatory region produces a change in transcription rate of the gene. • Some nutrients activate transmembrane receptors, which use intracellular signaling pathways to initiate or modify gene expression.

45. Regulation of gene expression by nutrients ….. • Single nucleotide polymorphisms and epigenetic changes can modify the expression of some gene. • Nutrient effects on mRNA processing, editing, stability, and translation have been documented. • Nutrients which have a direct effect on gene transcription include vitamin A (retinoic acid), vitamin D (calcitriol), zinc, n-3 polyunsaturated fatty acids, and specific sterols. • In contrast, iron, and perhaps other nutrients, has a direct effect on gene regulation through control of translation or stability of specific mRNA.

46. Regulation of gene expression by nutrients.. • Frequently, gene regulation by nutrients is more complex, where multiple and interconnected factors, including nutrient effects on signal transduction pathway, epigenetic effects on specific genes, mRNA splicing and translation, and posttranslational modifications, merge to define indirect effects on expression of a specific gene. • Although the primary focus of nutritional genomics is the understanding of nutrient-gene interactions, expression of genetic information also is influenced by numerous environmental factors. • For example, cytokine levels are unusually sensitive to environmental changes and serve as good markers of environmental influences that may alter protein and RNA expression.

47. Examples • Some examples of non-nutrient environmental factors affecting cytokine concentrations are: • Overall sleep time and sleep continuity. • Oxygen tension, which is related to altitude. • Over-the-counter drugs (nonsteroidal anti-inflammatory drugs). • Water intake relative to tea and other beverages. • Psychological factors like stress. • Exposure to allergens and pollutants. • Balance between energy intake and expenditure.

48. Genotype – Environment Interactions • Genes that cause chronic diseases must be regulated directly or indirectly by calorie intake and/or by specific chemicals in the diet because diet alters disease incidence and severity. • The progressive and sometimes slow change in phenotype from health to disease must occur, at least in part, through changes in gene expression. • These are gene-environment interactions. • The precise, statistical definition of gene-environment interaction is “a different effect of an environment exposure on disease risk in persons with different genotypes” or, alternatively, “a different effect of a genotype on disease risk in persons with different environmental exposures”. • In other words, nutrients affect expression of genetic information and genetic makeup affects how nutrients are metabolized.

49. Genotype – Environment Interactions ….. • A dietary chemical or its metabolite may alter the expression of a susceptibility gene or its variant that in turn affects other gene-gene interactions. • The consequence of such gene-environment interactions may not only be apparent on the gene of interest, but may also affect the action of that gene on other interacting genes. • Different functional classes of genes may have greater importance than others: affecting the expression of a nuclear receptor or signal transduction pathways may affect more processes than altering the expression of a gene encoding an enzyme in a metabolic pathway.

50. Genotype – Environment Interactions ….. • In the short term, the environment almost never improves genes by changing the DNA sequence; however, the control of genes can be changed, and potentially improved, by modulating epigenetics and early development through diet. • Epigenetic changes are those heritable changes in gene expression that do not require changes in DNA sequence. • These usually involve enzymatic DNA methylation and concomitant changes in histone modifications, such as methylation and acetylation, and in other modifications of chromatin structure. • Many effects are considered epigenetic if, without mutation, they change the long-term physiological, metabolic, or anatomical state of plants or animals even if the specific gene expression has not been identified.