Analysis of individual purine and pyrimidine nucleoside di- and triphosphates and other cellular metabolites in PCA extracts by using multinuclear high resolution NMR spectroscopy

Enhanced Standard Operating Procedures for 31P NMR-Based Metabolomics in Tissue Extracts

Phosphorylated metabolites, here referred to as phosphometabolites, are sufficiently abundant and widely distributed to provide a condensed representation of metabolism that can be readily accessed through NMR spectroscopy. This study addresses the challenge of precisely quantifying phosphometabolites via quantitative 31P NMR from tissue extracts. We optimized standard operating procedures for enhanced spectral resolution, signal intensity, and accuracy. By amply evaluating solvent and buffer conditions, reference compounds, and paramagnetic relaxation enhancers, we identified optimal conditions for metabolite analysis, including the use of trimethylphosphine oxide for accurate signal referencing due to its short T1 relaxation time and minimal offset and glycine buffer (in D2O) at pD 9.5, where virtually invariant 31P signal frequencies and sample osmolarities are observed, along with maximal NMR detection sensitivity and temperature stability of the pH. These methodological advancements significantly improve the reliability and reproducibility of phosphometabolite characterization, allowing the assignment of up to 60 independent signals in the one-dimensional (1D) 31P spectrum (of a total of 94 peaks), that resulted in the proper quantification of 44 phosphometabolites from different tissular samples.

Methodological Developments for Metabolic NMR Spectroscopy from Cultured Cells to Tissue Extracts: Achievements, Progress and Pitfalls

This is a broad overview and critical review of a particular group of closely related ex vivo and in vitro metabolic NMR spectroscopic methods. The scope of interest comprises studies of cultured cells and excised tissue, either intact or after physicochemical extraction of metabolites. Our detailed discussion includes pitfalls that have led to erroneous statements in the published literature, some of which may cause serious problems in metabolic and biological interpretation of results. To cover a wide range of work from relevant research areas, we consider not only the most recent achievements in the field, but also techniques that proved to be valid and successful in the past, although they may not have generated a very significant number of papers more recently. Thus, this comparative review also aims at providing background information useful for judiciously choosing between the metabolic ex vivo/in vitro NMR methods presented. Finally, the methods of interest are discussed in the context of, and in relation to, other metabolic analysis protocols such as HR-MAS and cell perfusion NMR, as well as the mass spectrometry approach.

Effects of manganese and arsenic species on the level of energy related nucleotides in human cells

Cellular adenine and pyridine nucleotides play important roles in the cellular energy and redox state. An imbalance in the cellular levels of these tightly regulated energy related nucleotides can lead to oxidative stress and thus is discussed to contribute to neurotoxic and carcinogenic processes. Here we established a reliable ion-pair reversed phase HPLC based method for the parallel quantification of six energy related nucleotides (ATP, ADP, ADP-ribose, AMP, NAD(+), NADH) in cells and subsequently applied it to determine effects of manganese and arsenic species in cultured human cells. In human lung cells, MnCl(2) (≥50 μM) decreased the levels of ATP, NAD(+) and NADH as well as the NAD(+)/NADH ratio. This reflects a decline in the cellular energy metabolism, most likely resulting from a disturbance of the mitochondrial function. In contrast, cultured astrocytes were more resistant towards manganese. Regarding the arsenicals, a disturbance of the cellular energy related nucleotides was detected in lung cells for arsenite (≥50 μM), monomethylarsonous (≥1 μM), dimethylarsinous (≥1 μM) and dimethylarsinic acid (≥100 μM). Thereby, the single arsenicals seem to disturb the cellular energy and redox state by different mechanisms. Taken together, this study provides further evidence that cellular energy related nucleotides serve as sensitive indicators for toxic species exposure. When searching for a molecular mechanism of toxic compounds, the data illustrate the necessity of quantifying several energy related nucleotides in parallel, especially since ATP depletion, redox state alterations and oxidative stress are known to potentiate each other.

Isotopomer profiling of Leishmania mexicana promastigotes reveals important roles for succinate fermentation and aspartate uptake in tricarboxylic acid cycle (TCA) anaplerosis, glutamate synthesis, and growth

Leishmania parasites proliferate within nutritionally complex niches in their sandfly vector and mammalian hosts. However, the extent to which these parasites utilize different carbon sources remains poorly defined. In this study, we have followed the incorporation of various (13)C-labeled carbon sources into the intracellular and secreted metabolites of Leishmania mexicana promastigotes using gas chromatography-mass spectrometry and (13)C NMR. [U-(13)C]Glucose was rapidly incorporated into intermediates in glycolysis, the pentose phosphate pathway, and the cytoplasmic carbohydrate reserve material, mannogen. Enzymes involved in the upper glycolytic pathway are sequestered within glycosomes, and the ATP and NAD(+) consumed by these reactions were primarily regenerated by the fermentation of phosphoenolpyruvate to succinate (glycosomal succinate fermentation). The initiating enzyme in this pathway, phosphoenolpyruvate carboxykinase, was exclusively localized to the glycosome. Although some of the glycosomal succinate was secreted, most of the C4 dicarboxylic acids generated during succinate fermentation were further catabolized in the TCA cycle. A high rate of TCA cycle anaplerosis was further suggested by measurement of [U-(13)C]aspartate and [U-(13)C]alanine uptake and catabolism. TCA cycle anaplerosis is apparently needed to sustain glutamate production under standard culture conditions. Specifically, inhibition of mitochondrial aconitase with sodium fluoroacetate resulted in the rapid depletion of intracellular glutamate pools and growth arrest. Addition of high concentrations of exogenous glutamate alleviated this growth arrest. These findings suggest that glycosomal and mitochondrial metabolism in Leishmania promastigotes is tightly coupled and that, in contrast to the situation in some other trypanosomatid parasites, the TCA cycle has crucial anabolic functions.

NMR-based metabolomic analysis of cerebrospinal fluid and serum in neurological diseases--a diagnostic tool?

We sought to evaluate the diagnostic accuracy of metabolomic biomarker profiles in neurological conditions (idiopathic intracranial hypertension (IIH), multiple sclerosis (MS) and cerebrovascular disease (CVD) compared to controls with either no neurological disease or mixed neurological diseases). Spectra of CSF (n = 87) and serum (n = 72) were acquired using (1)H NMR spectroscopy. Multivariate pattern recognition analysis was used to identify disease-specific metabolite biomarker profiles. The metabolite profiles were then used to predict the diagnosis of a second cohort of patients (n = 25). CSF metabolite profiles were able to predict diagnosis with a sensitivity and specificity of 80% for both IIH and MS. The CVD serum metabolite profile was 75% sensitive and specific. On analysing the second patient cohort, the established metabolite biomarker profiles generated from the first cohort showed moderate ability to segregate patients with IIH and MS (sensitivity:specificity of 63:75% and 67:75%, respectively). These findings suggest that NMR spectroscopic metabolic profiling of CSF and serum can identify differences between IIH, MS, CVD and mixed neurological diseases. Metabolomics may, therefore, have the potential to be developed into a clinically useful diagnostic tool. The identification of disease-unique metabolites may also impart information on disease pathology.

Characterization of breast cancers and therapy response by MRS and quantitative gene expression profiling in the choline pathway

Tumor choline metabolites have potential for use as diagnostic indicators of breast cancer phenotype and can be non-invasively monitored in vivo by MRS. Extract studies have determined that the principle diagnostic component of these peaks is phosphocholine (PCho), the biosynthetic precursor to the membrane phospholipid, phosphatidylcholine (PtdCho). The ability to resolve and quantify PCho in vivo would improve the accuracy of this putative diagnostic tool. In addition, determining the biochemical mechanisms underlying these metabolic perturbations will improve the understanding of breast cancer and may suggest potential molecular targets for drug development. Reported herein is the in vivo resolution and quantification of PCho and glycerophosphocholine (GPC) in breast cancer xenografts in SCID mice via image-guided 31P MRS, localized to a single voxel. Tumor metabolites are also detected using ex vivo extracts and high-resolution NMR spectroscopy and are quantified in the metastatic tumor line, MDA-mb-231. Also reported is the quantification of cytosolic and lipid metabolites in breast cells of differing cancer phenotype, and the identification of metabolites that differ among these cell lines. In cell extracts, PCho and the PtdCho breakdown products, lysophosphatidylcholine, GPC and glycerol 3-phosphate, are all raised in breast cancer lines relative to an immortalized non-malignant line. These metabolic differences are in direct agreement with differences in expression of genes encoding enzymes in the choline metabolic pathway. Results of this study are consistent with previous studies, which have concluded that increased choline uptake, increased choline kinase activity, and increased phosholipase-mediated turnover of PtdCho contribute to the observed increase in PCho in breast cancer. In addition, this study presents evidence suggesting a specific role for phospholipase A2-mediated PtdCho catabolism. Gene expression changes following taxane therapy are also reported and are consistent with previously reported changes in choline metabolites after the same therapy in the same tumor model.

Conditions of wound healing and cutaneous growth affect metabolic performance of skin following plastic surgery

The mechanical and structural properties of skin subjected to expansion have been widely investigated in the context of plastic surgery. To determine the actual metabolic state of skin following skin expander placement, we determined the basic biochemical parameters for various conditions of postsurgical wound healing and cutaneous growth. Studying, for the first time, comprehensive metabolic profiles ("metabolomics") of the skin in a minipig model, we found that the lactate/alanine ratios were significantly increased (p<0.05) in skin attached to noninflated expanders vs. control skin, indicating increased anaerobic glycolysis. Furthermore, creatine/phosphocreatine ratios were decreased in skin from inflated vs. noninflated expanders, implying an improved energetic state for stretched skin. In contrast, no significant differences were detected for these parameters on comparing skin from four inflated expanders with different surface structures, even where the histologically determined capsule thickness was significantly different. Overall, the metabolic performance of skin recovering and growing under stretch was found to be superior to that of skin from noninflated expanders, and comparable to that of control skin. Our results are consistent with the assumptions of (i) major hypoxia/ischemia due to reduced perfusion in skin recovering from surgery without an appropriate supportive structure and (ii) minimal metabolic effects of expander surface structures.

Critical study of preanalytical and analytical phases of adenine and pyridine nucleotide assay in human whole blood

Intracellular redox and energetic status play a crucial role in cardiovascular diseases and metabolic disorders. The physiological status of reducing agents, such as NADPH and NADH, and of high-energy molecules, such as ATP, is required for antioxidant system activity. For these reasons, an accurate measurement of adenine and pyridine nucleotides is fundamental. In this study we examined the preanalytical phase of reduced pyridine (RPN) and adenine and oxidized pyridine (AOPN) nucleotide assay in human whole blood. Different experimental conditions were applied to RPN alkaline and AOPN acid extracts to find the best analytical performance. Our results show that a good RPN and AOPN linearity (r from 0.994 to 0.999), recovery (near to 100%), and precision (coefficient of variation < 5%) were obtained when supernatant from acid and ultrafiltrate from alkaline extracts were neutralized, frozen, and thawed just before HPLC injection. Since NADH decays rapidly at -80 degrees C, RPN levels must be assayed within 72 h while AOPN can be stored for 1 month at the same temperature. An accurate and quantitative method for nucleotide determination can be obtained by applying the preanalytical conditions proposed in this study.

Changes in phosphate metabolism in thymoma cells suggest mechanisms for resistance to dexamethasone-induced apoptosis. A 31P NMR spectroscopic study of cell extracts

Treatment of the mouse thymoma-derived WEHI7.2 cell line with dexamethasone, a synthetic glucocorticoid, causes the cells to undergo apoptosis. Previous studies have shown that WEHI7.2 cell variants with an increased antioxidant defense exhibit increased resistance to dexamethasone-induced apoptosis, suggesting that oxidative stress may play a role in glucocorticoid-induced apoptosis. In this work we compared metabolic profiles of WEHI7.2 parental cells with those of WEHI7.2 variants with an increased antioxidant defense or overexpressing bcl-2, to determine whether bolstering the antioxidant defense results in altered metabolic parameters that could translate into increased resistance to dexamethasone-induced apoptosis. WEHI7.2 parental cells and cells overexpressing catalase, thioredoxin or bcl-2, or selected for resistance to 200 micro M H(2)O(2) were cultured in low-glucose DMEM medium supplemented with 10% calf serum, and extracted using chloroform-methanol-water (1:1:1). Metabolites contained in the aqueous and organic phases of the extracts were processed separately and subjected to high-resolution (31)P NMR spectroscopy. In most of the steroid-resistant variants, ATP levels and energetic status were decreased compared with the steroid-sensitive parental cell line, while the concentrations of hexose and triose phosphates were increased. Furthermore, the ratio of choline-containing phospholipids to ethanolamine-containing phospholipids was generally reduced in steroid-resistant cells. Phosphatidylethanolamine and its derivatives contain a higher amount of polyunsaturated fatty acids (PUFA) than the choline-containing analogs, and PUFA are readily oxidized by reactive oxygen species. Therefore, an increased initial amount of phosphatidylethanolamine may increase the 'buffering capacity' of this antioxidant and may thus contribute to the steroid resistance of WEHI7.2 variants.