Nutrient–gene interactions in benefit–risk analysis

Metabolic and immunological responses of Drosophila melanogaster to dietary restriction and bacterial infection differ substantially between genotypes in a population

To respond to changing environmental conditions, a population may either shift toward better‐adapted genotypes or adapt on an individual level. The present work aimed to quantify the relevance of these two processes by comparing the responses of defined Drosophila melanogaster populations to different stressors. To do this, we infected two homogeneous populations (isofemale lines), which differ significantly in fitness, and a synthetic heterogeneous population with a specific pathogen and/or exposed them to food restriction. Pectobacterium carotovorum was used to infect Drosophila larvae either fed standard or protein‐restricted diet. In particular, the two homogeneous groups, which diverged in their fitness, showed considerable differences in all parameters assessed (survivorship, protein and lipid contents, phenol‐oxidase (PO) activity, and antibacterial rate). Under fully nutritious conditions, larvae of the homogeneous population with low fitness exhibited lower survivorship and protein levels, as well as higher PO activity and antibacterial rate compared with the fitter population. A protein‐restricted diet and bacterial infection provoked a decrease in survivorship, and antibacterial rate in most populations. Bacterial infection elicited an opposite response in protein and lipid content in both isofemale lines tested. Interestingly, the heterogeneous population showed a complex response pattern. The response of the heterogeneous population followed the fit genotype in terms of survival and antibacterial activity but followed the unfit genotype in terms of PO activity. In conclusion, our results show that defined genotypes exhibit highly divergent responses to varying stressors that are difficult to predict. Furthermore, the responses of heterogeneous populations do not follow a fixed pattern showing a very high degree of plasticity and differences between different genotypes.

Genes and Diet in the Prevention of Chronic Diseases in Future Generations

Nutrition is a modifiable key factor that is able to interact with both the genome and epigenome to influence human health and fertility. In particular, specific genetic variants can influence the response to dietary components and nutrient requirements, and conversely, the diet itself is able to modulate gene expression. In this context and the era of precision medicine, nutrigenetic and nutrigenomic studies offer significant opportunities to improve the prevention of metabolic disturbances, such as Type 2 diabetes, gestational diabetes, hypertension, and cardiovascular diseases, even with transgenerational effects. The present review takes into account the interactions between diet, genes and human health, and provides an overview of the role of nutrigenetics, nutrigenomics and epigenetics in the prevention of non-communicable diseases. Moreover, we focus our attention on the mechanism of intergenerational or transgenerational transmission of the susceptibility to metabolic disturbances, and underline that the reversibility of epigenetic modifications through dietary intervention could counteract perturbations induced by lifestyle and environmental factors.

Foodomics for human health: current status and perspectives

INTRODUCTION

In the post-genomic era, the opportunity to combine and integrate cutting-edge analytical platforms and data processing systems allowed the birth of foodomics, 'a discipline that studies the Food and Nutrition domains through the application of advanced omics technologies to improve consumer's well-being, health, and confidence'. Since then, this discipline has rapidly evolved and researchers are now facing the daunting tasks to meet consumers' needs in terms of food traceability, sustainability, quality, safety and integrity. Most importantly, today it is imperative to provide solid evidence of the mechanisms through which food can promote human health and well-being. Areas covered: In this review, the complex relationships connecting food, nutrition and human health will be discussed, with emphasis on the relapses for the development of functional foods and nutraceuticals, personalized nutrition approaches, and the study of the interplay among gut microbiota, diet and health/diseases. Expert commentary: Evidence has been provided supporting the role of various omic platforms in studying the health-promoting effects of food and customized dietary interventions. However, although associated to major analytical challenges, only the proper integration of multi-omics studies and the implementation of bioinformatics tools and databases will help translate findings from clinical practice into effective personalized treatment strategies.

Nutriepigenomics and malnutrition

Epigenetics is defined as the modulation of gene expression without changes to the underlying DNA sequence. Epigenetic alterations, as a consequence of in utero malnutrition, may play a role in susceptibility to develop adulthood diseases and inheritance. However, the mechanistic link between epigenetic modifications and abnormalities in nutrition remains elusive. This review provides an update on the association of suboptimal nutritional environment and the high propensity to produce adult-onset chronic illnesses with a particular focus on modifications in genome functions that occur without alterations to the DNA sequence. We will mention the drivers of the phenotype and pattern of epigenetic markers set down during the reprogramming along with novel preventative and therapeutic strategies. New knowledge of epigenetic alterations is opening a gate toward personalized medicine.

Nutritional Strategies for the Individualized Treatment of Non-Alcoholic Fatty Liver Disease (NAFLD) Based on the Nutrient-Induced Insulin Output Ratio (NIOR)

Nutrients play a fundamental role as regulators of the activity of enzymes involved in liver metabolism. In the general population, the action of nutrients may be affected by gene polymorphisms. Therefore, individualization of a diet for individuals with fatty liver seems to be a fundamental step in nutritional strategies. In this study, we tested the nutrient-induced insulin output ratio (NIOR), which is used to identify the correlation between the variants of genes and insulin resistance. We enrolled 171 patients, Caucasian men (n = 104) and women (n = 67), diagnosed with non-alcoholic fatty liver disease (NAFLD). From the pool of genes sensitive to nutrient content, we selected genes characterized by a strong response to the NIOR. The polymorphisms included Adrenergic receptor (b3AR), Tumor necrosis factor (TNFα), Apolipoprotein C (Apo C III). Uncoupling Protein type I (UCP-1), Peroxisome proliferator activated receptor γ2 (PPAR-2) and Apolipoprotein E (APOEs). We performed three dietary interventions: a diet consistent with the results of genotyping (NIOR (+)); typical dietary recommendations for NAFLD (Cust (+)), and a diet opposite to the genotyping results (NIOR (−) and Cust (−)). We administered the diet for six months. The most beneficial changes were observed among fat-sensitive patients who were treated with the NIOR (+) diet. These changes included improvements in body mass and insulin sensitivity and normalization of blood lipids. In people sensitive to fat, the NIOR seems to be a useful tool for determining specific strategies for the treatment of NAFLD.

Selenium and cancer: a story that should not be forgotten-insights from genomics

Selenium (Se) is an essential micronutrient that is incorporated into selenoproteins. Although epidemiological studies suggest that low Se intake is associated with increased risk of various cancers, the results of supplementation trials have been confusing. These conflicting results may be due to different baseline Se status and/or genetic factors. In addition, mechanistic links between Se intake, selenoproteins and carcinogenesis are not clear. In this article, we discuss the functional significance of single-nucleotide polymorphisms (SNP) in selenoprotein genes and the evidence as to whether or not they influence risk of colorectal, prostate, lung or breast cancers. Both in vitro and in vivo studies have shown that a small number of SNPs in genes encoding glutathione peroxidases 1 and 4, selenoprotein P, selenoprotein S and 15-kDa selenoprotein have functional consequences. Data from case-control studies suggest that a variant at codon 198 in glutathione peroxidase 1 influences the effect of Se status on prostate cancer and risk, and it has also been associated with breast cancer and lung cancer risk, whereas variants in glutathione peroxidase 4, selenoprotein P and selenoprotein S may influence the risk of colorectal cancer. In addition, the results of gene microarray (transcriptomic) studies have identified novel selenoprotein biomarkers of Se status and novel downstream Se-targeted pathways. The work highlights the need to take baseline Se status and genetic factors into account in the design of future intervention trials.

An insight into the public acceptance of nutrigenomic-based personalised nutrition

It is predicted that non-communicable diseases will account for over 73 % of global mortality in 2020. Given that the majority of these deaths occur in developed countries such as the UK, and that up to 80 % of chronic disease could be prevented through improvements in diet and lifestyle, it is imperative that dietary guidelines and disease prevention strategies are reviewed in order to improve their efficacy. Since the completion of the human genome project our understanding of complex interactions between environmental factors such as diet and genes has progressed considerably, as has the potential to individualise diets using dietary, phenotypic and genotypic data. Thus, there is an ambition for dietary interventions to move away from population-based guidance towards 'personalised nutrition'. The present paper reviews current evidence for the public acceptance of genetic testing and personalised nutrition in disease prevention. Health and clear consumer benefits have been identified as key motivators in the uptake of genetic testing, with individuals reporting personal experience of disease, such as those with specific symptoms, being more willing to undergo genetic testing for the purpose of personalised nutrition. This greater perceived susceptibility to disease may also improve motivation to change behaviour which is a key barrier in the success of any nutrition intervention. Several consumer concerns have been identified in the literature which should be addressed before the introduction of a nutrigenomic-based personalised nutrition service. Future research should focus on the efficacy and implementation of nutrigenomic-based personalised nutrition.

Personalised nutrition: ready for practice?

The efficacy by which dietary interventions influence risk markers of multi-factorial diseases is mainly determined by taking population-based approaches. However, there exists considerable inter-individual variation in response to dietary interventions, and some interventions may benefit certain individuals or population subgroups more than others. This review evaluates the application of nutrigenomic technologies to further the concept of personalised nutrition, as well as the process to take personalised nutrition to the marketplace. The modulation of an individual's response is influenced by both genetic and environmental factors. Many nutrigenetics studies have attempted to explain variability in responses based on a single or a few genotypes so that a genotype may be used to define personalised dietary advice. It has, however, proven very challenging to define an individual's responsiveness to complex diets based on common genetic variations. In addition, there is a limited understanding of what constitutes an optimal response because we lack key health biomarkers and signatures. In conclusion, advances in nutrigenomics will undoubtedly further the understanding of the complex interplay between genotype, phenotype and environment, which are required to enhance the development of personalised nutrition in the future. At the same time, however, issues relating to consumer acceptance, privacy protection as well as marketing and distribution of personalised products need to be addressed before personalised nutrition can become commercially viable.

State of the art in benefit-risk analysis: food and nutrition

Benefit-risk assessment in food and nutrition is relatively new. It weighs the beneficial and adverse effects that a food (component) may have, in order to facilitate more informed management decisions regarding public health issues. It is rooted in the recognition that good food and nutrition can improve health and that some risk may be acceptable if benefit is expected to outweigh it. This paper presents an overview of current concepts and practices in benefit-risk analysis for food and nutrition. It aims to facilitate scientists and policy makers in performing, interpreting and evaluating benefit-risk assessments. Historically, the assessments of risks and benefits have been separate processes. Risk assessment is mainly addressed by toxicology, as demanded by regulation. It traditionally assumes that a maximum safe dose can be determined from experimental studies (usually in animals) and that applying appropriate uncertainty factors then defines the 'safe' intake for human populations. There is a minor role for other research traditions in risk assessment, such as epidemiology, which quantifies associations between determinants and health effects in humans. These effects can be both adverse and beneficial. Benefit assessment is newly developing in regulatory terms, but has been the subject of research for a long time within nutrition and epidemiology. The exact scope is yet to be defined. Reductions in risk can be termed benefits, but also states rising above 'the average health' are explored as benefits. In nutrition, current interest is in 'optimal' intake; from a population perspective, but also from a more individualised perspective. In current approaches to combine benefit and risk assessment, benefit assessment mirrors the traditional risk assessment paradigm of hazard identification, hazard characterization, exposure assessment and risk characterization. Benefit-risk comparison can be qualitative and quantitative. In a quantitative comparison, benefits and risks are expressed in a common currency, for which the input may be deterministic or (increasingly more) probabilistic. A tiered approach is advocated, as this allows for transparency, an early stop in the analysis and interim interaction with the decision-maker. A general problem in the disciplines underlying benefit-risk assessment is that good dose-response data, i.e. at relevant intake levels and suitable for the target population, are scarce. It is concluded that, provided it is clearly explained, benefit-risk assessment is a valuable approach to systematically show current knowledge and its gaps and to transparently provide the best possible science-based answer to complicated questions with a large potential impact on public health.

Nutrigenetics, nutrigenomics, and selenium

Selenium (Se) is an important micronutrient that, as a component of selenoproteins, influences oxidative and inflammatory processes. Its’ levels vary considerably, with different ethnic and geographic population groups showing varied conditions, ranging from frank Se deficiencies to toxic effects. An optimum Se level is essential for the maintenance of homeostasis, and this optimum may vary according to life stage, general state of health, and genotype. Nutrigenetic studies of different Se levels, in the presence of genetic variants in selenoproteins, suggest that an effective dietary Se intake for one individual may be very different from that for others. However, we are just starting to learn the significance of various genes in selenoprotein pathways, functional variants in these, and how to combine such data from genes into pathways, alongside dietary intake or serum levels of Se. Advances in systems biology, genetics, and genomics technologies, including genetic/genomic, epigenetic/epigenomic, transcriptomic, proteomic, and metabolomic information, start to make it feasible to assess a comprehensive spectrum of the biological activity of Se. Such nutrigenomic approaches may prove very sensitive biomarkers of optimal Se status at the individual or population level. The premature cessation of a major human Se intervention trial has led to considerable controversy as to the value of Se supplementation at the population level. New websites provide convenient links to current information on methodologies available for nutrigenetics and nutrigenomics. These new technologies will increasingly become an essential tool in optimizing the level of Se and other micronutrients for optimal health, in individuals and in population groups. However, definitive proof of such effects will require very large collaborative studies, international agreement on study design, and innovative approaches to data analysis.

Potential pitfalls of health claims from a public health nutrition perspective

The European Union is implementing a new regulatory framework for nutrition and health claims (HCs) that will greatly impact the communication of health messages on foodstuffs. In particular, approved HCs will be included in a positive register of generic claims. In the currently available literature, assessment of the relevance of HCs has mainly been related to scientific substantiation, and the issue of relevance in terms of public health has tended to be overlooked. Interestingly, the new regulation states that claims must be well understood by the average consumer. This article delves beyond the issue of scientific substantiation of claims and reviews possible discrepancies between consumer perception/understanding of HCs and the public health nutrition reality, which can confuse or mislead the consumer and ultimately impact public health nutrition. Six pitfalls are described herein and a comprehensive overview of the critical examination of any HC is proposed.

Integration of risk and benefit analysis-the window of benefit as a new tool?

Foods and food components can have positive and/or negative effects on our health, resulting in benefits and risks. At present these are evaluated in largely separated trajectories. In view of assessment, management, and communication, we here propose and argue for an integrated evaluation of risk and benefit of food components and foods. The window of benefit assessment concept is described as a framework to combine thresholds and scores. The recommended dietary allowance (RDA) and the tolerable upper intake level (UL) delimit the range of intakes that should be considered sufficient to prevent deficiency, while avoiding toxicity. Within these thresholds, two additional thresholds, the lower and upper level of additional benefit (LLAB and ULAB), define the range of intakes that constitute an additional benefit. Intake within these limits should thus be protective against a specified health or nutritional risk of public health relevance. To faithfully predict outcomes and to obtain the tools that are necessary to support scientific valid evaluations, a mechanism based systems biology understanding of the effects of foods and nutrients is seen as the way forward. Ultimately this should lead to an integrated risk-benefit assessment, which will allow better management and, especially, communication, to the benefit of the consumer.

Integrating anticipated nutrigenomics bioscience applications with ethical aspects

Nutrigenomics is a subspecialty of nutrition science which aims to understand how gene-diet interactions influence individuals' response to food, disease susceptibility, and population health. Yet ethical enquiry into this field is being outpaced by nutrigenomics bioscience. The ethical issues surrounding nutrigenomics face the challenges of a rapidly evolving field which bring forward the additional dimension of crossdisciplinary integrative research between social and biomedical sciences. This article outlines the emerging nutrigenomics definitions and concepts and analyzes the existing ethics literature concerning personalized nutrition and presents "points to consider" over ethical issues regarding future nutrigenomics applications. The interest in nutrigenomics coincides with a shift in emphasis in medicine and biosciences toward prevention of future disease susceptibilities rather than treatment of already established disease. Hence, unique ethical issues emerge concerning the extent to which nutrigenomics can alter our relation to food, boundaries between health and disease, and the folklore of medical practice. Nutrigenomics can result in new social values, norms, and responsibilities for both individuals and societies. Nutrigenomics is not only another new application of "-omics" technologies in the context of gene-diet interactions. Nutrigenomics may fundamentally change the way we perceive human illness while shifting the focus and broadening the scope of health interventions from patients to healthy individuals. In resource- and time-limited healthcare settings, this creates unique ethical dilemmas and distributive justice issues. Ethical aspects of nutrigenomics applications should be addressed proactively, as this new science develops and increasingly coalesces with other applications of genomics in medicine and public health.

Consumer acceptance of nutrigenomics-based personalised nutrition

Nutrigenomics is a new and promising development in nutritional science which aims to understand the fundamental molecular processes affected by foods. Despite general agreement on its promise for better understanding diet–health relationships, less consensus exists among experts on the potential of spin-offs aimed at the consumer such as personalised nutrition. Research into consumer acceptance of such applications is scarce. The present study develops a set of key hypotheses on public acceptance of personalised nutrition and tests these in a representative sample of Dutch consumers. An innovative consumer research methodology is used in which consumers evaluate short films which are systematically varied scenarios for the future of personalised nutrition. Consumer evaluations of these films, which are pre-tested in a pilot study, allow a formal test of how consumer perceptions of personalised nutrition drive consumer acceptance and through which fundamental psychological processes these effects are mediated. Public acceptance is enhanced if consumers can make their genetic profile available free at their own choice, if the actual spin-off products provide a clearly recognisable advantage to the consumer, and are easy to implement into the daily routine. Consumers prefer communication on nutrigenomics and personalised nutrition by expert stakeholders to be univocal and aimed at building support with consumers and their direct environments for this intriguing new development. Additionally, an exploratory segmentation analysis indicated that people have different focal points in their preferences for alternative scenarios of personalised nutrition. The insights obtained from the present study provide guidance for the successful further development of nutrigenomics and its applications.

High throughput ‘omics’ approaches to assess the effects of phytochemicals in human health studies

Human health is affected by many factors. Diet and inherited genes play an important role. Food constituents, including secondary metabolites of fruits and vegetables, may interact directly with DNA via methylation and changes in expression profiles (mRNA, proteins) which results in metabolite content changes. Many studies have shown that food constituents may affect human health and the exact knowledge of genotypes and food constituent interactions with both genes and proteins may delay or prevent the onset of diseases. Many high throughput methods have been employed to get some insight into the whole process and several examples of successful research, namely in the field of genomics and transcriptomics, exist. Studies on epigenetics and RNome significance have been launched. Proteomics and metabolomics need to encompass large numbers of experiments and linked data. Due to the nature of the proteins, as well as due to the properties of various metabolites, experimental approaches require the use of comprehensive high throughput methods and a sufficiency of analysed tissue or body fluids. In this contribution, we describe the basic tools currently used in nutrigenomics studies and indicate the general requirements for future technology methodological routings.

Evidence-based management of nutrigenomics expectations and ELSIs

Nutrigenomics is a new application context for genomics technologies that focuses on the bidirectional study of genetic factors influencing host (individuals' or populations') response to diet and the effects of bioactive constituents in food on host genome and gene expression. Nutrigenomics is considered the next wave after pharmacogenomics for individualization of health interventions. However, relatively little attention has been given to the specific ethical-legal-social issues (ELSIs) and sociotechnical expectations raised by nutrigenomics research. Some of the ELSIs, such as ensuring privacy of genetic information and implications of genetic testing for health insurance and employment, may be shared across the continuum of genomic technology applications in human disease genetics, pharmacogenomics and nutrigenomics. However, there are certain aspects of nutrigenomics research that may result in unique or unprecedented ELSIs. For example, nutrigenomics has a strong focus on public health and the prevention/modification of 'predisease phenotypes' in apparently healthy individuals. Thus, in contrast to previous applications of genomics technologies, where the goal is to distinguish existing disease from absence of disease, the aim of nutrigenomics is the discernment of nuanced differences in predisease states. Moreover, there is evidence to suggest that ELSIs may be different in biomarker discovery, translational research and clinical testing stages of nutrigenomics. Ideally, ELSI research and nutrigenomics bioscience should progress in parallel and in a commensurate manner. We suggest that qualitative research methods, using a hypothesis-free approach, can be employed to gain deeper insights on complex bioethics issues that do not ordinarily lend themselves to formal hypothesis testing with the quantitative methods used in biomedical sciences.

Personalised nutrition: status and perspectives

Personalised, genotype-based nutrition is a concept that links genotyping with specific nutritional advice in order to improve the prevention of nutrition-associated, chronic diseases. This review describes the current scientific basis of the concept and discusses its problems. There is convincing evidence that variant genes may indeed determine the biological response to nutrients. The effects of single-gene variants on risk or risk factor levels of a complex disease are, however, usually small and sometimes inconsistent. Thus, information on the effects of combinations of relevant gene variants appears to be required in order to improve the predictive precision of the genetic information. Furthermore, very few associations between genotype and response have been tested for causality in human intervention studies, and little is known about potential adverse effects of a genotype-derived intervention. These issues need to be addressed before genotyping can become an acceptable method to guide nutritional recommendations.

The biological revolution: understanding the impact of SNPs on diet-cancer interrelationships

Evidence is accumulating that individual risk of neoplasia depends on complex interactions among genetic inheritance, a range of exposures both in utero and in postnatal life, and the play of chance. Knowledge of the portfolio of genetic variants that confer susceptibility or resistance to cancer is limited, and there is potential for genome-wide scans and hypothesis-driven studies to reveal novel polymorphisms and haplotypes that modify risk. There is only fragmentary evidence of the scale and nature of diet-gene interactions that modulate risk of neoplasia, but it seems probable that such interactions will play a significant role as they do in other complex diseases including cardiovascular disease and type 2 diabetes. All existing evidence about diet-gene interactions and cancer risk comes from observational studies, and it will be necessary to undertake intervention studies to test the hypotheses generated by epidemiologic investigations. Because it is very unlikely that primary cancer will be an endpoint in dietary intervention studies in the foreseeable future, development of robust surrogate endpoints is a high priority. Emerging biological science using epigenomics, proteomics, and other molecular technologies appears to offer novel approaches to the discovery and validation of surrogate endpoints.