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REVIEW ARTICLE |
1 From the Nutrition Unit, Department of Clinical Medicine, Trinity College, Dublin, Ireland (MJG, MW, and HMR); the Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, University College, Dublin, Ireland (LB); the Department of Nutrition, University of California, Davis, CA and the Nestle Nutrition Research Centre, Lausanne, Switzerland (BG); and the TNO Quality of Life, TNO Voeding, Zeist, Netherlands (BvO)
2 Supported by the Irish Research Council for Science, Engineering, and Technology (postgraduate studentship to MW); the Health Research Board, Ireland (LM); an EU funded Integrated Project (Lipgene; www.lipgene.tcd.ie; principal investigator awards to MJG and HR); the Wellcome Trust New Blood Fellowship Programme (HR); an EU funded Network of Excellence (NuGo; www.nugo.org; directorship to BvO); and the Center for Childrens Environmental Health & The CHARGE Study University of California, Davis (grant P01 ES11269 to BG). 3 Reprints not available. Address correspondence to MJ Gibney, Nutrition Unit, Department of Clinical Medicine, Trinity Health Science Centre, St Jamess Hospital, Dublin 8, Ireland. E-mail: mgibney{at}tcd.ie.
| ABSTRACT |
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Key Words: Metabolomics metabonomics nutrigenomics metabolic pathways pattern recognition metabolic profiling
| INTRODUCTION |
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The 2 biggest challenges for metabolomics in human nutrition center around the vast output of spectral data on compounds in biofluids, which are generated by advanced 1- or 2-dimensional MS and NMR technologies (Figure 1
). The first challenge must be to identify all the chemicals in different biofluids that are linked to the human nutrition metabolome, and the priority must be to gain a consensus for the definition of a metabolome in human nutrition. The second biggest challenge associated with the large NMR and MS outputs is how to work with these large total data-capture data sets in which many compounds remain unidentified. Pattern-recognition techniques can be used to work with these partially resolved data sets and, thus far, have been very successful in identifying the metabolic signatures of many phenotypes. The extension of this technology to human nutrition offers enormous potential. These are the core issues of this review, which also includes discussions on other related areas such as the value of different biofluids in nutritional metabolomics, the issues of nonnutrient chemicals and large-bowel metabolites, and the linkage of metabolomics with the wider elements of nutrigenomics.
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Thus, a major initiative of the NIH roadmap is the construction of libraries of small molecules and their chemistry (5). As part of this initiative, the Molecular Libraries Screening Center Network was established, a new chemoinformatics database was constructed (9), and a plan for the development of better analytic platforms was established. Initially, PubChem will build up data on 500 000 chemicals. Many of these chemicals will be used in the rapidly expanding field of small-molecule microarrays for drug discovery (10). This technology allows for small molecules to be immobilized onto a variety of slides, which can then be used to sequester compounds that have a binding affinity with the small molecule. In the plant sciences, a new initiative to create a publicly accessible library of indexes on mass spectra and retention times has been established (8). The Standard Reference Database of the National Institute of Standards and Technology will also be valuable in this regard (11). The challenges for the nutrition sciences will be to create a consensus of small molecules that are important for the study of metabolomics and then to create the standards needed for their identification with MS, NMR, and other emerging technologies.
This then begs the question of how we might create a list of nutrients and metabolites that might populate the ideal metabolome. Recently, the enzyme classification number mapping of metabolically active enzymes to metabolic pathway and to genome data (12, 13) was carried out. In one study, the HumanCyc database was used to assign 2709 human enzymes to 135 predicted metabolic pathways (12). Many metabolites will exist in signaling, receptor binding, translocation, and other reaction pathways. However, it must be possible to begin to list the key metabolites of the various metabolic pathways that nutrients are involved in and to begin to build up a library of compounds that particularly interest nutritionists. A first priority must be to analyze the carbohydrate, fat, protein, and energy metabolism pathways along with the mineral, trace element, and vitamin metabolism pathways. These pathways will involve anabolic and catabolic pathways as well as transport and transformation pathways. Subsequently, we will need to address reproductive, inflammatory, satiety, and other such pathways as well as tissue-specific pathways, signaling pathways, and cell regulatory pathways. In all these endeavors, consideration must be given to their relevance in human nutrition.
Pattern-recognition techniques and their application to human nutrition
The large data sets produced with the use of metabolomic analyses in pharmacology and toxicology have been used to identify compounds that differ between 2 treated groups, similar to the uses described in the previous section, and they have also been used for the recognition of an overall pattern of NMR or MS spectral output but not for the recognition of specific compounds. In metabolomics, this pattern recognition is achieved through the use of principal component analysis, which is unsupervised, and with the use of partial least-squares discriminate analysis, which is supervised and separates classes of individuals or animals. To date, pattern-recognition techniques have been used in metabolomics research to successfully separate case and control subjects for cardiovascular disease (1), for multiple sclerosis (14), for hypertension (15), for epithelial ovarian cancer (16), for the detection of inborn errors of metabolism (17), for species of animals (18), for strains of animals within a species (19), for animals treated with drugs (3) or fed different diets, for humans fed different diets (20), or for humans from disparate geographic locations (21, 22). This application of metabolomics may have great potential in nutrition research, but the issues raised in ensuing parts of this review that relate to the nonnutrient elements of human foods will need to be factored in when comparing different diets. If these effects can be either eliminated or controlled for in some way, then pattern-recognition approaches offer enormous opportunities for the identification of the metabolic signatures of different diets. If a protocol for linking NMR or MS metabolomics to phenotypes can be established and annotated to an international standard, and if corresponding databases are created and made publicly available, then the science of human nutrition will experience a giant leap. So great is that potential leap, that testing the validity of this hypothesis is worth thorough and collaborative efforts. Thus, any expert group that sets out to define a consensus on the nutritional metabolome, as described in the previous section, should also be charged with setting up the standards that will allow the creation of databases that link metabolomes to phenotypes.
In pharmacology and toxicology, a major international collaborative project (the Consortium on Metabonomics in Toxicology) is underway to fully characterize the NMR-derived metabolomes of selected rat and mouse strains that were exposed to 150 drug-development compounds of interest (19). A similar initiative in human nutrition is clearly worth exploring. Notwithstanding the fact that the pattern-recognition element of metabolomics works with both the knowns and unknowns in the large NMR and MS outputs, in ensuing sections we discuss that in human nutrition we must ensure that pattern recognition does not confuse the strong effects of nonnutrients in the diet with those of the nutrients we wish to study and that the significant effect of all exogenous and endogenous factors that may influence the metabolome under question are taken into account (Figure 2
).
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Finally, we need to consider the chemical transformation of the food matrix after foods are cooked or digested. This brings animal food into consideration as sources of significant nonnutrient signals. In one study, concentrations of heterocyclic amines, which are produced when meats are grilled, were found to increase 1438-fold in urine on the day after grilled beef was eaten and returned to baseline concentrations within 4872 h after the cessation of meat intake (33). These compounds have also been detected in the urine of human volunteers who were fed a single meal of grilled chicken; in this study, most of the target metabolites were excreted within 12 h of the test meal, and very low concentrations were found at hour 18 (34). Clearly, careful chronic dietary interventions could be undone by the acute ingestion of different foods the evening before final biofluid samples are taken. Thus, dietary nonnutrients, which may not be important in pharmacology or toxicology, may be critically important in human dietary studies that seek to use metabolomics. A major consensus decision for the field of nutritional metabolomics will be how to address endogenous human metabolites and exogenous components of food that coexist at least transiently in human biofluids.
The microbiome
The gut microflora is often associated only with the large bowel, but, depending on the biofluid in question, the roles of the oral microflora and of gastric colonization by Helicobacter pylori may also need to be factored into nutritional metabolomics. Notwithstanding that caveat, most of our data relate to the large-bowel microflora. Healthy humans have
400500 microbial species in their large bowel that can directly deliver compounds from their metabolome, which are absorbed and either contribute to human metabolism (such as amino acids, vitamins, and energy substrates) or are not considered metabolically important. Regardless of their diverse origin, metabolites can be broadly classified as being either endogenous (from directly regulated reactions) or xenobiotic (not directly involved in metabolic function). However, because of the various interactions from entities such as the gut microflora, intermediate categories of metabolites have been proposed (35). These intermediate classes of metabolites have been categorized as symendogenous compounds, symxenobiotic compounds, and transxenobiotic compounds. The microflora can change constituents in food and make them available to themselves or to the host for additional metabolism. For example, microbial enzymes hydrolyze soy isoflavones to release aglycons, daidzein, genistein, and glycitein. These compounds may be absorbed as such and contribute to the metabolome or may enter the microbial metabolome for conversion to the following other compounds: daidzein to equol or to O-desmethylangolensin and genistein to p-ethyl phenol (35). These in turn can then enter the host metabolome. Perhaps these less defined and facile reactions are partly responsible for idiosyncrasies that are observed in response to a diet. It has been proposed that regulated metabolic pathways do not truly exist for xenobiotics, and this can result in various metabolic fates or endpoints. Major metabolites stem from reactions that have a high probability of occurring whereas micrometabolites stem from reactions that have a lower probability of occurring (35). Metabolomic studies in rat urine have shown very marked differences between rats with a germ-free status and rats with a conventional status (36). However, whereas large differences between the total absence of a gut microflora and its presence might be expected in urinary metabolomes, exactly how diet-related changes in the composition of the gut microflora of humans influence the metabolomic profiles of his different biofluids remains to be determined.
Which metabolome?
Having considered these various potential confounding factors in human nutrition metabolomics, the available biofluids and what role they might play in the field are worth considering. Blood, urine, and saliva are the most likely sources of biofluids for human metabolomics. Fecal water offers an opportunity to study gut microflora metabolomics but must be treated cautiously because this biofuluid cannot indicate the metabolites from the large-bowel microflora that are actually absorbed by the host. Obtaining other metabolomes (eg, cerebrospinal fluid, liver, gut, or muscle biopsy specimens) is more invasive, but we can anticipate the use of such tissues, as well as the use of cultured human cells such as peripheral blood mononuclear cells or fibroblasts, for metabolomic studies. Nonetheless, the 3 main biofluids that will probably be used in nutritional metabolomics are saliva, blood, and urine.
Saliva is not widely used in human nutrition research, but a case for its inclusion in nutritional metabolomics can be made. Saliva is a readily attainable biofluid that is rich in hormones such as 17-OH progesterone, testosterone, estradiol, and free cortisol (37). Its fatty acid composition has been used as a biomarker of plasma arachidonic acid (38), and it has been extensively studied for its antioxidant capacity (39). Although saliva has not been used in metabolomic studies, its potential for distinguishing between metabolic profiles and for monitoring changes in metabolic profiles induced by diet would be worth exploring. Both serum and plasma will undoubtedly be used for nutritional metabolomic analyses, but they will yield very different NMR and MS spectra because of the large number of small molecules that are released in the clotting process, which gives rise to serum. The nature of the anticoagulant used when the plasma samples are obtained may also have an effect on the metabolomic analysis.
A major difference between urine and plasma is the ratio of metabolites (signal) to nonmetabolites that are derived from plant food phytochemicals and chemicals that arise from cooking (noise); urine has a higher level of noise than does plasma. Blood is a rich source of nutrients and metabolites that are in transit from one organ to another. These metabolically active compounds are retained in blood as much as possible and only spill over into urine when their concentrations in plasma rise and exceed the relevant renal threshold. In contrast, the diet-derived nonnutrient compounds that are not involved in metabolism are rendered more polar to decrease their renal threshold, which favors their entry into urine. The major function of urine is to dispose of unwanted compounds in the body; consequently, the concentration of nonnutrient compounds is usually higher in urine than in plasma. In the study of the acute effects of onion ingestion on quercitin metabolism, 11 quercitin metabolites unique to urine were found, whereas only 5 quercitin metabolites were unique to plasma (28). Thus, if the objective is to study the direct effect of dietary intervention on the urinary metabolome, then a relative enrichment of urine in nonnutrient compounds represents an increase in noise. A second major difference is that lipid-soluble compounds can exist in plasma but not in urine. Urine, however, has become a major biofluid of choice in pharmacologic and toxicological metabolomics and, thus, is also likely to be of major importance for many nutritionists.
These examples point to the necessity of standardizing the application of metabolomics in nutrition studies, at least in terms of sample collection and preparation and of standardization of fluids, times, volumes, and processing aids. The use of databases for comparison of dietary or other treatment groups and the identification of discriminating metabolites makes sense only if certain minimal criteria are met for all elements of the data collection. Several initiatives are being undertaken to standardize approaches (40-42). Such standardization has been established for the application of metabolomics to plant sciences (43).
Adjusting metabolomic profiles for the experimental input
Toxicological and pharmacologic studies apply an external compound, drug, or toxin and then measure the effects on metabolomic profiles. However, the drug or chemical and their metabolites should not, as signals, be confused with the metabolic consequences of the signal and are normally deleted from the metabolic profile. From the limited number of animal studies that have used single nutrients as metabolic inputs (signals), such as ascorbic acid in metabolomics research, a similar approach of signal correction has been applied (44). Although the principle of correcting for the spectral effect of the test nutrient is possible for compounds such as vitamin C or folic acid, this correction will not be possible in nutritional studies that involve complex mixtures of nonnutrient small molecules. For example, a study of the differences between the effects of soy protein and the effects of cow milk protein will show very different urinary metabolomes, and the frequently used statistical techniques, which involve megavariate analyses, will show a significant separation of the 2 treatment groups. Will this difference be due to the metabolic consequences of differences in amino acid compositions, to differences in the metabolic effects of soy- or milk-derived peptides, or simply to the appearance of soy phytochemicals in biofluids?
Another example of the problems or challenges we face in nutrition is when removing the direct effect of the input is not feasible. The addition of fatty acids to a diet will lead to their incorporation into a metabolic pool of fixed size, such as in a pool of phospholipids, and will lead to the displacement of some fatty acids that are already present therein. In other instances, metabolic pools will resist change, eg, pools of ionizable calcium in plasma or pools of any mineral or trace elements in plasma. Finally, for complex dietary interventions, such as altering the intake of fruit and vegetables, the deletion of signal noise will be impossible with nonspecific techniques such as NMR and will only be possible with selective techniques such as MS.
Linking metabolomes with cell regulatory processes
The tendency exists to think that the connection of one gene to one transcript to one protein to specific metabolites can be universally applied and that through a systems biology approach, which integrates all connections, we will eventually obtain a qualitative, quantitative, and probabilistic overview of biological processes. Metabolism, however, is dynamic, and measurements of the flux of metabolites through metabolic pools, perhaps for very narrow or focused metabolomes (eg, the folate metabolome), will somehow need to be measured with the use of stable isotopes (45-47). Even with a comprehensive set of transcriptomic and proteomic data with some elements of dynamic measures, linking metabolites back to proteins and genes will not be simple. Cells operate many sensory, regulatory, and compensatory systems that regulate the flux of metabolites through pathways without involving hormonal or endocrine signals, and although these pathways are known, the exact sensor remains unclear (48). AMP-activated protein kinase is uniquely sensitive to the ratio of AMP to ATP in cells, whereas amino acids are positive regulators of mammalian target of rapamycin kinase, which regulates cell size. Recently, a direct effect of metabolic cofactors on gene expression has been discovered, but this effect does not involve any of the normal signal transduction pathways (12). A series of metabolic-related enzymes, which are named metabolic transcription factors, act independently of their catalytic properties and in direct association with enzyme cofactors such as ATP, NAD, NADP, FAD, and S-adenosylmethionine and appear to be key in the regulation of gene expression. For example, S-adenosylmethionine in association with histone methyltransferases regulates histones, and arginine 82 requires ATP binding to modulate the arginine- and phosphate-responsive gene transcription factor. Clearly, metabolic function does not necessarily lead to gene expression through hormones or through signal transduction pathways, which is an important fact for systems biology.
Metabolomicsnutrition compared with pharmacology and toxicology
Experimental pharmacology and toxicology differ from human nutrition in 3 major respects with regard to metabolomics. First, much of the research in pharmacology and toxicology is conducted in laboratory animals that are genetically and nutritionally more homogeneous than are humans. Second, experiments in both pharmacology and toxicology involve the direct administration of a xenobiotic at a dose that is intended to have an effect on metabolism. Finally, major metabolic signals that act in concert on the pathologic regulation of the disease have a profound effect on the human metabolome and will affect the application of metabolomics in clinical medicine for the detection of diseases, such as cardiovascular disease or multiple sclerosis. Because of these differences, the signal-to-noise ratio will be higher in pharmacology and toxicology research than in human nutrition research. Thus, it is clear that, in human nutrition research, a great effort should be made to maximize the accuracy and precision of metabolite measurements to ensure that the data obtained maintain the biological information that underlies the phenotype variations of interest. The field will need this level of accuracy to understand the separate effects of drugs, food supplements, stress, physical activity, body composition, age, sex, colonic flora, and reproductive factors.
| CONCLUSIONS |
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| ACKNOWLEDGMENTS |
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| REFERENCES |
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