Nutrigenomics: goals and strategies

A nutrigenomics database – integrated repository for publications and associated microarray data in nutrigenomics research

In the current situation where microarray data in the field of nutritional genomics (nutrigenomics) are accumulating rapidly, there is imminent need for an efficient data infrastructure to support research workflow. We have established a web-based, integrated database of the publications and microarray expression data in the field of nutrigenomics. The registered data include links to external databases such as PubMed of the National Center for Biotechnology Information and public microarray databases that contain Minimum Information About a Microarray Experiment-compliant microarray expression data. Using this database, all data sets created will be effectively utilized and shared with other researchers. This database is built on an open-source database system and is freely accessible via the World Wide Web (http://a-yo5.ch.a.u-tokyo.ac.jp/index.phtml</url).

The quest for cardiovascular health in the genomic era: nutrigenetics and plasma lipoproteins

Nutrigenetics and nutrigenomics are promising multidisciplinary fields that focus on studying the interactions between nutritional factors, genetic factors and health outcomes. Their goal is to achieve more efficient individual dietary intervention strategies aimed at preventing disease, improving quality of life and achieving healthy aging. Our studies, and those of many other investigators, using population-based and intervention studies have found evidence for interactions between dietary factors, genetic variants and biochemical markers of CVD. Now, the characterization of individuals who may respond better to one type of dietary recommendation than another can be begun. Thus, a low-fat low-cholesterol strategy may be particularly efficacious in lowering the plasma cholesterol levels of those subjects carrying the apoE4 allele at the APOE gene. HDL-cholesterol (HDL-C) levels are also modulated by dietary, behavioural and genetic factors. It has been reported that the effect of PUFA intake on HDL-C concentrations is modulated by an APOA1 genetic polymorphism. Thus, subjects carrying the A allele at the –75 G/A polymorphism show an increase in HDL-C with increased intakes of PUFA, whereas those homozygotes for the more common G allele have the expected lowering of HDL-C levels with increased intake of PUFA. Variability at the hepatic lipase gene is also associated with interactions between intake of fat and HDL-C concentrations that could shed some light on the different abilities of certain ethnic groups to adapt to new nutritional environments. This knowledge should lead to successful dietary recommendations partly based on genetic factors that may help to reduce cardiovascular risk more efficiently than the current universal recommendations.

Individualized nutritional recommendations: do we have the measurements needed to assess risk and make dietary recommendations?

Is the information currently available to adjust nutritional recommendations and develop individualized nutrition? No. There is not even the information needed for setting dietary recommendations with confidence now at the group level. Will it be available soon? The answer to this question depends on the drive and will of the nutritional community, the success in recruiting funding to the area, the education of nutritionists and the spawning of great ideas and approaches. The emerging tools of genomics, proteomics and metabolomics are enabling the in-depth study of relationships between diet, genetics and metabolism. The advent of technologies can be compared with the discovery of the microscope and the new dimensions of scientific visualization enabled by that discovery. Nutritionists stand at the crest of new waves of data that can be generated, and new methods for their digestion will be required. To date, the study of dietary requirements has been based largely on a black box approach. Subjects are supplemented or depleted and clinical outcomes are observed. Few recommendations are based on metabolic outcomes. Metabolomics and nutrigenomics promise tools with which recommendations can be refined to meet individual requirements and the potential of individualized nutrition can be explored. As yet, these tools are not being widely applied in nutritional research and are rarely being applied by nutritionists. The result is often interesting research that is frequently nutritionally flawed, resulting in inappropriate conclusions. Nutritional education is needed to put nutritionists at the forefront of the development of applications for these technologies, creating a generation of nutrigenomicists. A new generation of nutritionists should be working interdisciplinarily with geneticists, molecular biologists and bioinformaticians in the development of research strategies. The present paper reviews the current status of nutrigenomic research, the current controversies and limitations, and developments needed to advance nutrigenomics and explore fully the promise of individualized nutritional recommendations.

Nutrigenomics, individualism and public health

Issues arising in connection with genes and nutrition policy include both nutrigenomics and nutrigenetics. Nutrigenomics considers the relationship between specifc nutrients or diet and gene expression and, it is envisaged, will facilitate prevention of diet-related common diseases. Nutrigenetics is concerned with the effects of individual genetic variation (single nucleotide polymorphisms) on response to diet, and in the longer term may lead to personalised dietary recommendations. It is important also to consider the surrounding context of other issues such as novel and functional foods in so far as they are related to genetic modification. Ethical issues fall into a number of categories: (1) why nutrigenomics? Will it have important public health benefits? (2) questions about research, e.g. concerning the acquisition of information about individual genetic variation; (3) questions about who has access to this information, and its possible misuse; (4) the applications of this information in terms of public health policy, and the negotiation of the potential tension between the interests of the individual in relation to, for example, prevention of conditions such as obesity and allergy; (5) the appropriate ethical approach to the issues, e.g. the moral difference, if any, between therapy and enhancement in relation to individualised diets; whether the 'technological fix' is always appropriate, especially in the wider context of the purported lack of public confidence in science, which has special resonance in the sphere of nutrition.

Controlling the chromatin organization of vitamin D target genes by multiple vitamin D receptor binding sites

An essential prerequisite for the direct modulation of transcription by 1alpha,25-dihydroxy vitamin D(3) (1alpha,25(OH)(2)D(3)) is the location of at least one activated vitamin D receptor (VDR) protein close to the transcription start site of the respective primary 1alpha,25(OH)(2)D(3) target gene. This is achieved through the specific binding of VDR to a 1alpha,25(OH)(2)D(3) response element (VDRE). Although these elements are well characterized in vitro, the function of VDREs in living cells in the context of chromatin is still largely unknown. To resolve this issue, approximately 8kB of the promoter regions of the primary 1alpha,25(OH)(2)D(3) target genes CYP24, cyclin C and p21((Waf1/Cip1)) were screened by chromatin immunoprecipitation (ChIP) assays for VDR binding sites using antibodies against VDR and its partner proteins. This approach identified three to four functional VDREs per gene promoter. In parallel, in silico screening of the extended gene areas (i.e. 10kB of promoter, introns, exons and 10kB of the downstream region) of all six members of the insulin-like growth factor binding protein (IGFBP) gene family was performed. Gel shift, reporter gene and ChIP assays identified in total 10 functional VDREs in the genes IGFBP1, IGFBP3 and IGFBP5. Taken together, both screening approaches suggest that a reasonable proportion of all VDR target genes, if not all, are under the control of multiple VDREs.

Antidiabetic effects of cis-9, trans-11-conjugated linoleic acid may be mediated via anti-inflammatory effects in white adipose tissue

Adipose tissue may be the source of insulin desensitizing proinflammatory molecules that predispose to insulin resistance. This study investigated whether dietary fatty acids could attenuate the proinflammatory insulin-resistant state in obese adipose tissue. The potential antidiabetic effect of cis-9, trans-11-conjugated linoleic acid (c9,t11-CLA) was determined, focusing on the molecular markers of insulin sensitivity and inflammation in adipose tissue of ob/ob C57BL-6 mice. Feeding a c9,t11-CLA-enriched diet reduced fasting glucose (P < 0.05), insulin (P < 0.05), and triacylglycerol concentrations (P < 0.01) and increased adipose tissue plasma membrane GLUT4 (P < 0.05) and insulin receptor (P < 0.05) expression compared with the control linoleic acid-enriched diet. Interestingly, after the c9,t11-CLA diet, adipose tissue macrophage infiltration was less, with marked downregulation of several inflammatory markers in adipose tissue, including reduced tumor necrosis factor-alpha and CD68 mRNA (P < 0.05), nuclear factor-kappaB (NF-kappaB) p65 expression (P < 0.01), NF-kappaB DNA binding (P < 0.01), and NF-kappaB p65, p50, c-Rel, p52, and RelB transcriptional activity (P < 0.01). To define whether these observations were direct effects of the nutrient intervention, complimentary cell culture studies showed that c9,t11-CLA inhibited tumor necrosis factor-alpha-induced downregulation of insulin receptor substrate 1 and GLUT4 mRNA expression and promoted insulin-stimulated glucose transport in 3T3-L1 adipocytes compared with linoleic acid. This study suggests that altering fatty acid composition may attenuate the proinflammatory state in adipose tissue that predisposes to obesity-induced insulin resistance.

Design guidelines for the development of digital nutrigenomics learning material for heterogeneous target groups

Nutritional genomics, or nutrigenomics, can be considered as the combination of molecular nutrition and genomics. Students who attend courses in nutrigenomics differ with respect to their prior knowledge. This study describes digital nutrigenomics learning material suitable for students from various backgrounds and provides design guidelines for the development of the learning material. These design guidelines, derived from theories on cognitive science and instructional design, describe the selection of interaction types for learning tasks and the timing of information presentation. The learning material supports two learning goals: 1) the formulation of meaningful research questions in the field of nutrigenomics and 2) the development of feasible experiments to answer these questions. The learning material consists of two cases built around important nutrigenomics topics: 1) personalized diets and 2) the role of free fatty acids in the regulation of hepatic gene transcription. Each case consists of several activities to promote active learning by the student. Evaluation of the cases in a realistic academic educational setting indicates that the cases were useful.

Global reconstruction of the human metabolic network based on genomic and bibliomic data

Metabolism is a vital cellular process, and its malfunction is a major contributor to human disease. Metabolic networks are complex and highly interconnected, and thus systems-level computational approaches are required to elucidate and understand metabolic genotype-phenotype relationships. We have manually reconstructed the global human metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation of >50 years of legacy data (i.e., bibliomic data). Herein we describe the reconstruction process and demonstrate how the resulting genome-scale (or global) network can be used (i) for the discovery of missing information, (ii) for the formulation of an in silico model, and (iii) as a structured context for analyzing high-throughput biological data sets. Our comprehensive evaluation of the literature revealed many gaps in the current understanding of human metabolism that require future experimental investigation. Mathematical analysis of network structure elucidated the implications of intracellular compartmentalization and the potential use of correlated reaction sets for alternative drug target identification. Integrated analysis of high-throughput data sets within the context of the reconstruction enabled a global assessment of functional metabolic states. These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology.

Pharmacogenomics and nutrigenomics: synergies and differences

The success of the Human Genome Project and the spectacular development of broad genomics tools have catalyzed a new era in both medicine and nutrition. The terms pharmacogenomics and nutrigenomics are relatively new. Both have grown out of their genetic forbears as large-scale genomics technologies have been developed in the last decade. The aim of both disciplines is to individualize or personalize medicine and food and nutrition, and ultimately health, by tailoring the drug or the food to the individual genotype. This review article provides an overview of synergies and differences between these two potentially powerful science areas. Individual genetic variation is the common factor on which both pharmacogenomics and nutrigenomics are based. Each human is genetically (including epigenetics) unique and phenotypically distinct. One of the expectations of both technologies is that a wide range of gene variants and related single-nucleotide polymorphism will be identified as to their importance in health status, validated and incorporated into genotype based strategies for the optimization of health and the prevention of disease. Pharmacogenomics requires rigorous genomic testing that will be regulated and analyzed by professionals and acted on by medical practitioners. As further information is obtained on the importance of the interaction of food and the human genotype in disease prevention and health, pharmacogenomics can provide an opportunity driver for nutrigenomics. As we move from disease treatment to disease prevention, the two disciplines will become more closely aligned.

The vitamin D receptor as a therapeutic target

The vitamin D receptor (VDR) is a member of the large family of nuclear receptor transcription factors and specifically binds the micronutrient-derived hormone 1alpha,25(OH)2D3. A central endocrine role for this receptor in bone health was established at the beginning of the 20th century. Over the last 25 years, additional roles, perhaps through autocrine and paracrine mechanisms, have been established for VDR to regulate cell proliferation and differentiation, and more recently to exert immunomodulatory and antimicrobial functions. These findings, from in vitro and in vivo experiments, have generated considerable interest in targeting the VDR in multiple therapeutic settings. As with many potential therapeutics, it has also become clear that cells and tissues may also display de novo and acquired mechanisms of resistance to these actions. Consequently, a range of experimental and clinical options are being developed to bring about more targeted actions, overcome resistance and enhance efficacy of VDR-centred therapeutics.

Bioethics in human nutrigenomics research: European Nutrigenomics Organisation workshop report

As part of its work on setting standards and establishing guidelines for nutrigenomics research, the European Nutrigenomics Organisation (NuGO) is developing bioethical guidelines for those engaged in human nutrigenomics studies. A NuGO working group developed a set of draft guidelines addressing four areas: (1) information and consenting prior to a nutrigenomics study; (2) the generation and use of genotype information; (3) the establishment and maintenance of biobanks; (4) the exchange of samples and data. NuGO convened a workshop with a panel of invited external experts to assess the draft guidelines. The panel of experts confirmed that these areas are important and that the development of specific bioethical guidelines for nutrigenomics research would therefore enhance the application of established international guidelines in this field of biomedical research.

Nutrition and Genes in the Development of Orofacial Clefting

Clefts of the lip, alveolus, and/or palate, which are called orofacial clefts (OFC), occur in 0.5 to 3 per 1000 live and stillbirths. The pathogenesis of these congenital malformations remains largely unknown, but evidence is increasing that both nutritional and genetic factors are involved. Unlike genetic factors, nutritional causes can be corrected and may therefore contribute to the prevention of OFC. The goal of this review is to summarize the embryogenesis and genes involved in OFC, and to give an overview of the nutrients and related genes in humans. Improving our knowledge of the role of nutrition, genes, and their interactions in the pathogenesis of OFC may stimulate the development of nutritional interventions for OFC prevention in the future.

Nutritional modulation of ageing: Genomic and epigenetic approaches

Dietary factors have a profound effect on many aspects of health including ageing and do so, at least partly, through interactions with the genome which result in altered gene expression. The application of high throughput genomics technologies in nutritional research (nutrigenomics) offers a new approach to understanding the molecular mechanisms by which nutrition affects ageing. To date, transcriptional profiling techniques have been applied in studies of the mode of action of energy (caloric) restriction. Two further areas which appear to be particularly promising are (i) nutritional modulation of DNA damage and repair and (ii) nutritional modulation of epigenetic markings. Epigenetic-mediated changes in gene expression in response to dietary and other lifestyle exposures appear to be a major molecular mechanism linking environmental factors with the genome with consequences for cell function and health throughout the life course.

Nutrigenomics, proteomics, metabolomics, and the practice of dietetics

The human genome is estimated to encode over 30,000 genes, and to be responsible for generating more than 100,000 functionally distinct proteins. Understanding the interrelationships among genes, gene products, and dietary habits is fundamental to identifying those who will benefit most from or be placed at risk by intervention strategies. Unraveling the multitude of nutrigenomic, proteomic, and metabolomic patterns that arise from the ingestion of foods or their bioactive food components will not be simple but is likely to provide insights into a tailored approach to diet and health. The use of new and innovative technologies, such as microarrays, RNA interference, and nanotechnologies, will provide needed insights into molecular targets for specific bioactive food components and how they harmonize to influence individual phenotypes. Undeniably, to understand the interaction of food components and gene products, there is a need for additional research in the "omics" of nutrition. It is incumbent upon dietetics professionals to recognize that an individual's response to dietary intervention will depend on his or her genetic background and that this information may be used to promote human health and disease prevention. The objectives of this review are to acquaint nutritional professionals with terms relating to "omics," to convey the state of the science to date, to envision the possibilities for future research and technology, and to recognize the implications for clinical practice.

Nutrigenomics: From Molecular Nutrition to Prevention of Disease

Until recently, nutrition research concentrated on nutrient deficiencies and impairment of health. The advent of genomics-interpreted broadly as a suite of high throughput technologies for the generation, processing, and application of scientific information about the composition and functions of genomes-has created unprecedented opportunities for increasing our understanding of how nutrients modulate gene and protein expression and ultimately influence cellular and organismal metabolism. Nutritional genomics (nutrigenomics), the junction between health, diet, and genomics, can be seen as the combination of molecular nutrition and genomics. The diverse tissue and organ-specific effects of bioactive dietary components include gene-expression patterns (transcriptome); organization of the chromatin (epigenome); protein-expression patterns, including posttranslational modifications (proteome); as well as metabolite profiles (metabolome). Nutrigenomics will promote an increased understanding of how nutrition influences metabolic pathways and homeostatic control, how this regulation is disturbed in the early phases of diet-related disease, and the extent to which individual sensitizing genotypes contribute to such diseases. Eventually, nutrigenomics will lead to evidence-based dietary intervention strategies for restoring health and fitness and for preventing diet-related disease. In this review, we provide a brief overview of nutrigenomics from our point of view by describing current strategies, future opportunities, and challenges.

Gene-gene, gene-environment & multiple interactions in colorectal cancer

This review comprehensively evaluates the influence of gene-gene, gene-environment and multiple interactions on the risk of colorectal cancer (CRC). Methods of studying these interactions and their limitations have been discussed herein. There is a need to develop biomarkers of exposure and of risk that are sensitive, specific, present in the pathway of the disease, and that have been clinically tested for routine use. The influence of inherited variation (polymorphism) in several genes has been discussed in this review; however, due to study limitations and confounders, it is difficult to conclude which ones are associated with the highest risk (either individually or in combination with environmental factors) to CRC. The majority of the sporadic cancer is believed to be due to modification of mutation risk by other genetic and/or environmental factors. Micronutrient deficiency may explain the association between low consumption of fruit/vegetables and CRC in human studies. Mitochondrial modulation by dietary factors influences the balance between cell renewal and death critical in colon mucosal homeostasis. Both genetic and epigenetic interactions are intricately dependent on each other, and collectively influence the process of colorectal tumorigenesis. The genetic and environmental interactions present a good prospect and a challenge for prevention strategies for CRC because they support the view that this highly prevalent cancer is preventable.

Nutrigenomics and nutrigenetics: the emerging faces of nutrition

The recognition that nutrients have the ability to interact and modulate molecular mechanisms underlying an organism's physiological functions has prompted a revolution in the field of nutrition. Performing population-scaled epidemiological studies in the absence of genetic knowledge may result in erroneous scientific conclusions and misinformed nutritional recommendations. To circumvent such issues and more comprehensively probe the relationship between genes and diet, the field of nutrition has begun to capitalize on both the technologies and supporting analytical software brought forth in the post-genomic era. The creation of nutrigenomics and nutrigenetics, two fields with distinct approaches to elucidate the interaction between diet and genes but with a common ultimate goal to optimize health through the personalization of diet, provide powerful approaches to unravel the complex relationship between nutritional molecules, genetic polymorphisms, and the biological system as a whole. Reluctance to embrace these new fields exists primarily due to the fear that producing overwhelming quantities of biological data within the confines of a single study will submerge the original query; however, the current review aims to position nutrigenomics and nutrigenetics as the emerging faces of nutrition that, when considered with more classical approaches, will provide the necessary stepping stones to achieve the ambitious goal of optimizing an individual's health via nutritional intervention.

Vitamin D and cancer

The impact of dietary intake upon cell and tissue physiology, as well as pathophysiology, has emerged as being highly significant to the etiology of a number of high-profile malignancies. The vitamin D receptor (VDR) is a member of a large transcription factor family of nuclear receptors and responds specifically to a hormonal micronutrient (1α25(OH)₂D₃). A central endocrine role for this receptor in bone health was established at the beginning of the 20th century. An alternative role has been established over the last 25 years for the VDR to regulate cell growth and division, and promote differentiation through autocrine and paracrine mechanisms. These findings from in vitro and in vivo experiments have generated considerable interest in the potential to target the VDR in either chemoprevention or chemotherapy cancer settings. As with many potential cancer therapeutics, it has become equally clear that cancer cells display de novo and acquired mechanisms of resistance to these actions. Consequently, researchers are developing a range of experimental and clinical options to bring about more targeted actions, overcome resistance and enhance the efficacy of VDR-centered therapeutics.

Nutrition and food science go genomic

The wealth of genomic information and high-throughput profiling technologies are now being exploited by scientists in the disciplines of nutrition and food science. Diet and food components are prime environmental factors that affect the genome, transcriptome, proteome and metabolome, and this life-long interaction defines the health or disease state of an individual. For the first time the interaction of foods, and individual food constituents, with the biological systems can be defined on a molecular basis. Profiling technologies are used in basic-science applications for identifying the mode of action of foods or particular ingredients, and are similarly taken into the science-driven development of foods with a defined biofunctionality. Biomarker profiles and patterns derived from genomics applications in humans should guide nutrition and food science in developing evidence-based dietary recommendations and health-promoting foods.

Interleukin 1 genetics, inflammatory mechanisms, and nutrigenetic opportunities to modulate diseases of aging

Inflammation plays a central role in many diseases of aging, and genetic differences in the inflammatory response appear to influence different disease courses among individuals. Variations in the genes for the family of interleukin 1 (IL-1) proteins are inherited together in a small set of patterns and provide an example of the role of inflammatory genetics as a modifier of diseases of aging. The IL-1 genetic variations are associated with variation in both the inflammatory response and the clinical presentation of a range of diseases, including coronary artery disease, Alzheimer disease, gastric cancer, and periodontitis. This growing understanding of the role of genetic variation in inflammation and chronic disease presents opportunities to identify healthy persons who are at increased risk of disease and to potentially modify the trajectory of disease to prolong healthy aging. Nutrition represents one of the promising approaches to modulation of the risk of diseases of aging because of the effects of certain nutrients on gene expression. One of the most practical applications of nutritional modulation of chronic disease may be nutrients that regulate the expression of key inflammatory genes.

Emerging concepts in nutrigenomics: a preview of what is to come

This article provides an overview of the fundamental principles of genetics and emerging concepts related to the ways in which nutrients and bioactive food components may interact with the genome and subsequently affect human health. This exciting area of research is likely to have far-reaching implications for the assessment and treatment of critically and chronically ill individuals that will affect nutrition standards of care and practice. A brief overview of some of the ethical, legal, and social implications of genomic research and genome-based health care and a list of genetics resources also are provided.

The case for strategic international alliances to harness nutritional genomics for public and personal health

Nutrigenomics is the study of how constituents of the diet interact with genes, and their products, to alter phenotype and, conversely, how genes and their products metabolise these constituents into nutrients, antinutrients, and bioactive compounds. Results from molecular and genetic epidemiological studies indicate that dietary unbalance can alter gene-nutrient interactions in ways that increase the risk of developing chronic disease. The interplay of human genetic variation and environmental factors will make identifying causative genes and nutrients a formidable, but not intractable, challenge. We provide specific recommendations for how to best meet this challenge and discuss the need for new methodologies and the use of comprehensive analyses of nutrient-genotype interactions involving large and diverse populations. The objective of the present paper is to stimulate discourse and collaboration among nutrigenomic researchers and stakeholders, a process that will lead to an increase in global health and wellness by reducing health disparities in developed and developing countries.

Nutrigenomics: The Impact of Biomics Technology on Nutrition Research

The interaction between the human body and nutrition is an extremely complex process involving multi-organ physiology with molecular mechanisms on all levels of regulation (genes, gene expression, proteins, metabolites). Only with the recent technology push have nutritional scientists been able to address this complexity. Both the challenges and promises that are offered by the merge of 'biomics' technologies and mechanistic nutrition research are huge, but will eventually evolve in a new nutrition research concept: nutritional systems biology. This review describes the principles and technologies involved in this merge. Using nutrition research examples, including gene expression modulation by carbohydrates and fatty acids, this review discusses applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, and systems biology. Furthermore, reference is made to gene polymorphisms that underlie individual differences in nutrient utilization, resulting in, e.g., different susceptibility to develop obesity.

Impact of microarray technology in nutrition and food research

Microarrays have become standard tools for gene expression profiling as the mRNA levels of a large number of genes can be measured in a single assay. Many technical aspects concerning microarray production and laboratory usage have been addressed in great detail, but it remains still crucial to establish this technology in new research fields such as human nutrition and food-related areas. The correlation between diet and inter-individual variation in gene expression is an important and relatively unexplored issue in human nutrition. Therefore, nutritionists changed their research field dramatically from epidemiology and physiology towards the "omics" sciences. Nutrigenomics as a field of research is based on the complete knowledge of the human genome and refers to the entire spectrum of human genes that determine the interactions of nutrition with the organism. Nutrigenetics is based on the inter-individual, genetically determined differences in metabolism. Nutrigenomics and nutrigenetics carry the hope that individualized diet can improve human health and prevent nutrition-related diseases. In this article we give an overview of current DNA and protein microarray techniques (including fabrication, experimental procedure and data analysis), we describe their applications to nutrition and food research and point out the limitations, problems and pitfalls of microarray experiments.

Nutrient-gene interaction: metabolic genotype-phenotype relationship

The U.S. Department of Health and Human Services (DHHS)/USDA Dietary Guidelines for Americans is a science and population evidence-based guide on diet and physical activity, providing advice and recommendations to promote a healthier lifestyle and reduce the risk of chronic diseases, including cancer. These recommendations are supported by the comprehensive evidence-based review on diet and cancer prevention conducted by the American Institute for Cancer Research, National Cancer Institute, World Health Organization/International Agency for Research on Cancer, and others. However, influencing dietary effects are the individual genetic predispositions that are the basis for considerable interindividual variations in cancer risk within the population and in nutrient homeostasis, which is maintained by genomic-nutrient and metabolic-phenotype interactions. Although genetics is an important component, it accounts for only a portion of this variation. An individual's overall phenotype, including health status, is achieved and maintained by the sum of metabolic activities functioning under differing circumstances within the life cycle and the complex interactions among genotype, metabolic phenotype, and the environment. In this postgenomic era, high-throughput groups of technologies in genomics, proteomics, and metabolomics measure and analyze DNA sequences, RNA transcripts, proteins, and nutrient-metabolic fluxes in a single experiment. These advances have transformed biomarker studies on nutrient-gene interactions from a reductionist concept into a holistic practice in which many regulated genes involved in metabolism, along with its metabolic phenotypes, can be measured through functional genomics and metabolic profiling. The overall integration of data and information from the building blocks of metabolism-based nutrient-gene interaction can lead to future individualized dietary recommendations to diminish cancer risk.

Nutrition-/diet-induced changes in gene expression in white adipose tissue

Nutrients regulate metabolic fluxes and homeostasis through transcriptional and translational control of enzyme concentrations and allosteric modulation of enzyme activity. Dietary omega-3 polyunsaturated fatty acids (PUFAs) have been shown to exert a variety of beneficial health effects such as reducing adiposity and increasing insulin sensitivity in rodents. It is now clear that PUFAs regulate fundamental adipose cell and liver functions through modulation of activity and abundance of key transcription factors that act as nutrient sensors, including peroxisome proliferator-activated receptors (PPARalpha/delta/gamma), sterol regulatory element binding proteins (SREBP-1/2), and liver X receptors (LXRalpha/beta). However, in the state of obesity, where adipose tissue shows elevated storage of triglycerides, many lipogenic genes that are essential for adipose cell function including PPARgamma, SREBP-1c, CCAAT-enhancer binding protein alpha and stearoyl-CoA desaturase-1 are downregulated, apparently due to desensitization of the very same crucial nutrient sensors. This chapter will summarize recent studies of PUFA- and obesity-induced changes in gene expression in white adipose tissue.

Pharmacogenomics, nutrigenomics and therapeutic optimization in Alzheimer’s disease

The molecular neuropharmacology of Alzheimer’s disease (AD) is still at an early stage. During the past 20 years, only five drugs, four cholinesterase inhibitors (tacrine, donepezil, rivastigmine and galantamine) and one NMDA receptor partial antagonist (memantine), with poor cost-effectiveness, have been approved for the treatment of AD. Patients with dementia receive many different drugs daily to palliate cognitive and noncognitive symptoms, as well as for the treatment of concomitant disorders present in the elderly population. Polypharmacy, drug–drug interactions and adverse events may combine to deteriorate the frail condition of AD patients. In recent times, the partial elucidation of the pathogenic mechanisms underlying AD-related neurodegeneration, in which many different genes are involved, has helped to foster the development of novel drugs and pharmacogenomics studies. Functional genomics studies have revealed the association of specific mutations in primary loci (APP,PS1, PS2) and/or apolipoprotein (APO)-E-related polymorphic variants with the phenotypic expression of biological traits (e.g., age at onset, brain atrophy, cognitive decline rate, β-amyloid deposition, lipid metabolism dysfunction, immunologic dysregulation or therapeutic outcome). In most pharmacogenomics studies, patients harboring the APOE-4 allele (especially homozygotes) are the worst responders. Genetic clusters integrating 3–4 AD-related genes, representing 25–30% of the AD population, have allowed the identification of selective genotype clusters of good responders. Furthermore, approximately 15% of the European population with AD show mutant CYP2D6 alleles (poor and ultrarapid metabolizers) potentially responsible for efficacy and safety problems with cholinesterase inhibitors and psychotropic drugs. Nutritional factors may also contribute to the deterioration of cognition and brain function in dementia. Novel nutraceutical products obtained from marine sources with biotechnologic procedures have demonstrated atheroprotective properties and lipid-lowering effects and are devoid of hepatotoxic activity. Some of these nutraceuticals exhibit a genotype-dependent therapeutic effect, reflecting a nutrigenomic profile. Nutrigenetics/nutrigenomics- and pharmacogenetics/pharmacogenomics-associated factors may represent major determinants of drug efficacy and safety and therapeutics optimization in dementia and other CNS disorders.

Dietary rapeseed oil affects the expression of genes involved in hepatic lipid metabolism in Atlantic salmon (Salmo salar L.)

Supplies of marine fish oils (FO) are limited, and sustainable production in aquaculture dictates that alternatives that do not compromise fish health and product quality, such as vegetable oils, must be found. Nutrigenomics will increase our understanding of how nutrition influences metabolic pathways and homeostatic control, and may be used to measure and validate subtle changes in organ-specific, metabolic gene expression signatures. We compared 2 groups of Atlantic salmon fed diets containing 100% FO or 75% rapeseed oil (RO) for 42 wk. A small-scale cDNA microarray was constructed to screen for changes in the expression of lipid metabolism genes in the liver resulting from this partial substitution of RO for FO. Delta5 fatty acid desaturase gene expression was significantly greater in fish fed 75% RO than in fish fed the control diet; this was confirmed by quantitative real time PCR analysis. In addition, several genes, among these mitochondrial proteins, peroxisome proliferator-activated receptor gamma, as well as other transcription factors, coactivators, and signal transducers, showed significant differential regulation. This partially validated microarray may be used for further gene expression profiling using other dietary comparisons, and for further characterization of selected genes.

SINGLE NUCLEOTIDE POLYMORPHISMS THAT INFLUENCE LIPID METABOLISM: Interaction with Dietary Factors

Cardiovascular disease (CVD) risk is the result of complex interactions between genetic and environmental factors. During the past few decades, much attention has focused on plasma lipoproteins as CVD risk factors. The current evidence supports the concept that gene-environment interactions modulate plasma lipid concentrations and potentially CVD risk. The findings from studies examining gene-diet interactions and lipid metabolism have been highly promising. Several loci (i.e., APOA1, APOA4, APOE, and LIPC) are providing proof-of-concept for the potential application of genetics in the context of personalized nutritional recommendations for CVD prevention. However, the incorporation of these findings to the clinical environment is not ready for prime time. There is a compelling need for replication using a higher level of scientific evidence. Moreover, we need to evolve from the simple scenarios examined nowadays (i.e., one single dietary component, single nucleotide polymorphism, and risk factor) to more realistic situations involving interactions between multiple genes, dietary components, and risk factors. In summary, there is need for both large population studies and well-standardized intervention studies.

Colonic microbiota signatures across five northern European countries

The composition of the colonic microbiota of 91 northern Europeans was characterized by fluorescent in situ hybridization using 18 phylogenetic probes. On average 75% of the bacteria were identified, and large interindividual variations were observed. Clostridium coccoides and Clostridium leptum were the dominant groups (28.0% and 25.2%), followed by the Bacteroides (8.5%). According to principal component analysis, no significant grouping with respect to geographic origin, age, or gender was observed.

A perspective on DNA microarray technology in food and nutritional science

PURPOSE OF REVIEW

The functions of nutrients and other foods have been revealed at the level of gene regulation. The advent of DNA microarray technology has enabled us to analyze the body's response to these factors in a much more holistic manner than before. This review is intended to overview the present status of this DNA microarray technology, hoping to provide food and nutrition scientists, especially those who are planning to introduce this technology, with hints and suggestions.

RECENT FINDINGS

The number of papers examining transcriptomics analysis in food and nutrition science has expanded over the last few years. The effects of some dietary conditions and administration of specific nutrients or food factors are studied in various animal models and cultured cells. The target food components range from macronutrients and micronutrients to other functional food factors. Such studies have already yielded fruitful results, which include discovery of novel functions of a food, uncovering hitherto unknown mechanisms of action, and analyses of food safety.

SUMMARY

The potency of DNA microarray technology in food and nutrition science is broadly recognized. This technique will surely continue to provide researchers and the public with valuable information on the beneficial and adverse effects of food factors. It should also be acknowledged, however, that there remain problems such as standardization of the data and sharing of the results among researchers in this field.

DROSOPHILANUTRIGENOMICS CAN PROVIDE CLUES TO HUMAN GENE-NUTRIENT INTERACTIONS

Nutrigenomics refers to the complex effects of the nutritional environment on the genome, epigenome, and proteome of an organism. The diverse tissue- and organ-specific effects of diet include gene expression patterns, organization of the chromatin, and protein post-translational modifications. Long-term effects of diet range from obesity and associated diseases such as diabetes and cardiovascular disease to increased or decreased longevity. Furthermore, the diet of the mother can potentially have long-term health impacts on the children, possibly through inherited diet-induced chromatin alterations. Drosophila is a unique and ideal model organism for conducting nutrigenomics research for numerous reasons. Drosophila, yeast, and Caenorhabditis elegans all have sophisticated genetics as well as sequenced genomes, and researchers working with all three organisms have made valuable discoveries in nutrigenomics. However, unlike yeast and C. elegans, Drosophila has adipose-like tissues and a lipid transport system, making it a closer model to humans. This review summarizes what has already been learned in Drosophila nutrigenomics (with an emphasis on lipids and sterols), critically evaluates the data, and discusses fruitful areas for future research.

Kinetics of biomarkers: biological and technical validity of isoprostanes in plasma

Isoprostanes, non-enzymatic peroxidation products of arachidonic acid, are attractive biomarkers of oxidative stress in research in biology, medicine and nutrition. For the appropriate use of biomarkers it is required that these are both biologically and technically valid. Whereas the biological validity of isoprostanes is well-established, it is technically quite complicated to measure isoprostanes and its metabolites in body fluids, and its rapid disappearance from plasma may hamper practical application. This paper shortly introduces isoprostanes as a biomarker for studies with humans, describes a novel fast and sensitive method for measuring isoprostanes in plasma by high-performance liquid chromatography and tandem mass spectrometry, and provides several examples of the use of the method in studies in humans. By taking care of the biological and technical validity of this biomarker it is possible to establish the antioxidant effects of some food ingredients in studies with human volunteers.

The emergence of a new paradigm of pharmacogenomics

A series of qualitatively new properties of the complex polygenic systems are transforming the dominant, genome-centric approach of pharmacogenomics towards a more integrative, holistic paradigm. The recent concepts of interposition of regulatory networks between genotype and phenotype, and the emergence of epigenotype as the locus of integration of genetic background with nutritional and lifestyle influences, render problematic any prediction of the consequences of individual gene alterations. In addition, the redefinition of the traditional boundaries of clinical phenotypes, with the promotion of the endophenotypes as methodological strategy, and the initiative of the phenome elucidation, reshape both the research, as well as the application, of pharmacogenomics. These concepts and developments can explain some of the complexity, and the multifactorial nature, of most drug responses and imply another understanding of education in the field, which aims at stimulating a critical reflection on these major shifts prior to a practical training on the immediate application of pharmacogenomics.

Changes in adipose tissue gene expression with energy-restricted diets in obese women

BACKGROUND

The effect of energy restriction and macronutrient composition on gene expression in adipose tissue is not well defined.

OBJECTIVE

The aim of the study was to investigate the effect of different low-energy diets on gene expression in human adipose tissue.

DESIGN

Forty obese women were randomly assigned to a moderate-fat, moderate-carbohydrate diet or a low-fat, high-carbohydrate hypoenergetic (-600 kcal/d) diet for 10 wk. Subcutaneous adipose tissue samples were obtained before and after the diet period. High-quality RNA samples were obtained from 23 women at both time points, and these samples were hybridized to microarrays containing the 8500 most extensively described human genes. The results were confirmed by separate messenger RNA measurements.

RESULTS

Both diets resulted in weight losses of approximately 7.5% of baseline body weight. A total of 52 genes were significantly up-regulated and 44 were down-regulated as a result of the intervention, and no diet-specific effect was observed. No major effect on lipid-specific transcription factors or genes regulating signal transduction, lipolysis, or synthesis of acylglycerols was observed. Most changes were modest (<25% of baseline), but all genes regulating the formation of polyunsaturated fatty acids from acetyl-CoA and malonyl-CoA were markedly down-regulated (35-60% decrease).

CONCLUSIONS

Macronutrients have a secondary role in changes in adipocyte gene expression after energy-restricted diets. The most striking alteration after energy restriction is a coordinated reduction in the expression of genes regulating the production of polyunsaturated fatty acids.

The Human Peroxisome Proliferator-activated Receptor δ Gene is a Primary Target of 1α,25-Dihydroxyvitamin D3 and its Nuclear Receptor

Peroxisome proliferator-activated receptor (PPAR) delta is the most widely expressed member of the PPAR family of nuclear receptor fatty acid sensors. Real-time PCR analysis of breast and prostate cancer cell lines demonstrated that PPARdelta expression was increased 1.5 to 3.2-fold after three hours stimulation with the natural vitamin D receptor (VDR) agonist, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). In silico analysis of the 20 kb of the human PPARdelta promoter revealed a DR3-type 1alpha,25(OH)2D3 response element approximately 350 bp upstream of the transcription start site, which was able to bind VDR-retinoid X receptor (RXR) heterodimers and mediate a 1alpha,25(OH)2D3-dependent upregulation of reporter gene activity. Chromatin immuno-precipitation assays demonstrated that a number of proteins representative for 1alpha,25(OH)2D3-mediated gene activation, such as VDR, RXR and RNA polymerase II, displayed a 1alpha,25(OH)2D3-dependent association with a region of the proximal PPARdelta promoter that contained the putative DR3-type VDRE. This was also true for other proteins that are involved in or are the subject of chromatin modification, such as the histone acetyltransferase CBP and histone 4, which displayed ligand-dependent association and acetylation, respectively. Finally, real-time PCR analysis demonstrated that 1alpha,25(OH)2D3 and the synthetic PPARdelta ligand L783483 show a cell and time-dependent interference in each other's effects on VDR mRNA expression, so that their combined application shows complex effects on the induction of VDR target genes, such as CYP24. Taken together, we conclude that PPARdelta is a primary 1alpha,25(OH)2D3-responding gene and that VDR and PPARdelta signaling pathways are interconnected at the level of cross-regulation of their respective transcription factor mRNA levels.

Intake of soy protein isolate alters hepatic gene expression in rats

Soy protein isolate (SPI) can elicit various physiological effects such as cholesterol lowering and antiobesity effects. To examine whether hepatic gene expression is altered by SPI intake, rats were fed an SPI or casein diet for 8 weeks. After 8 weeks of feeding, liver weight and plasma triglyceride and cholesterol levels were significantly lower in the SPI group than in the casein group. Hepatic gene expression was investigated using DNA microarrays. The expression profiles and statistical analysis showed clear and significant differences between the SPI and casein groups (p < 0.05); in the SPI group, 63 genes were up-regulated and 57 genes were down-regulated, most involved in various physiological functions such as lipid metabolism, antioxidant activity, transcriptional regulation, and energy metabolism. Especially in lipid metabolism, the down-regulated genes are related to fatty acid synthesis and the up-regulated genes are related to cholesterol synthesis and steroid catabolism. These results suggest that SPI intake could maintain homeostasis primarily by modulating lipid and energy metabolism.

Beta-carotene and the application of transcriptomics in risk–benefit evaluation of natural dietary components

Beta-carotene is a natural food component that is present in fruits and vegetables and is also used as a food colorant and a supplement. Beta-carotene is an anti-oxidant and a source of vitamin A. It is endowed with health beneficial properties, but a number of studies showed that with high intakes it may increase the risk for lung cancer in at risk individuals (heavy smokers, asbestos workers and alcohol users). To establish the window of benefit, it is necessary to identify early markers of effect and to obtain insight in the mechanism of action of beta-carotene, in the absence and presence of environmental risk factors. Genomics technologies are well suited to dissect the mechanisms of action and identify the markers of effect. Human cell lines can be used to analyse the effects of beta-carotene, but exposure studies with beta-carotene show that cell lines display a widely variant behaviour, which hampers translation to the in vivo situation in humans. Alternatively, animal studies can be used. Especially the ferret seems to be a good model, but little sequence information of this species is available. However, heterologous hybridization on human cDNA seems possible and provides and a new tool for molecular analysis of health effects of beta-carotene.

Folic acid - vitamin and panacea or genetic time bomb?

We live in a health-conscious age - many of us supplement our diet with essential micronutrients through the discretionary use of multivitamin pills or judicious selection of foods that have a health benefit beyond that conferred by the nutrient content alone - the so-called 'functional foods'. Indeed, the citizens of some nations have little choice, with a mandatory fortification policy in place for certain vitamins. But do we ever stop to consider the consequences of an increased exposure to micronutrients? We examine this issue in relation to the B-group vitamin folic acid, and ask whether supplementation with this vitamin could introduce a strong genetic selection pressure - one that has the side effect of increasing the prevalence of some of the most significant, human life-threatening diseases. Are we affecting our genetics - is this a case of human evolution in progress by altering our diet?

Environmental health research in the post-genome era: new fields, new challenges, and new opportunities

The human genome sequence provides researchers with a genetic framework to eventually understand the relationships of gene-environment interactions. This wealth of information has led to the birth of several related areas of research, including proteomics, functional genomics, pharmacogenomics, and toxicogenomics. Developing techniques such as DNA/protein microarrays, small-interfering RNA (siRNA) applications, two-dimensional gel electrophoresis, and mass spectrometry in conjunction with advanced analysis software and the availability of Internet databases offers a powerful set of tools to investigate an individual's response to specific stimuli. This review summarizes these emerging scientific fields and techniques focusing specifically on their applications to the complexities of gene-environment interactions and their potential role in environ-mental biosecurity.