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Nutrigenomic Approach

Nutrigenomic Approach

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Blackwell Publishing LtdOxford, UKOBRObesity Reviews1467-7881© 2007 Queen’s Printer and Controller of HMSO; published with permission;

Journal compilation © 2007 The International Association for the Study of Obesity? 20078••7781Review ArticleNutrigenomic approaches for obesity research R. M. Elliott & I. T. Johnson

obesity reviews

Nutrigenomic approaches for obesity research
R. M. Elliott and I. T. Johnson

Institute of Food Research, Colney, Norwich, UK

Keywords: Genetics, genomics, nutrition, obesity.

Accepted 27 November 2006

Address for correspondence: Dr RM Elliott and Professor IT Johnson, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK. E-mail: ruan.elliott@bbsrc.ac.uk; ian.johnson@bbsrc.ac.uk

OnlineOpen: This article is available free online at www.blackwell-synergy.com

obesity reviews (2007) 8 (Suppl. 1), 77–81

Background
At the individual level, weight gain is essentially the result of energy intake exceeding expenditure for significant periods of time, but this obvious truth provides no insight into the strategies needed to deal with the ever-increasing problem of obesity in Western populations. It is equally obvious, however, that certain individuals are more prone to developing obesity than others. This phenomenon invites the nutrition research community to explore the physiological basis for such differences and ultimately to design more targeted and personalized approaches to the control of body weight (1). Novel research strategies are required to understand the molecular mechanisms controlling energy balance. In parallel with such studies, there is still much to be learned about the metabolic consequences that follow when an appropriate energy balance is not maintained, and how this relates to risks of diseases such as hypertension, heart disease, stroke, diabetes and certain cancers. The developing fields of nutrigenetics and nutrigenomics, with their accompanying battery of high-throughput technologies, provide an unprecedented opportunity to cope with the complexity of this condition and to develop the knowledge base required.

interactions). Although the term ‘nutrigenomics’, in its broadest sense, encompasses nutrigenetics, more commonly the main focus of nutrigenomics is considered to be on how diet regulates gene function (transcription and translation) and metabolism (i.e. diet → gene interactions) (2).

Nutrigenetics and obesity
Genetic differences play an important role in the development of obesity, although it is clear that these are by no means the only contributing factors. Environmental and social factors are also very important. The relative contributions of genetic and socioeconomic factors to the development of obesity, and the ways in which these interact in human societies, are largely unknown. The genetic code (DNA sequence) carried by any two unrelated people is approximately 99.9% identical. It is the variation in the sequence of the remaining 0.1% that determines the genetic component of inter-individual differences in disease risk, and presumably also their differing responses to the nutritional environment. Sites in the DNA where the sequences of individuals differ commonly (e.g. in at least 1% of the population) are called polymorphisms; the most common form being a single letter change in the code termed a ‘single nucleotide polymorphism’ (SNP). As each cell contains two copies of every gene (except those present on the sex chromosomes), one individual may carry various combinations of a polymorphism. The term ‘genotype’ refers to the combination of sequences in the two copies of a gene for a particular polymorphism.

Terminology: nutrigenetics and nutrigenomics
The term ‘nutrigenetics’ is generally used to refer to the impact of genetic variation on optimal dietary requirements for an individual (i.e. in the simplest terms: gene → diet

This paper was commissioned by the Foresight programme of the Office of Science and Innovation, Department of Trade and Industry © 2007 Queen’s Printer and Controller of HMSO; published with permission Journal compilation © 2007 The International Association for the Study of Obesity. obesity reviews 8 (Suppl. 1), 77–81

77

M. Transcriptomics is performed using microarray technology.org/) (5). syndromes of obesity because of single-gene mutations have been described for at least 10 different genes. markers and chromosomal regions that have been associated or linked with human obesity. A set of such associated SNPs is termed a ‘haplotype’ and it turns out that most chromosome regions have only a few common haplotypes. some combinations of genotypes may interact to enhance or reduce risk to a greater extent than the sum of the effect of each genotype considered in isolation. However. More limited work has been performed with samples from human subjects. appears a truly daunting task. However. characterizing all the genes involved in obesity. obesity reviews 8 (Suppl. Appropriate study design and improved statistical approaches will be vital (8–10). and the fact that many more may yet be identified. bringing together the large and well-defined cohorts of human subjects that have already been established. This potential is now starting to be realized. rather than inevitably leading to severe and intractable weight gain. For example.18). Their effects are more difficult to detect reliably in a diverse population with varied lifestyles.edu/) (3). most notably appetite. proteomics and metabolomics) in nutrition has been reviewed extensively (12–16). and the avoidance of false positives. 1). So. such syndromes are extremely rare and therefore of limited relevance to the majority of obese individuals. Ultimately. Some regional differences in gene expression within different fat depots have been described and a number of studies have examined the effects of weight loss/caloric restriction on patterns of gene expression in adipose tissue from obese subjects (19). that influence the development of obesity. which enables the transcript levels for many tens of thousands of genes to be studied simultaneously. the history of genetic association studies addressing subtle and complex associations indicates that the reliable detection of true associations. while a chromosome region may contain many SNPs. it is possible that analysing only a few ‘tag’ SNPs can provide most of the information on the pattern of genetic variation in that region. To date. In spite of the rapid pace of technical developments. and more are added to this list with each update (http://obesitygene. some recent developments help to make this work more feasible. will continue to be a significant challenge (6. Preliminary studies have also been performed on the patterns of gene expression in regions of the human brain that are known to show differential responses to nutritional stimuli in obese vs. published with permission Journal compilation © 2007 The International Association for the Study of Obesity. the effects of each polymorphism are more subtle. this type of work will require studies involving very large numbers of human subjects. and to their contributions to key processes. This scale currently still exceeds the capacity of the new platform technologies. Nutrigenomics and obesity The potential impact of functional genomic approaches (transcriptomics. particular combinations of genotypes may cancel each other out. There are currently more than 600 genes. interactions between genotypes for obesity-linked genes may be important. but SNPs that are located close together in the DNA sequence on the same chromosome tend to be inherited together. revealing characteristic and tissue-specific alterations in the expression of genes involved in adipogenesis. This technology is ideally suited to the study of the metabolic syndrome and the associated inflammatory signals that underlie many of the comorbidities linked to the obese state.78 Nutrigenomic approaches for obesity research R. Second. Microarrays have been used to define the changes in patterns of gene expression at the level of RNA in the adipose and other tissues of different strains of lean and obese mice. Johnson obesity reviews The most recent update of the human obesity gene map emphasizes just how complex the genetic component of obesity alone is. First. These types of studies provide a much broader perspective on the effects of obesity than was possible before the development of microarrays and a wealth of new information and research leads.7). These include the development of technologies capable of parallel genotyping analysis for hundreds of thousands of SNPs from a single small blood or tissue sample (4). with the publication of an increasing flow of nutrigenomic studies each giving new mechanistic insights. Department of Trade and Industry © 2007 Queen’s Printer and Controller of HMSO. a more comprehensive and focused programme will be required to obtain a robust overview for the changes in gene expression related to obesity and their biological significance in relation to health.pbrc. lean individuals (20). Given the number of genes implicated so far. It is estimated that there are about 10 million SNPs in human populations. The effects of the common genetic polymorphisms associated with ‘sporadic’ obesity at the population level are much harder to study for two main reasons. inflammation and gluconeogenesis (17. generally modulating the risk of developing obesity by perhaps a few percent. However. 77–81 . T. There is therefore an obvious need to promote new international collaborations. These cases provide immensely valuable insights into the roles of these genes.hapmap. Alternatively. let alone examining their possible interactions. to achieve the study power necessary (11). Transcriptomics The transcriptome is the complete collection of RNA transcripts produced from the DNA in a genome. This paper was commissioned by the Foresight programme of the Office of Science and Innovation. Defining these haplotype blocks and the most reliable tag SNPs are the goals of the International HapMap Project (http://www. Elliott & I. Realizing these goals will help to bring the complexity of genetic studies down towards a level that may be manageable.

obesity reviews Nutrigenomic approaches for obesity research R. Refinements to these data capture systems are likely to include appropriate data-quality metrics and specialty-specific metadata. Epigenetic marks have recently been shown to change in response to environmental factors over an individual’s lifetime (32). both as causes and possible consequences of obesity. These approaches have already been demonstrated to be sensitive enough to detect the often subtle effects of dietary modification. http:// www. tic/classification analyses. both between individuals with differing susceptibilities to chronic weight gain. etc. It is ideally suited. Before this concept can be developed further. The use of protein expression patterns as ‘biomarkers of vulnerability’ to obesity-related diseases such as colorectal cancer is one approach (22).). As the massive task of mapping the human epigenome progresses. and is the newest of the ‘omic’ technologies.g.nugo. the absence of the full range of identified metabolites limits the biological interpretation of the data. M. physical activity and gut microflora) has to be defined. The next challenge is to develop tools to integrate the different types of data and start to realize the vision of nutritional systems biology. it has proven possible not only to obtain lists of gene products and metabolites that change in response under defined conditions but also to gain insights into the overall biological processes involved. The challenges and potential of nutrigenomics and nutrigenetics The potential of nutrigenomic and nutrigenetic approaches is starting to be realized. A great deal of progress has already been made and. by applying new analytical tools to the data already generated. gender. Standardization of data capture for microarray studies has already been addressed (33) and equivalent procedures are in development for proteomic and metabolomic studies (34. an organ. Studies relating directly to the physiology and biochemistry of obesity have examined patterns of protein expression in adipocytes during differentiation (23. rather than drown in the flood. For example. the influence of potential confounding factors (e.24). The mass spectrometry and nuclear magnetic resonance techniques that are used to analyse the composition of these fluids are capable of very high sample throughput at comparatively low cost (after the initial set-up of the machinery). or in body fluids. including all subsequent modifications that the proteins may undergo. Continuing development of improved statistical and bioinformatic tools means that the conclusions of the data analyses are becoming more robust and sensitive. and within individuals who are undergoing significant changes in body weight and adiposity (28. Department of Trade and Industry © 2007 Queen’s Printer and Controller of HMSO. This can be defined as the study of heritable epigenetic signals. While these profiles may be used with multivariate statistical tools for diagnos- This paper was commissioned by the Foresight programme of the Office of Science and Innovation. Not least among the many challenges are the needs for quality control. Johnson 79 Proteomics The proteome is the full complement of proteins produced from the transcriptome.org) is working to identify bottlenecks and emerging technical requirements and seeking solutions to them. The ‘omic’ tools produce vast quantities of data rapidly. age. To date. data capture and storage of nutrigenomic and nutrigenetic data. standardization. In addition to its use in the analysis of gene expression in tissues. Another emerging challenge that may well carry implications for the development of obesity research is that of ‘epigenomics’. the European Nutrigenomics Organization (NuGO. It is therefore possible to generate large datasets very fast. proteomics has been used less extensively in nutrigenomic studies than transcriptomics but it has just as much potential (21). If we are to make use of this information. encoded in patterns of DNA methylation and histone acetylation within the chromatin. There is also increasing interest in the use of metabolomic profiles as markers of dietary habits and as a descriptor of nutritional phenotype (30). 77–81 . it will become possible to explore the role of epigenetic effects. proteomics provides a possible route for the identification and validation of new protein biomarkers that can be detected in plasma. T. The international HuPO Plasma Proteome Project is providing new resources (protein databases and optimized experimental standards) that will be essential for this kind of work (27).29). published with permission Journal compilation © 2007 The International Association for the Study of Obesity. New text-mining tools are starting to make it easier to interrogate the full body of scientific literature and thus to place new findings within the context of current scientific knowledge. both from a technical and scientific standpoint. the effects of a high-fat diet on protein expression in different target tissues in mice (25) and have compared skeletal muscle of lean and obese women (26). to the global analysis of metabolite patterns in body fluids (plasma/serum/urine. that modulate the expression of genes (31). NuGO is working with international organiza- Metabolomics Metabolomics is the study of the sum total of endogenous and exogenous metabolites in a cell. Another challenge is that present metabolomic technologies generate metabolite profiles for which the majority of signals are not immediately identified. obesity reviews 8 (Suppl.35). it is essential that the data collected are of high quality and are captured in a manner that enables them to be stored and exchanged readily. In all these areas. and should lend themselves readily to the detection of metabolic differences. ethnicity. so even identical twins may ultimately develop differing susceptibilities to adverse environmental factors. Elliott & I. 1). which are comparatively easy to access in human volunteers.

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