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,3
* Nestle Research Center, Lausanne 26, Switzerland;
University of California, Davis, CA 95616;
** Nestle Purina Pet Care, St. Louis, MO 63164; and
Lipomics Technologies, Inc., West Sacramento, CA
3To whom correspondence should be addressed. E-mail: jbgerman{at}ucdavis.edu.
| ABSTRACT |
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KEY WORDS: lipomics nutrition lipids genetics metabolite
The arrival of the human genome has changed the way biological research is conducted and will soon change the way science is applied to nutrition and health. Nutrition research and its public health applications have achieved a major impact on the prevention of diseases caused by deficiencies of essential nutrients. The absolute quantitative levels of essential nutrients that are necessary in the diet to prevent these conditions have been established for the human population at various stages of growth and physiology and are the basis of population-wide surveillance and intervention (1). The diseases that are produced by a deficiency of each of these nutrients have been characterized and point-of-care diagnostics developed to recognize those individuals who are actively experiencing deficiencies (2). Finally, the risks of deficiencies of essential vitamins, minerals, amino acids and fatty acids have been successfully reduced by multinational programs of fortification, enrichment and process modification throughout the food industry, and population-wide dietary guidelines and food education programs have been aimed at the consuming public. Nevertheless, variations in food choices throughout the world continuously lead to the emergence of subpopulations at risk of deficiencies of essential nutrients emphasizing that constant personalized surveillance remains important (3).
Unfortunately, identifying nutrient deficiencies does not necessarily resolve all nutritional problems. New sets of issues associated with diet continue to emerge. Rather than diseases caused by deficiencies of essential nutrients, these new health problems are the result of dietary imbalances and the inability to control metabolism accurately within a range of lifestyles (4). Metabolic disturbances involve more than the essential nutrients; they extend to macronutrient fuels and nonessential nutrients. The rapid increase in the incidence of metabolic disorders of energy regulation, from obesity to diabetes and atherosclerosis, now includes the majority of citizens of many countries including the most developed countries of the world (5). Such prevalence has caused the public and its oversight health agencies to reevaluate all aspects of environment and lifestyle, from diet to exercise to leisure activities (6). While many common themes are emerging, scientists are agreed in one aspectno single causal agent is responsible for the problem in all persons affected (7). That is, the same diet practiced by one individual may support their health and quality of life and yet this same diet practiced by another may lead to obesity and subsequent metabolic problems compromising their quality of life. The genetic basis of these differences is being established in the newly emerging fields of genomics, nutrigenetics and nutrigenomics (8). Nevertheless, even before all of the genetic and molecular reasons that can explain the differences between individuals are discovered, it is clear that diversity of the human population is a nutritional reality. Once this diversity is realized, it becomes imperative that the problems of metabolic regulation, and their causes and interventions, will need to be personalized in order to be addressed and finally solved.
| Metabolic phenotype |
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where phenotype is the sum of all functional attributes related to health, viz., "The observable physical or biochemical characteristics of an organism."
| Genotype |
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| Environment |
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| Metabolic memory |
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| Phenotypic variation in humans |
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| Assessment strategies for personalizing metabolic phenotype |
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The principles of individual cholesterol measurement and action are applicable to all aspects of metabolic regulation. The basic steps are illustrated in Figure 2. Technologies for broad scale and parallel analysis of metabolites need to be developed. The technologies, once applied to large clinical assessments of populations, can produce databases that are simultaneously annotated according to various aspects of the effective phenotypes of the individuals involved. These databases provide information resources to explore the statistical relationship between concentrations of metabolites in individuals and their phenotypic outcomes. Scientists, with their access to all the tools of modern biology and genomics, will apply them to molecular, cellular or whole animal models of metabolism to establish the mechanisms that are responsible for these relationships. The knowledge that is being built from this process will become the guideposts to provide each individual actionable advice based on their own personal metabolic profile. The cholesterol program was successful for drug development but did not go far enough for foods by deciding to focus on a single metabolite and by assuming that the same mode of intervention would be successful for all individuals. Assuming that cholesterol could be acted upon in isolation was a mistake because the simple presence even of relatively high levels of cholesterol in blood does not constitute a disease. Therefore, any action designed to change cholesterol should ensure that metabolic regulation as a whole is not compromised. Various authors are beginning to argue that focusing health recommendations based solely on cholesterol has been a problem with recommending low fat diets to all individuals. While assisting many individuals to lower their cholesterol, such a dietary change precipitated a shift in metabolism that aggravated obesity and diabetes in others (22,23).
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| Assessment and health |
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The experience with cholesterol reveals the importance of measuring a larger number of metabolites as metabolism assessment rather than a single biomarker or subset group of biomarkers as disease risk. While measuring cholesterol per se can provide a quantitative estimate of disease risk in a population and an individual, the simple measurement of cholesterol does not provide sufficient information to deduce why that individual accumulated the cholesterol nor does it suggest the appropriate intervention to resolve the problem. As an example, cholesterol can be high in the blood of an individual due to several mechanisms, but three are illustrative: 1) the individual can absorb cholesterol inordinately well through the intestine, or 2) they can produce too much through endogenous biosynthesis, or 3) they can fail to convert cholesterol to bile acids sufficiently. The measurement of total blood cholesterol does not distinguish these three, but if the analytical measurements are simply expanded to include more sterol metabolites, it is possible to obtain sufficient information. Those who absorb excessive cholesterol absorb both cholesterol and phytosterols more than the average individual (24), and the levels of phytosterols in plasma reflect absolute absorption of sterols from the intestine. Individuals who hyperabsorb can be distinguished by including the quantitative analysis of phytosterols in cholesterol measurements. For these individuals, an intervention strategy that targets intestinal absorption of cholesterol is appropriate (25). Those individuals who produce excessive quantities of cholesterol via endogenous biosynthesis have increased levels of mevalonic acid in plasma as a direct quantitative reflection (26), and for these individuals, inhibitors of cholesterol biosynthesis are more appropriate. Finally, the causal mechanisms of insufficient bile acid conversion are detected in those individuals by the amounts of 7alpha-hydroxy-4-cholesten-3-one in plasma (27).
| Comprehensive metabolomic analysis of plasma lipids |
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The technologies that are available to address most of the metabolite classes are equally as available as those for fatty acids and complex lipids. Thus, no significant technological hurdle stands in the way of using these technologies to assemble metabolite databases of humans and experimental animals for amino acids and small peptides, sterols, organic acids, sugars and alcohols, vitamins, nucleotides, etc. So long as the data are qualitative and quantitative, such data from various human and animal investigations are directly comparable, i.e., capable of producing legacy databases and appropriate for subsequent data mining. Studies conducted in separate laboratories, using entirely different analytical technologies years apart, will produce directly comparable data if the data are qualitative and quantitative. These data are thus analytical platform independent, and as the technologies needed for higher throughput are developed, they will build upon existing databases and not obsolesce them. An obvious consideration that such an approach raises is the importance of annotating subjects and animals that are the sources of the metabolic data. It will be possible to relate metabolism only to those physiological, health and behavioral endpoints that are measured coincident with the metabolic data. Researchers should be considering how to convert these endpoints to quantitative and comprehensive analyses to improve the ability of bioinformatics to mine the relationships between endpoint and metabolism. Rather than simply bias the outcome by including only disease endpoints, the databases should include multiple biologic (physiological, neurological, genetic, anatomical, etc.), behavioral, cognitive and other dimensions of health that can then be used for examining specific hypotheses, and perhaps more importantly, for generating new hypotheses in a wide range of health.
| Bioinformatics of metabolite profiles |
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A next step for integrating nutrition is to annotate the metabolome in order to relate changes in metabolites within specific pathways to genetic and environmental influences. The science is in many cases already well underway and only needs to be applied to this annotation task. For example to annotate the products of lipid metabolism, each metabolite and its absolute amounts in biofluids would be linked to mechanistic information about the various endogenous and exogenous inputs that alter its level in these same biofluids. The absolute amount of arachidonic acid is an example of a metabolite that illustrates the extent of the scientific information that already exists to annotate the biology of this molecule as a part of the metabolome. The dietary, genetic, hormonal, pharmacologic and toxicologic influences on gene expression of the lipid metabolic enzymes that produce and remove arachidonic acid have been studied from various perspectives. Growth hormone stimulates the expression of the delta 5 and delta 6 desaturase enzymes and growth hormone leads to increased abundance of the metabolic products of these enzymes, including arachidonic acid (36,37). Pharmaceutical intervention data will also be useful in these same annotations and again, such information has been the subject of pharmaceutical research. To continue using the same example of arachidonic acid, statin drugs affect the delta 6 and delta 5 desaturase enzymes that produce arachidonic acid causing a preferential increase in delta 5 desaturase (38). The effects of environmental toxicants on the metabolites and the pathways that produce them will provide further annotation information. Once again, many studies have produced data on the effects of toxins on arachidonic acids metabolic pathways as illustrated by the research demonstrating the effects of PCBs on inhibiting the desaturase enzymes and reducing arachidonic acid levels in plasma (39).
Software tools will need to be developed to examine metabolites in a broad scope rather than as individual biomarkers. A first generation approach has been developed for lipid metabolites (28). This approach uses a straightforward calculation and visualization tool adapted from gene array analysis tools to take advantage of the growing familiarity of scientists with such three-dimensional visualization strategies. Visualization algorithms can be used to present fatty acid data quantitatively according to various criteria of lipid family, lipid class, tissue of origin and metabolic origin. The format of difference maps enables scientists to examine differences between samples across as many criteria as possible. Informatic software can visualize quantitative differences in various formats, such as color coding of changes between samples much as is used to advantage in visualizing gene array data. Additionally, extensive bioinformatic efforts will continue to target metabolic data via statistical clustering and quality analyses and ultimately will directly link metabolic pathways to all other phenotypic determinants as systems biology (40,41,42).
| Examples of metabolic analysis and interpretation |
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A number of studies have now taken steps to observe the metabolic consequences of diet using omic approaches (43,44,31,45). In one study, the effects of PUFA, either alone or in combination, were studied using a combined genomicmetabolomic approach (31). This study showed clear evidence of both correlated gene function and lipid metabolite level, as well as other instances of disconcordance, where apparent gene expression changes were not reflected by predicted changes in lipid metabolites. Both cases are interesting, but it is the discordance that most likely points to a lack of understanding for the basic cellular and physiological controls on metabolism. New studies using a quantitative metabolic analysis combined with other omic techniques will continue to aid our understanding and complete our grasp of integrative metabolism.
The inappropriateness of relying on the traditional biomarker approach of disease diagnostics for metabolic dysregulation is shown in various recent studies. First, the use of a metabolic intervention may alter one target appropriately, but compromise metabolism elsewhere. Second, individuals may vary with respect to a particular dietary intervention. Third, the metabolic state of an individual can significantly affect the net metabolic consequences, and an individual in one metabolic state may be benefited by a particular intervention, while in another metabolic statei.e., overweightthe same intervention may be net deleterious.
The effects of alternative pharmaceutical strategies on the metabolic condition of diabesity (the comorbidities of obesity and diabesity) illustrate the problems of ignoring disparate metabolic consequences of a single intervention. The animal model (NZOxNO)F1 male mouse (46) provides a genetically modified experimental animal with many of the metabolic dysregulations of humans with these conditions. In affected animals, the three diagnostic markers typically used in humans (serum glucose, insulin and triglycerides) are all elevated at the same time that the animals become obese on specific diets. The pharmaceuticals roziglitazone, a PPAR agonist, is a successful drug for type 2 diabetes. Animals treated with high doses of roziglitazone responded with changes to the three biomarkers (glucose, insulin and triglycerides). These three biomarkers are considered to be the hallmark of a therapeutic benefit. The metabolic consequences to these animals, at the doses of roziglitazone applied, was to exacerbate hepatic lipidosis in the model. Metabolomic analysis (quantitative fatty acid analysis of all lipid classes) in liver, blood and muscle identified significant metabolic differences and highlighted the lipid metabolic abnormalities by which hepatic lipidosis was caused by roziglitazone (28).
| Summary |
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| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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2 Supported by the National Institutes of Health (DK-35747). ![]()
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