Diseases that are known to be associated with the interactions between multiple genetic and environmental factors such as diet include many cancers, diabetes, heart disease, obesity, and some psychiatric disorders. Therefore, both disciplines aim to unravel diet–genome interactions; however, their approaches and immediate objectives are distinct. Nutrigenomics will unravel the optimal diet from within a series of nutritional alternatives, whereas nutrigenetics will yield critically important information that will assist clinicians in identifying the optimal diet for a given individual, i.e., personalized nutrition [10]. The following five tenets of nutritional genomics serve as a conceptual basis for understanding the focus and promise of this budding field: [7]

Cancer is a process composed of multiple stages in which gene expression, and protein and metabolite function, begins to operate aberrantly [14]. In the post-genomic era, the cellular events mediating the onset of carcinogenesis, in addition to their modulation by dietary factors, have yielded significant information in understanding of this disease [15]. Inherited mutations in genes can increase one’s susceptibility for cancer. Evidences of genome and epigenome damage biomarkers, in the absence of overt exposure of genotoxins, are themselves sensitive indicators of deficiency in micronutrients required as cofactors or as components of DNA repair enzymes, for maintenance methylation of CpG sequences and prevention of DNA oxidation and/or uracil incorporation into DNA [16]. Diet is considered as a source of either carcinogens (intrinsic or cooking generated) present in certain foods or constituents acting in a protective manner (vitamins, antioxidants, detoxifying enzyme-activating substances, etc.) [17]. It is clear that carcinogen metabolism-affecting polymorphisms may modify the chance of contact between carcinogens and target cells, thus acting at the stage of cancer initiation. Influences of polymorphisms of gene encoding factors involved in hormonal regulation are most strongly manifested in hormone-dependent tumors such as breast, prostate, ovarian, and endometrial cancers. Polymorphisms in sex hormone receptor genes comprising those encoding estrogen receptor, progesterone receptor, and androgen receptor have been shown to be associated with cancer risk modulation [18]. Dietary factors can undoubtedly interact with hormonal regulation. Obesity strongly affects hormonal status. At the same time, some food components, such as phytoestrogens, are known to be processed by the same metabolic pathways as sex hormones [19]; thus their cancer-preventive effect can be modulated by the polymorphisms.

An important emerging part of nutrient–gene interaction studies with the potential for both intra- and transgenerational effects is epigenetics [20]. Epigenetics refers to the processes that regulate how and when certain genes are turned on and off, while epigenomics pertains to analysis of epigenetic changes in a cell or the entire organism. Epigenetic processes have a sturdy influence on normal growth and development, and this process is deregulated in diseases such as cancer. Diet on its own or by interaction with other environmental factors can cause epigenetic changes that may turn certain genes on or off. Table 6.2 provides a brief description of the nutrients and chemicals involved in DNA methylation. Epigenetic silencing of genes that would usually protect against a disease, as a result, could make people more susceptible to developing that disease later in life. The epigenome, which is heritable and modifiable by diet, is the global epigenetic pattern determined by global and gene-specific DNA methylation, histone modifications, and chromatin-associated proteins that control expression of housekeeping genes and restrains the expression of parasitic DNA such as transposons. Table 6.3 represents the dietary chemicals, DNA methylation, and its mechanism of action.

One study has demonstrated that sulforaphane, butyrate, and allyl sulfur are effective inhibitors of histone deacetylase (HDAC). HDAC inhibition was associated with global increases in histone acetylation, enhanced interactions of acetylated histones with the promoter regions of the P21 and BAX genes, and higher expression of p21Cip1/Waf1 and BAX proteins [33]. Importantly, sulforaphane has been reported to reduce HDAC activity in humans [33]. Future research likely needs to relate HDAC changes in humans to a change in a cancer-related process. Furthermore, since acetylation is only one method to regulate histone homeostasis [34], greater concentration needs to be given to how nutrition might influence the other types of histone modifications.

The field of nutrigenomics harnesses multiple disciplines and includes dietary effects on genome stability (DNA damage at the molecular and chromosome level), epigenome alterations (DNA methylation), RNA and micro-RNA expression (transcriptomics), protein expression (proteomics), and metabolite changes (metabolomics), all of which can be studied independently or in an integrated manner to diagnose health status and/or disease trajectory. However, of these biomarkers, only DNA damage is a clear biomarker of fundamental pathology that may be mitigated by promotion of apoptosis of genetically aberrant cells or by reducing the rate of DNA damage accumulation. Changes at the epigenome, transcriptome, proteome, and metabolome levels may simply reflect modifiable homeostatic responses to altered nutritional exposure and on their own may not be sufficient to indicate definite irreversible pathology at the genome level.

DNA damage can be diagnosed in a number of complementary ways as follows: (1) damage to single bases (e.g., DNA adducts such as the addition of a hydroxyl radical to guanine caused by oxidative stress), (2) basic sites in the DNA sequence (measurable by use of the aldehyde-reactive probe), (3) DNA strand breaks (commonly measured using the Comet assay), (4) telomere shortening (measured by terminal restriction fragment length analysis, quantitative PCR, or flow cytometry), (5) chromosome breakage or loss (usually measured using micronucleus cytome assays or metaphase chromosome analysis), and (6) mitochondrial DNA damage (usually measured as deletions or base damage in the circular mitochondrial DNA sequence). These DNA damage biomarkers are presently at different levels of validation based on evidence relating to the association with nutrition (cross-sectional epidemiological and intervention studies) and disease (cross-sectional epidemiology and prospective cohort studies) [35]. The micronucleus assay in cytokinesis-blocked lymphocytes is currently the best validated biomarker for nutritional genomic studies of DNA damage.

Given the advances in diagnostic technologies assessing DNA damage, it has now become feasible to determine dietary reference values for DNA damage prevention and to start translating into practice the Genome Health Clinic concept of DNA damage prevention [35]. The latter is based on the recognition that damage to the genome is the most elementary cause of developmental and degenerative diseases, which can be accurately diagnosed and prevented by appropriate diet and lifestyle intervention at a genetic subgroup and personalized level. The ability of diet to affect the flow of genetic information can occur at multiple sites of regulation [10]. Advances in genomics, transcriptomics, proteomics, and metabolomics have enabled a more rapid and comprehensive understanding of how bioactive compounds affect human health. Dietary bioactive compounds can be tested for their potential health-promoting properties by applying these different technologies to cell culture, and animal or human studies. Each experimental approach offers unique strengths and has certain limitations.

Several studies of sporadic breast cancers have shown that fruits and vegetables [36], fish, monounsaturated and polyunsaturated fatty acids [37], vitamin D, calcium, and phytoestrogens may reduce the risk of breast cancer, although there are inconsistencies in the literature. High intake of meat, poultry, total energy, and total fat and saturated fatty acids has been reported to be associated with increased risk for breast cancer [38]. Malmö Diet and Cancer cohort examined the association between dietary folate equivalents (DFE) and breast cancer among carriers of two genetic polymorphisms for MTHFR gene (MTHFR 677C/T and 1298A/C). A positive association between DFE and breast cancer among women carriers of MTHFR 677CT/TT-1298AA occurred while an inverse association was observed in 677CT-1298 AC women [39]. In a nested case-control study, Maruti et al. reported that postmenopausal women with two copies of variant T alleles (TT genotype) had increased risk of breast cancer. In addition, the intake of other B vitamins may influence the relationship between the MTHFR genetic variants and breast cancer risk. It has been found that the most pronounced MTHFR-breast cancer risk was observed among women with the lowest intakes of dietary folate and vitamin B6 [40].

In a nested case-control study within the Singapore Chinese Health Study, it has been observed that there is an inverse relationship between breast cancer risk and low folate intake and weekly/daily green tea intake compared with reduced green tea intake. Also, women carrying the high-activity MTHFR/TYMS genotypes with 0–1 variant allele and weekly/daily green tea intake had a lower breast cancer risk, especially women who also had low folate intake. No association was observed among women carriers of two variant alleles. These findings suggest one of the mechanisms through which green tea can provide protection against breast cancer is through folate regulation [41]. The anticancer effect of the EGCG (tea polyphenol (−)-epigallocatechin-3-gallate) may be mediated by the regulation of epigenetic processes. It was found that EGCG can lead to ERα reactivation in the ERα-negative breast cancer cell lines by remodeling the chromatin structure of the ERα promoter by the alteration of the histone acetylation and methylation status [42]. Further, it has been reported that EGCG inhibits the telomerase by decreasing the hTERT promoter methylation and ablating the histone H3 Lys9 acetylation in the MCF-7 cell lines [43].

Another study reported the inverse relationship between green tea intake and breast cancer risk among Asian-Americans [44] as a function of the catechol-O-methyltransferase (COMT) genotype. This enzyme is recognized to be involved in the metabolism of the tea polyphenols. More specifically, a reduced risk of breast cancer was observed only among tea (green and black) drinker carriers of at least one low-activity COMT allele. These findings of reduced breast cancer risk with tea catechins, especially in women who had the low-activity COMT alleles, suggest that these women were less efficient in eliminating tea catechins, therefore optimizing the benefits from the tea and its associated bioactive constituent [45].

The Shanghai Breast Cancer Study examined the relationship between breast cancer risk, GSTP1 genetic variants, and other diet components, the cruciferous vegetables. The GSTP1 Val/Val genotype was associated with increased breast cancer risk, especially in premenopausal women with low intake of cruciferous vegetables. Thus, cruciferous vegetable intake with high isothiocyanates may reduce breast cancer risk and modify the effect of the GSTP1 genotype [45], and not necessarily be beneficial to all women.

Finally, the response to marine n-3 fatty acids with breast cancer risk may depend on genetics. Women with genetic variants that encode lower or no enzymatic activity of GSTT1 have a 30 % lower breast cancer risk from the marine n-3 fatty acids, when compared with women with high-activity genotypes. These data suggest that the peroxidation products of n-3 fatty acids may be involved in the protection against breast cancer [46]. This is not that unusual since other food components have been reported to inhibit tumors by generating free radicals [47]. Watercress, a rich source of phenethyl isothiocyanates (PEITC), has been proposed to have anticancer activity. A crude watercress extract was reported to inhibit cancer cell growth and hypoxia-inducible factor (HIF) activity and reduced angiogenesis by decreasing the phosphorylation of the translation regulator 4E binding protein 1 (4E-BP1) [48].

In a breast case-control study that examined the association of the 5-lipoxygenase gene (ALOX) and 5-lipoxygenase-activating protein gene (ALOX5AP) polymorphisms and dietary linoleic acid intake with breast cancer risk, it was found that women carriers of two variant alleles for the ALOX5AP 4900 A/G who had a diet rich in linoleic acid had a greater breast cancer risk compared with women carrying AG or GG genotypes. These results propose that genetic predisposition related to n-6 polyunsaturated fatty acid metabolism should be taken into account when the relation between dietary fat and breast cancer risk is examined [49]. Furthermore, dietary omega-3 polyunsaturated fatty acids downregulate the expression of the polycomb group (PcG) protein, enhancer of zeste homologue 2 (EZH2) in breast cancer cells. This study reported a decrease in histone 3 lysine 27 trimethylation (H3K27me3) activity of EZH2 and upregulation of E-cadherin and insulin-like growth factor-binding protein 3. The treatment with omega-3 PUFAs led to decrease in the invasion capacity of the breast cancer cells [50].

Additionally, a nested case-control study of postmenopausal women examined the interaction between oxidative stress-related genes including catalase (CAT) C262T, myeloperoxidase (MPO) G463A, endothelial nitric oxide synthase (NOS3) G894T, and heme oxygenase-1 (HO-1) GT (n) dinucleotide length polymorphism and level of vegetable and fruit intake on breast cancer risk. The study found that women with low intake of vegetables and fruits and the low-risk CAT CC genotypes appeared to be associated with increased breast cancer risk, especially those women with four or more low-risk alleles, suggestive of the role of endogenous and exogenous antioxidants in breast carcinogenesis [51].

Iwasaki et al. examined the effect of four SNPs in cytochrome P450c17alpha (CYP17), aromatase (CYP19), 17beta-hydroxysteroid dehydrogenase type I (17beta-HSD1), and sex hormone-binding globulin (SHBG) genes on the association between isoflavone intake and breast cancer risk. The study identified an inverse association between isoflavone intake and breast cancer risk among women with at least one variant allele for the 17beta-HSD1 polymorphism and among postmenopausal Japanese women with GG genotype for the SHBG gene, indicating that genetic variants of the 17beta-HSD1 and SHBG genes may modify the relationship between isoflavone intake and breast cancer risk [52]. The association between isoflavones and breast cancer risk may be explained by the antiestrogenic effect of the isoflavones and the effect on the DNA methylation. It has been reported that the daily administration of isoflavones to healthy premenopausal women led to dose-specific changes in RARbeta2 and CCND2 gene promoter methylation, changes that correlated with genistein levels. Additionally, an inverse correlation between estrogenic marker complement C3 and genistein was observed, suggesting an antiestrogenic effect [53]. Furthermore, genistein has been associated with specific epigenetic changes. For example, the long-term exposure to genistein of the MCF-7 breast cancer cell lines has been found to lead to reduced expression of the acetylated histone 3 (H3). Additionally, this exposure was associated with alteration in growth responses to mitogenic factors and histone deacetylase inhibitors [54].

Dietary berries have been suggested to influence breast cancer risk (AICR Report), although considerable variability in response is observed. Preclinical studies demonstrate that tumor formation is suppressed as a result of the levels of E(2)-metabolizing enzymes during the early phase of E(2) carcinogenesis [55].

A nested case-control study within the Singapore Chinese Health Study Cohort showed a significant interaction between the level of green tea drinking and the activity of the angiotensin-converting enzyme (ACE) with respect to breast cancer risk depending on ACE gene polymorphism [56]. Even the BRCA breast cancer-associated gene is affected by diet. A diet rich in fruits and vegetables protects a woman from the BRCA gene becoming activated [57]. Olive oil is an integral ingredient of the “Mediterranean diet” and accumulating evidence suggests that it may have a potential role in lowering the risk of several types of cancers. A number of epidemiological studies have linked consumption of olive oil with a reduced risk of cancer, and researchers are increasingly investigating this association further in laboratory studies. The mechanisms by which the cancer-preventing effects of olive oil as having novel anticancer actions may relate to the ability of its monounsaturated fatty acid (MUFA) oleic acid (OA; 18:1n-9) to specifically regulate cancer-related oncogenes. Exogenous supplementation of cultured breast cancer cells with physiological concentrations of OA was found to suppress the overexpression of HER2 (Her-2/neu, erbB-2), a well-characterized oncogene playing a key role in the etiology, progression, and response to chemotherapy and endocrine therapy in approximately 20 % of breast carcinomas.

OA treatment was also found to synergistically enhance the efficacy of trastuzumab (Herceptin) a humanized monoclonal antibody binding with high affinity to the ectodomain (ECD) of the Her2-coded p185(HER2) oncoprotein. Moreover, OA exposure significantly diminished the proteolytic cleavage of the ECD of HER2 and, consequently, its activation status, a crucial molecular event that determines both the aggressive behavior and the response to trastuzumab of Her2-overexpressing breast carcinomas. Recent findings further reveal that OA exposure may suppresses HER2 at the transcriptional level by upregulating the expression of the Ets protein PEA3 -a DNA-binding protein that specifically blocks HER2 promoter activity in breast, ovarian, and stomach cancer cell lines. This anti-HER2 property of OA offers a previously unrecognized molecular mechanism by which olive oil may regulate the malignant behavior of cancer cells. From a clinical perspective, it could provide an effective means of influencing the outcome of Her-2/neu-overexpressing human carcinomas with poor prognosis. Indeed, OA-induced transcriptional repression of HER2 oncogene may represent a novel genomic explanation linking olive oil and cancer, as it seems to equally operate in various types of Her-2/neu-related carcinomas [58].

In another study, OA treatment in Her-2/neu-overexpressing cancer cells was found to induce upregulation of the Ets protein polyomavirus enhancer activator 3 (PEA3), a transcriptional repressor of Her-2/neu promoter. Also, an intact PEA3 DNA-binding site at endogenous Her-2/neu gene promoter was essential for OA-induced repression of this gene. Moreover, OA treatment failed to decrease Her-2/neu protein levels in MCF-7/Her2-18 transfectants, which stably express full-length human Her-2/neu cDNA controlled by a SV40 viral promoter. OA-induced transcriptional repression of Her-2/neu occurs through the action of PEA3 protein at the promoter level [59].

All main signaling pathways are deregulated in cancer, including cell proliferation, apoptosis, DNA repair, carcinogen metabolism, inflammation, immunity, differentiation, and angiogenesis. Increasingly, evidence points to each of these as molecular targets for cancer prevention. Since several of these sites appear to be tailored by multiple dietary components, it becomes challenging to tease apart nutrient–nutrient interactions and thus what constitutes an ideal diet for health promotion [2]. For example, the apoptosis or programmed cell death that is essential in the fight against cancer through two pathways—either the intrinsic, mitochondrial-mediated pathway, or the extrinsic, death receptor-mediated pathway—could be a target for dietary bioactive agents including genistein, curcumin, resveratrol, luteolin, lupeol, indole 3-carbinol, etc. [4]. Dietary components can modulate apoptosis through effects at different levels, all of which culminate in changes in gene expression. Table 6.4 provides details on transcription factor pathways mediating nutrient–gene interactions.

Compounds such as Japanese knotweed (Polygonum c.), 20 % resveratrol, ginger, (Zingiber off.) 5 % gingerols, Rosemary (Rosemarinus off.), 6 % carnosic acid, 1 % rosemarinic acid, 1.5 % ursolic aicd, etc have demonstrated broad-spectrum, multi-targeting, anticancer effects, as well as disease-preventive and health-promoting benefits. The other important aspect of these compound-rich foods, spices, and herbs is that have been regularly used by many cultures throughout the world. Cancer prevention studies have exposed that all of the major signaling pathways deregulated in different types of cancer are affected by nutrients. Pathways studied include carcinogen metabolism, DNA repair, cell proliferation/apoptosis, differentiation, inflammation, oxidant/antioxidant balance, and angiogenesis [61].

So far, more than 1,000 different phytochemicals have been identified with cancer-preventive activities [62]. Dietary fibers have a protective effect against bowel cancer. Long-chain polyunsaturated fatty acids (LC-PUFA) beneficially affect physiological processes, including growth; neurological development; lean and fat mass accretion; reproduction; innate and acquired immunity; infectious pathologies of viruses, bacteria, and parasites; and the incidence and severity of virtually all chronic and degenerative diseases including cancer, atherosclerosis, stroke, arthritis, diabetes, osteoporosis, neurodegenerative, inflammatory, and skin diseases [63]. Fish oil, rich in omega-3 fatty acids, inhibits the growth of colonic tumors in both in vitro and in vivo systems [64].

Bioactive components present in fruits and vegetables can prevent carcinogenesis by several mechanisms, such as blocking metabolic activation through increasing detoxification. Plant foods can modulate detoxification enzymes as flavonoids, phenols, isothiocyanates, allyl sulfur compounds, indoles, and selenium [65]. As a result of carcinogen activation, covalent adducts with the individual nucleic acids of DNA or RNA are formed. It has also been found that reactive oxygen species (ROS) such as superoxide anions, hydrogen peroxide, and hydroxyl radicals attack DNA bases, resulting in potential mistranscription of DNA sequence [66]. Such disruptions can interfere with DNA replication and thus produce mutations in oncogenes and tumor-suppressor genes. ROS can also result in breakage of DNA strand, resulting in mutations or deletions of genetic material [67].