Nicholas V. Reo

NMR-BASED METABOLOMICS

ABSTRACT Similar to genomics and proteomics which yield vast amounts of data about the expression of genes and proteins, metabolomics refers to the whole metabolic profile of the cell. The focus of this report concerns the use of nuclear magnetic resonance (NMR) spectroscopy for metabolic analyses and, in particular, its use in toxicology for examining the metabolic profile of biofluids. Examples from the literature will demonstrate how 1H NMR and pattern recognition methods are used to obtain the urinary metabolic profile, and how this profile is affected by exposure to various toxicants. These particular studies which focus on the metabolic profiles of biofluids, specifically urine, are referred to as metabonomics. NMR-based metabonomics provides a means to categorize organ-specific toxicity, monitor the onset and progression of toxicological effects, and identify biomarkers of toxicity. A future challenge, however, is to describe the cellular metabolome for purposes of understanding cellular functions (i.e., metabolomics). Thus the capabilities and advantages of multinuclear NMR to provide metabolic information in cells and tissues will also be discussed. Such information is essential if metabolomics is to provide a complementary dataset which together with genomics and proteomics can be used to construct computer network models to describe cellular functions.

Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease.

Obesity is becoming the new pediatric epidemic. Non-alcoholic fatty liver disease (NAFLD) is frequently associated with obesity and has become the most common cause of pediatric liver disease. The gut microbiome is the major metabolic organ and determines how calories are processed, serving as a caloric gate and contributing towards the pathogenesis of NAFLD. The goal of this study is to examine gut microbial profiles in children with NAFLD using phylogenetic, metabolomic, metagenomic and proteomic approaches. Fecal samples were obtained from obese children with or without NAFLD and healthy lean children. Stool specimens were subjected to 16S rRNA gene microarray, shotgun sequencing, mass spectroscopy for proteomics and NMR spectroscopy for metabolite analysis. Children with NAFLD had more abundant Gammaproteobacteria and Prevotella and significantly higher levels of ethanol, with differential effects on short chain fatty acids. This group also had increased genomic and protein abundance for energy production with a reduction in carbohydrate and amino acid metabolism and urea cycle and urea transport systems. The metaproteome and metagenome showed similar findings. The gut microbiome in pediatric NAFLD is distinct from lean healthy children with more alcohol production and pathways allocated to energy metabolism over carbohydrate and amino acid metabolism, which would contribute to development of disease.

Dynamic adaptive binning: an improved quantification technique for NMR spectroscopic data

The interpretation of nuclear magnetic resonance (NMR) experimental results for metabolomics studies requires intensive signal processing and multivariate data analysis techniques. A key step in this process is the quantification of spectral features, which is commonly accomplished by dividing an NMR spectrum into several hundred integral regions or bins. Binning attempts to minimize effects from variations in peak positions caused by sample pH, ionic strength, and composition, while reducing the dimensionality for multivariate statistical analyses. Herein we develop an improved novel spectral quantification technique, dynamic adaptive binning. With this technique, bin boundaries are determined by optimizing an objective function using a dynamic programming strategy. The objective function measures the quality of a bin configuration based on the number of peaks per bin. This technique shows a significant improvement over both traditional uniform binning and other adaptive binning techniques. This improvement is quantified via synthetic validation sets by analyzing an algorithm’s ability to create bins that do not contain more than a single peak and that maximize the distance from peak to bin boundary. The validation sets are developed by characterizing the salient distributions in experimental NMR spectroscopic data. Further, dynamic adaptive binning is applied to a 1H NMR-based experiment to monitor rat urinary metabolites to empirically demonstrate improved spectral quantification.

Evidence that Plasmalogen is Protective Against Oxidative Stress in the Rat Brain

The antioxidant capabilities of phosphatidylethanolamine plasmalogen (PlsEtn), in vivo, against lipid peroxidation were investigated via acute phosphine (PH3) administration in rats. Oxidative stress was assessed from measures of malondialdehyde and various enzyme activities, while NMR analyses of lipid and aqueous tissue extracts provided metabolic information in cerebellum, brainstem, and cortex. Brainstem had the highest basal [PlsEtn], and showed only moderate PH3-induced oxidative damage with no loss of ATP. The lowest basal [PlsEtn] was observed in cortex, where PH3 caused a 51% decrease in [ATP]. The largest oxidative effect occurred in cerebellum, but [ATP] was unaffected. Myo-inositol+ethanolamine pretreatment attenuated all PH3 effects. Specifically, the pretreatment attenuated the ATP decrease in cortex, and elevated brain [PlsEtn] in the cerebellum, nearly abolishing the cerebellar oxidative effects. Our data suggest a high basal [PlsEtn], or the capacity to synthesize new ethanolamine lipids (particularly PlsEtn) may protect against PH3 toxicity.

Comparative Metabolomic and Genomic Analyses of TCDD-Elicited Metabolic Disruption in Mouse and Rat Liver

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) elicits a broad spectrum of species-specific effects that have not yet been fully characterized. This study compares the temporal effects of TCDD on hepatic aqueous and lipid metabolite extracts from immature ovariectomized C57BL/6 mice and Sprague-Dawley rats using gas chromatography-mass spectrometry and nuclear magnetic resonance-based metabolomic approaches and integrates published gene expression data to identify species-specific pathways affected by treatment. TCDD elicited metabolite and gene expression changes associated with lipid metabolism and transport, choline metabolism, bile acid metabolism, glycolysis, and glycerophospholipid metabolism. Lipid metabolism is altered in mice resulting in increased hepatic triacylglycerol as well as mono- and polyunsaturated fatty acid (FA) levels. Mouse-specific changes included the induction of CD36 and other cell surface receptors as well as lipases- and FA-binding proteins consistent with hepatic triglyceride and FA accumulation. In contrast, there was minimal hepatic fat accumulation in rats and decreased CD36 expression. However, choline metabolism was altered in rats, as indicated by decreases in betaine and increases in phosphocholine with the concomitant induction of betaine-homocysteine methyltransferase and choline kinase gene expression. Results from these studies show that aryl hydrocarbon receptor-mediated differential gene expression could be linked to metabolite changes and species-specific alterations of biochemical pathways.

The networks of human gut microbe–metabolite associations are different between health and irritable bowel syndrome

The goal of this study was to determine if fecal metabolite and microbiota profiles can serve as biomarkers of human intestinal diseases, and to uncover possible gut microbe–metabolite associations. We employed proton nuclear magnetic resonance to measure fecal metabolites of healthy children and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS-D). Metabolite levels were associated with fecal microbial abundances. Using several ordination techniques, healthy and irritable bowel syndrome (IBS) samples could be distinguished based on the metabolite profiles of fecal samples, and such partitioning was congruent with the microbiota-based sample separation. Measurements of individual metabolites indicated that the intestinal environment in IBS-D was characterized by increased proteolysis, incomplete anaerobic fermentation and possible change in methane production. By correlating metabolite levels with abundances of microbial genera, a number of statistically significant metabolite–genus associations were detected in stools of healthy children. No such associations were evident for IBS children. This finding complemented the previously observed reduction in the number of microbe–microbe associations in the distal gut of the same cohort of IBS-D children.

Relationship between total magnesium concentration and free intracellular magnesium in sheep red blood cells

The cellular free magnesium concentration of ionophore A23187 permeabilized high potassium sheep erythrocytes was measured by 31P nuclear magnetic resonance spectroscopy, and the total cellular magnesium concentration was determined by atomic absorption spectroscopy. The free versus total cellular magnesium concentrations yield a linear relationship on a log-log scale in the concentration range from 0.3 to 1.92 mmol Mg/liter cells. Thus, free intracellular magnesium concentrations can be calculated from atomic absorption data. The method permits the estimation of physiologically or experimentally induced variations of intracellular free magnesium concentrations between 7 and 405 microM magnesium in cell water. This range encompasses the free magnesium concentration of 335 +/- 60 microM in cell water determined for untreated erythrocytes.

Perfluorodecanoic acid, a peroxisome proliferator, activates phospholipase C, inhibits CTP:phosphocholine cytidylyltransferase, and elevates diacylglycerol in rat liver

Perfluorooctanoic acid (PFOA) and perfluorodecanoic acid (PFDA) are peroxisome proliferators that cause hepatotoxicity in rodents. This study shows that PFDA activates liver phospholipase C (PLC) and inhibits CTP:phosphocholine cytidylyltransferase (CT). PLC cytosolic and microsomal activities were increased 1.4- and 1.7-fold, respectively. CT activates were decreased to 58% (cytosol) and 36% (microsome) of control values. PFDA also caused a threefold increase in liver diacylglycerol (DAG) concentration. PFOA had no effect on the enzyme activities or DAG concentration. Together with previous results, these data suggest that PFDA activates a phosphatidylcholine-specific PLC causing an increase in liver phosphocholine and DAG. These effects are discussed in relation to cellular signalling processes that may provide a mechanism for PFDA-induced hepatotoxicity.

Dose–response hepatotoxicity of the peroxisome proliferator, perfluorodecanoic acid and the relationship to phospholipid metabolism in rats

Perfluorodecanoic acid (PFDA) is a potent peroxisome proliferator that causes hepatotoxicity but lacks tumor-promoting activity in rats. We previously showed that a single dose of PFDA at 50 mg/kg (approximately LD50) causes an elevation in liver phosphocholine (PCho) and other effects related to phospholipid metabolism. In this study, we examined metabolic effects in the dose range 2-50 mg/kg in rats. At doses < or =20 mg/kg, PFDA is significantly less hepatotoxic than the LD50 as manifested by electron microscopy and measurements of daily food consumption and body weight. At 50 mg/kg rat serum tumor necrosis factor (TNF)-alpha concentration was increased 8-fold, while at 15 mg/kg there was no apparent increase in this cytokine. This lower dose, however, induces metabolic effects similar to those seen at the LD50. Liver fatty acyl-CoA oxidase activity showed a dose-dependent increase from 5-25 mg/kg PFDA. Treatments at 15 and 50 mg/kg caused a significant increase in liver phosphatidylcholine (28 and 66%) and phosphatidylethanolamine (31 and 74%). Both doses caused a significant increase in liver PCho but did not affect liver ATP levels, as manifested in 31P nuclear magnetic resonance (NMR) spectra from rat livers in vivo. These data suggest that the increase in liver [PCho] observed following PFDA exposure in rats represents a specific metabolic response, rather than a broad-range hepatotoxic effect.

Studies of myo-inositol and plasmalogen metabolism in rat brain.

Plasmalogens are ether-linked phospholipids that are abundant in nervous tissues. Their biological role is unclear, but may involve membrane structure/function and antioxidant activities. This study further investigates a recent report that chronic administration of myo-inositol in rats increased brain phosphatidylethanolamine plasmalogen (PlsEtn). We examined the effects of myo-inositol administration on the incorporation of [2-13C]ethanolamine ([2-13C]Etn) into rat brain phospholipids using NMR spectroscopy. Rats received either acute myo-inositol (single dose) ± [2-13C]Etn, or chronic myo-inositol (10-day treatment) + [2-13C]Etn. Controls received saline rather than myo-inositol. Acute myo-inositol produced a 68% increase in brain [myo-inositol] and an increase in the incorporation of [2-13C]Etn into phospholipids (P < .05). The PlsEtn/phosphatidylethanolamine ratio and the [PlsEtn] were increased by 27% and 30%, respectively. The PlsEtn content as a mole percentage of total phospholipids was elevated (P ≤ .05). Acute administration of myo-inositol + ethanolamine illustrates a positive correlation between the brain [myo-inositol] and the biosynthesis of ethanolamine phospholipids, with preferential synthesis of PlsEtn.