High-resolution magic angle spinning 1H NMR spectroscopy and reverse transcription-PCR analysis of apoptosis in a rat glioma

Approaches to Integrating Metabolomics and Multi-Omics Data: A Primer

Metabolomics deals with multiple and complex chemical reactions within living organisms and how these are influenced by external or internal perturbations. It lies at the heart of omics profiling technologies not only as the underlying biochemical layer that reflects information expressed by the genome, the transcriptome and the proteome, but also as the closest layer to the phenome. The combination of metabolomics data with the information available from genomics, transcriptomics, and proteomics offers unprecedented possibilities to enhance current understanding of biological functions, elucidate their underlying mechanisms and uncover hidden associations between omics variables. As a result, a vast array of computational tools have been developed to assist with integrative analysis of metabolomics data with different omics. Here, we review and propose five criteria-hypothesis, data types, strategies, study design and study focus- to classify statistical multi-omics data integration approaches into state-of-the-art classes under which all existing statistical methods fall. The purpose of this review is to look at various aspects that lead the choice of the statistical integrative analysis pipeline in terms of the different classes. We will draw particular attention to metabolomics and genomics data to assist those new to this field in the choice of the integrative analysis pipeline.

Monitoring apoptosis in intact cells by high-resolution magic angle spinning 1 H NMR spectroscopy

Apoptosis maintains an equilibrium between cell proliferation and cell death. Many diseases, including cancer, develop because of defects in apoptosis. A known metabolic marker of apoptosis is a notable increase in ¹ H NMR-observable resonances associated with lipids stored in lipid droplets. However, standard one-dimensional NMR experiments allow the quantification of lipid concentration only, without providing information about physical characteristics such as the size of lipid droplets, viscosity of the cytosol, or cytoskeletal rigidity. This additional information can improve monitoring of apoptosis-based cancer treatments in intact cells and provide us with mechanistic insight into why these changes occur. In this paper, we use high-resolution magic angle spinning (HRMAS) ¹ H NMR spectroscopy to monitor lipid concentrations and apparent diffusion coefficients of mobile lipid in intact cells treated with the apoptotic agents cisplatin or etoposide. We also use solution-state NMR spectroscopy to study changes in lipid profiles of organic solvent cell extracts. Both NMR techniques show an increase in the concentration of lipids but the relative changes are 10 times larger by HRMAS ¹ H NMR spectroscopy. Moreover, the apparent diffusion rates of lipids in apoptotic cells measured by HRMAS ¹ H NMR spectroscopy decrease significantly as compared with control cells. Slower diffusion rates of mobile lipids in apoptotic cells correlate well with the formation of larger lipid droplets as observed by microscopy. We also compared the mean lipid droplet displacement values calculated from the two methods. Both methods showed shorter displacements of lipid droplets in apoptotic cells. Our results demonstrate that the NMR-based diffusion experiments on intact cells discriminate between control and apoptotic cells. Apparent diffusion measurements in conjunction with ¹ H NMR spectroscopy-derived lipid signals provide a novel means of following apoptosis in intact cells. This method could have potential application in enhancing drug discovery by monitoring drug treatments in vitro, particularly for agents that cause portioning of lipids such as apoptosis.

Metabolomics facilitates the discrimination of the specific anti-cancer effects of free- and polymer-conjugated doxorubicin in breast cancer models

Metabolomics is becoming a relevant tool for understanding the molecular mechanisms involved in the response to new drug delivery systems. The applicability of this experimental approach to cell cultures and animal models makes metabolomics a useful tool for establishing direct connections between in vitro and in vivo data, thus providing a reliable platform for the characterization of chemotherapeutic agents. Herein, we used metabolomic profiles based on nuclear magnetic resonance (NMR) spectroscopy to evaluate the biochemical pathways involved in the response to a chemotherapeutic anthracycline drug (Doxorubicin, Dox) and an N-(2-hydroxypropyl) methacrylamide (HPMA) copolymer-conjugated form (HPMA-Dox) in an in vitro cell culture model and an in vivo orthotopic breast cancer model. We also used protein expression and flow cytometry studies to obtain a better coverage of the biochemical alterations associated with the administration of these compounds. The overall analysis revealed that polymer conjugation leads to increased apoptosis, reduced glycolysis, and reduced levels of phospholipids when compared to the free chemotherapeutic drug. Our results represent a first step in the application of integrated in vitro and in vivo metabolomic studies to the evaluation of drug delivery systems.

Present and foreseeable future of metabolomics in forensic analysis

The revulsive publications during the last years on the precariousness of forensic sciences worldwide have promoted the move of major steps towards improvement of this science. One of the steps (viz. a higher involvement of metabolomics in the new era of forensic analysis) deserves to be discussed under different angles. Thus, the characteristics of metabolomics that make it a useful tool in forensic analysis, the aspects in which this omics is so far implicit, but not mentioned in forensic analyses, and how typical forensic parameters such as the post-mortem interval or fingerprints take benefits from metabolomics are critically discussed in this review. The way in which the metabolomics-forensic binomial succeeds when either conventional or less frequent samples are used is highlighted here. Finally, the pillars that should support future developments involving metabolomics and forensic analysis, and the research required for a fruitful in-depth involvement of metabolomics in forensic analysis are critically discussed.

Applications of NMR spectroscopy to systems biochemistry

The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other 'omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.

Metabolic impact of anti-angiogenic agents on U87 glioma cells

BACKGROUND

Glioma cells not only secrete high levels of vascular endothelial growth factor (VEGF) but also express VEGF receptors (VEGFR), supporting the existence of an autocrine loop. The direct impact on glioma cells metabolism of drugs targeting the VEGF pathway, such as Bevacizumab (Bev) or VEGFR Tyrosine Kinase Inhibitor (TKI), is poorly known.

MATERIAL AND METHODS

U87 cells were treated with Bev or SU1498, a selective VEGFR2 TKI. VEGFR expression was checked with FACS flow cytometry and Quantitative Real-Time PCR. VEGF secretion into the medium was assessed with an ELISA kit. Metabolomic studies on cells were performed using High Resolution Magic Angle Spinning Spectroscopy (HR-MAS).

RESULTS

U87 cells secreted VEGF and expressed low level of VEGFR2, but no detectable VEGFR1. Exposure to SU1498, but not Bev, significantly impacted cell proliferation and apoptosis. Metabolomic studies with HR MAS showed that Bev had no significant effect on cell metabolism, while SU1498 induced a marked increase in lipids and a decrease in glycerophosphocholine. Accordingly, accumulation of lipid droplets was seen in the cytoplasm of SU1498-treated U87 cells.

CONCLUSION

Although both drugs target the VEGF pathway, only SU1498 showed a clear impact on cell proliferation, cell morphology and metabolism. Bevacizumab is thus less likely to modify glioma cells phenotype due to a direct therapeutic pressure on the VEGF autocrine loop. In patients treated with VEGFR TKI, monitoring lipids with magnetic resonance spectroscopic (MRS) might be a valuable marker to assess drug cytotoxicity.

Integrated analysis of transcriptomics and metabolomics profiles

BACKGROUND

Integrated analysis of transcriptomics and metabolomics data has the potential greatly to increase our understanding of metabolic networks and biological systems leading to various potential clinical applications.

OBJECTIVE

The aim is to present different applications as well as analysis tools utilized for the parallel study of gene and metabolite expressions.

METHODS

Publications dealing with integrated analysis of gene and metabolite expression data as well as publications describing tools that can be used for integrated analysis are reviewed.

RESULTS/CONCLUSION

The full benefit of integrated analysis can be achieved only if data from all utilized methods are treated equally by multidisciplinary teams. This approach can lead to advances in functional genomics with possible clinical developments in diagnostics and improved drug target selection.

Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery

Breast cancer is the most common cancer in women worldwide, and the development of new technologies for better understanding of the molecular changes involved in breast cancer progression is essential. Metabolic changes precede overt phenotypic changes, because cellular regulation ultimately affects the use of small-molecule substrates for cell division, growth or environmental changes such as hypoxia. Differences in metabolism between normal cells and cancer cells have been identified. Because small alterations in enzyme concentrations or activities can cause large changes in overall metabolite levels, the metabolome can be regarded as the amplified output of a biological system. The metabolome coverage in human breast cancer tissues can be maximized by combining different technologies for metabolic profiling. Researchers are investigating alterations in the steady state concentrations of metabolites that reflect amplified changes in genetic control of metabolism. Metabolomic results can be used to classify breast cancer on the basis of tumor biology, to identify new prognostic and predictive markers and to discover new targets for future therapeutic interventions. Here, we examine recent results, including those from the European FP7 project METAcancer consortium, that show that integrated metabolomic analyses can provide information on the stage, subtype and grade of breast tumors and give mechanistic insights. We predict an intensified use of metabolomic screens in clinical and preclinical studies focusing on the onset and progression of tumor development.

Using magnetic resonance imaging and spectroscopy in cancer diagnostics and monitoring: preclinical and clinical approaches

Nuclear Magnetic Resonance (MR) based imaging has become an integrated domain in today's oncology research and clinical management of cancer patients. MR is a unique imaging modality among numerous other imaging modalities by providing access to anatomical, physiological, biochemical and molecular details of tumour with excellent spatial and temporal resolutions. In this review we will cover established and investigational MR imaging (MRI) and MR spectroscopy (MRS) techniques used for cancer imaging and demonstrate wealth of information on tumour biology and clinical applications MR techniques offer for oncology research both in preclinical and clinical settings. Emphasis is given not only to the variety of information which may be obtained but also the complementary nature of the techniques. This ability to determine tumour type, grade, invasiveness, degree of hypoxia, microvacular characteristics, and metabolite phenotype, has already profoundly transformed oncology research and patient management. It is evident from the data reviewed that MR techniques will play a key role in uncovering molecular fingerprints of cancer, developing targeted treatment strategies and assessing responsiveness to treatment for personalized patient management, thereby allowing rapid translation of imaging research conclusions into the benefit of clinical oncology.

Magnetic resonance spectroscopy of cancer metabolism and response to therapy

Magnetic resonance spectroscopy allows noninvasive in vivo measurements of biochemical information from living systems, ranging from cultured cells through experimental animals to humans. Studies of biopsies or extracts offer deeper insights by detecting more metabolites and resolving metabolites that cannot be distinguished in vivo. The pharmacokinetics of certain drugs, especially fluorinated drugs, can be directly measured in vivo. This review briefly describes these methods and their applications to cancer metabolism, including glycolysis, hypoxia, bioenergetics, tumor pH, and tumor responses to radiotherapy and chemotherapy.

The fast spiral-SelMQC technique for in vivo MR spectroscopic imaging of polyunsaturated fatty acids in human breast tissue

The selective multiple-quantum coherence transfer method has been applied to image polyunsaturated fatty acids (PUFA) distributions in human breast tissues in vivo for cancer detection, with complete suppression of the unwanted lipid and water signals in a single scan. The Cartesian k-space mapping of PUFA in vivo using the selective multiple-quantum coherence transfer (Sel-MQC) chemical shift imaging (CSI) technique, however, requires excessive MR scan time. In this article, we report a fast Spiral-SelMQC sequence using a rapid spiral k-space sampling scheme. The Spiral-SelMQC images of PUFA distribution in human breast were acquired using two-interleaved spirals on a 3 T GE Signa magnetic resonance imaging scanner. Approximately 160-fold reduction of acquisition time was observed as compared with the corresponding selective multiple-quantum coherence transfer CSI method with an equivalent number of scans, permitting acquisition of high-resolution PUFA images in minutes. The reconstructed Spiral-SelMQC PUFA images of human breast tissues achieved a sub-millimeter resolution of 0.54 × 0.54 or 0.63 × 0.63 mm(2) /pixel for field of view = 14 or 16 cm, respectively. The Spiral-SelMQC parameters for PUFA detection were optimized in 2D selective multiple-quantum coherence transfer experiments to suppress monounsaturated fatty acids and other lipid signals. The fast in vivo Spiral-SelMQC imaging method will be applied to study human breast cancer and other human diseases in extracranial organs.

1H NMR spectroscopy analysis of metabolites in the kidneys provides new insight into pathophysiological mechanisms: applications for treatment with Cordyceps sinensis

BACKGROUND

The number of patients with chronic kidney disease (CKD) is continuously growing worldwide. Treatment with traditional Chinese medicine might slow the progression of CKD.

METHODS

In this study, we evaluated the renal protective effects of the Chinese herb Cordyceps sinensis in rats with 5/6 nephrectomy. Male Sprague-Dawley mice (weighing 150-200 g) were subjected to 5/6 nephrectomy. The rats were divided into three groups: (i) untreated nephrectomized group (OP group, n = 16), (ii) oral administration of C. sinensis-treated (4 mg/kg/day) nephrectomized group (CS group, n = 16) and (iii) sham-operated group (SO group, n = 16). The rats were sacrificed at 4 and 8 weeks after 5/6 nephrectomy, and the kidneys, serum and urine were collected for (1)H nuclear magnetic resonance spectral analysis. Multivariate statistical techniques and statistical metabolic correlation comparison analysis were performed to identify metabolic changes in aqueous kidney extracts between these groups.

RESULTS

Significant differences between these groups were discovered in the metabolic profiles of the biofluids and kidney extracts. Pathways including the citrate cycle, branched-chain amino acid metabolism and the metabolites that regulate permeate pressure were disturbed in the OP group compared to the SO group; in addition, these pathways were reversed by C. sinensis treatment. Biochemistry and electron microscopic images verified that C. sinensis has curative effects on chronic renal failure. These results were confirmed by metabonomics results.

CONCLUSION

Our study demonstrates that C. sinensis has potential curative effects on CKD, and our metabonomics results provided new insight into the mechanism of treatment of this traditional Chinese medicine.

In vitro metabonomic study detects increases in UDP-GlcNAc and UDP-GalNAc, as early phase markers of cisplatin treatment response in brain tumor cells

O-linked β-N-acetylglucosamine glycosylation (O-GlcNAcylation) is important in a number of biological processes and diseases including transcription, cell stress, diabetes, and neurodegeneration and may be a marker of tumor metastasis. Uridine diphospho-N-acetylglucosamine (UDP-GlcNAc), the donor molecule in O-GlcNAcylation, can be detected by (1)H nuclear magnetic resonance spectroscopy ((1)H NMR), giving the potential to measure its level noninvasively, providing a novel biomarker of prognosis and treatment monitoring. In this in vitro metabonomic study, four brain cancer cell lines were exposed to cisplatin and studied for metabolic responses using (1)H NMR. The Alamar blue assay and DAPI staining were used to assess cell sensitivity to cisplatin treatment and to confirm cell death. It is shown that in the cisplatin responding cells, UDP-GlcNAc and uridine diphospho-N-acetylgalactosamine (UDP-GalNAc), in parallel with (1)H NMR detected lipids, increased with cisplatin exposure before or at the onset of the microscopic signs of evolving cell death. The changes in UDP-GlcNAc and UDP-GalNAc were not detected in the nonresponders. These glycosylated UDP compounds, the key substrates for glycosylation of proteins and lipids, are commonly implicated in cancer proliferation and malignant transformation. However, the present study mechanistically links UDP-GlcNAc and UDP-GalNAc to cancer cell death following chemotherapeutic treatment.

Semi-parametric time-domain quantification of HR-MAS data from prostate tissue

High Resolution--Magic Angle Spinning (HR-MAS) spectroscopy provides rich biochemical profiles that require accurate quantification to permit biomarker identification and to understand the underlying pathological mechanisms. Meanwhile, quantification of HR-MAS data from prostate tissue samples is challenging due to significant overlap between the resonant peaks, the presence of short T₂* metabolites such as citrate or polyamines (T₂ from 25 to 100 msec) and macromolecules, and variations in chemical shifts and T₂*s within a metabolite's spin systems. Since existing methods do not address these challenges completely, a new quantification method was developed and optimized for HR-MAS data acquired with an ultra short T(E) and over 30,000 data points. The proposed method, named HR-QUEST (High Resolution--QUEST), iteratively employs the QUEST time-domain semi-parametric strategy with a new model function that incorporates prior knowledge from whole and subdivided metabolite signals. With these features, HR-QUEST is able to independently fit the chemical shifts and T₂*s of a metabolite's spin systems, a necessity for HR-MAS data. By using the iterative fitting approach, it is able to account for significant contributions from macromolecules and to handle shorter T₂ metabolites, such as citrate and polyamines. After subdividing the necessary metabolite basis signals, the root mean square (RMS) of the residual was reduced by 52% for measured HR-MAS data from prostate tissue. Monte Carlo studies on simulated spectra with varied macromolecular contributions showed that the iterative fitting approach (6 iterations) coupled with inclusion of long T₂ macromolecule components in the basis set improve the quality of the fit, as assessed by the reduction of the RMS of the residual and of the RMS error of the metabolite signal estimate, by 27% and 71% respectively. With this optimized configuration, HR-QUEST was applied to measured HR-MAS prostate data and reliably quantified 16 metabolites and reference signals with estimated Cramér Rao Bounds ≤5%.

Metabolomic profiling with NMR discriminates between biphosphonate and doxorubicin effects on B16 melanoma cells

The metabolomic profiles of B16 melanoma cells were investigated in vitro with high resolution-magic angle spinning proton magnetic resonance spectroscopy and OPLS multivariate statistical analyse. We compared the profiles for untreated melanoma B16-F10 cells and Ca(2+) chelating EGTA, doxorubicin or BP7033 bisphosphonate treated cells. The two last molecules are known to induce anti-proliferative effects by different mechanisms of action in cells. Untreated and EGTA treated cells had similar profiles and were considered together as control cells. Several spectral regions could discriminate control from doxorubicin as well as BP7033 treated cells. Doxorubicin and BP7033 displayed distinct metabolic profiles. Important changes in neutral lipids and inositol were related to doxorubicin activity whereas BP7033 affected essentially phospholipids and alanine/lactate metabolism. These results provide new putative targets for both drugs. Metabolomics by NMR is shown here to be a good tool for the investigation of the mechanisms of action of drugs in pre-clinical studies.

1H magnetic resonance spectroscopy metabolites as biomarkers for cell cycle arrest and cell death in rat glioma cells

BACKGROUND

Improved non-invasive imaging biomarkers of treatment response contribute to optimising cancer management and metabolites detected by proton magnetic resonance spectroscopy ((1)H MRS) show promise in this area. Understanding (1)H MRS changes occurring in cells during cell stress and cell death in vitro should aid the selection of pertinent biomarkers for clinical use.

METHODS

BT4C glioma cells in culture were exposed to either 50 μM cis-dichlorodiammineplatinum II (cisplatin) or starvation by culture in phosphate buffered saline. High resolution magic angle spinning (1)H MRS was performed on cells using a Varian 600 MHz nanoprobe and metabolites were quantified by a time domain fitting method. Cell viability was assessed by trypan blue, H&E, 4',6-diamino-2-phenylindole (DAPI), DNA laddering and annexin V-FITC labelled flow cytometry; propidium iodide flow cytometry was used to assess the cell cycle phase.

RESULTS

With cisplatin exposure, cells initially accumulated in the G1 stage of the cell cycle with low numbers of apoptotic and necrotic cells and this was associated with decreases in phosphocholine, succinate, alanine, taurine, glycine and glutamate and increases in lactate and glycerophosphocholine (GPC). Starvation, leading to necrotic cell death within 6-18 h, caused decreases in succinate, alanine, glycine, and glutamate and increases in GPC. Principal component analysis revealed two patterns of metabolite changes, one common to both types of cell stress and another specific for necrosis secondary to cell starvation.

CONCLUSIONS

(1)H MRS reveals alterations in multiple metabolites during cell cycle arrest and cell death which may provide early biomarker profiles of treatment efficacy in vivo.

Metabolic, pathologic, and genetic analysis of prostate tissues: quantitative evaluation of histopathologic and mRNA integrity after HR-MAS spectroscopy

The impact of high-resolution magic angle spinning (HR-MAS) spectroscopy on the histopathologic and mRNA integrity of human prostate tissues was evaluated. Forty prostate tissues were harvested at transrectal ultrasound (TRUS) guided biopsy (n = 20) or radical prostatectomy surgery (n = 20), snap-frozen on dry ice, and stored at -80°C until use. Twenty-one samples (n = 11 biopsy, n = 10 surgical) underwent HR-MAS spectroscopy prior to histopathologic and cDNA microarray analysis, while 19 control samples (n = 9 biopsy, n = 10 surgical) underwent only histopathologic and microarray analysis. Frozen tissues were sectioned at 14-µm intervals and placed on individual histopathology slides. Every 8th slide was stained with hematoxylin and eosin (H&E) and used to target areas of predominantly epithelial tissue on the remaining slides for mRNA integrity and cDNA microarray analysis. Histopathologic integrity was graded from 1 (best) to 5 (worst) by two 'blinded' pathologists. Histopathologic integrity scores were not significantly different for post-surgical tissues (HR-MAS vs controls); however, one pathologist's scores were significantly lower for biopsy tissues following HR-MAS while the other pathologist's scores were not. mRNA integrity assays were performed using an Agilent 2100 Bioanalyzer and the electrophoretic traces were scored with an RNA integrity number (RIN) from 1 (degraded) to 10 (intact). RIN scores were not significantly different for surgical tissues, but were significantly lower for biopsy tissues following HR-MAS spectroscopy. The isolated mRNA then underwent two rounds of amplification, conversion to cDNA, coupling to Cy3 and Cy5 dyes, microarray hybridization, imaging, and analysis. Significance analysis of microarrays (SAM) identified no significantly over- or under-expressed genes, including 14 housekeeping genes, between HR-MAS and control samples of surgical and biopsy tissues (5% false discovery rate). This study demonstrates that histopathologic and genetic microarray analysis can be successfully performed on prostate surgical and biopsy tissues following HR-MAS analysis; however, biopsy tissues are more fragile than surgical tissues.

Methods for metabolic evaluation of prostate cancer cells using proton and (13)C HR-MAS spectroscopy and [3-(13)C] pyruvate as a metabolic substrate

Prostate cancer has been shown to undergo unique metabolic changes associated with neoplastic transformation, with associated changes in citrate, alanine, and lactate concentrations. (13)C high resolution-magic angle spinning (HR-MAS) spectroscopy provides an opportunity to simultaneously investigate the metabolic pathways implicated in these changes by using (13)C-labeled substrates as metabolic probes. In this work, a method to reproducibly interrogate metabolism in prostate cancer cells in primary culture was developed using HR-MAS spectroscopy. Optimization of cell culture protocols, labeling parameters, harvesting, storage, and transfer was performed. Using [3-(13)C] pyruvate as a metabolic probe, (1)H and (13)C HR-MAS spectroscopy was used to quantify the net amount and fractional enrichment of several labeled metabolites that evolved in multiple cell samples from each of five different prostate cancers. Average enrichment across all cancers was 32.4 +/- 5.4% for [3-(13)C] alanine, 24.5 +/- 5.4% for [4-(13)C] glutamate, 9.1 +/- 2.5% for [3-(13)C] glutamate, 25.2 +/- 5.7% for [3-(13)C] aspartate, and 4.2 +/- 1.0% for [3-(13)C] lactate. Cell samples from the same parent population demonstrated reproducible fractional enrichments of alanine, glutamate, and aspartate to within 12%, 10%, and 10%, respectively. Furthermore, the cells produced a significant amount of [4-(13)C] glutamate, which supports the bioenergetic theory for prostate cancer. These methods will allow further characterization of metabolic properties of prostate cancer cells in the future. Magn Reson Med, 2009. (c) 2009 Wiley-Liss, Inc.

Evaluation of the ERETIC method as an improved quantitative reference for 1H HR-MAS spectroscopy of prostate tissue

The Electronic REference To access In vivo Concentrations (ERETIC) method was applied to (1)H HR-MAS spectroscopy. The accuracy, precision, and stability of ERETIC as a quantitative reference were evaluated in solution and human prostate tissue samples. For comparison, the reliability of 3-(trimethylsilyl)propionic-2,2,3,3-d(4) acid (TSP) as a quantitation reference was also evaluated. The ERETIC and TSP peak areas were found to be stable in solution over the short-term and long-term, with long-term relative standard deviations (RSDs) of 4.10% and 2.60%, respectively. Quantification of TSP in solution using the ERETIC peak as a reference and a calibrated, rotor-dependent conversion factor yielded results with a precision < or =2.9% and an accuracy error < or =4.2% when compared with the expected values. The ERETIC peak area reproducibility was superior to TSP's reproducibility, corrected for mass, in both prostate surgical and biopsy samples (4.53% vs. 21.2% and 3.34% vs. 31.8%, respectively). Furthermore, the tissue TSP peaks exhibited only 27.5% of the expected area, which would cause an overestimation of metabolite concentrations if used as a reference. The improved quantification accuracy and precision provided by ERETIC may enable the detection of smaller metabolic differences that may exist between individual tissue samples and disease states.

Experimental estimation of postmortem interval using multivariate analysis of proton NMR metabolomic data

Nuclear magnetic resonance (NMR) spectroscopy has recently been applied to metabolic studies. In particular, metabolic profiles of tissues or of the whole body can easily be acquired through multivariate analysis of NMR spectra. The present study investigates metabolic changes after death in rat femoral muscles using pattern recognition of proton NMR spectra. Rats were killed by suffocation, cocaine overdose and induced respiratory failure, and then low molecular weight metabolites extracted using perchlorate from excised tissues were measured using proton NMR. All spectral data were processed and assessed by multivariate analysis to obtain metabolic profiles of the tissues. The results of principal component analysis (PCA) score plots soon after death showed that the metabolic profiles of the tissues differed according to the mode of death. The principal component (PC) scores of the data varied hourly and correlated with postmortem interval. The present results showed that NMR-based metabolic profiling could provide useful information with which to estimate postmortem intervals and causes of death.

Monitoring of gliomas in vivo by diffusion MRI and (1)H MRS during gene therapy-induced apoptosis: interrelationships between water diffusion and mobile lipids

The measurement of water diffusion by diffusion-weighted MRI (DWI) in vivo offers a non-invasive method for assessing tissue responses to anti-cancer therapies. The pathway of cell death after anti-cancer treatment is often apoptosis, which leads to accumulation of mobile lipids detectable by (1)H MRS in vivo. However, it is not known how these discrete MR markers of cell death relate to each other. In a rodent tumour model [i.e. ganciclovir-treated herpes simplex thymidine kinase (HSV-tk) gene-transfected BT4C gliomas], we studied the interrelationships between water diffusion (Trace{D}) and mobile lipids during apoptosis. Water diffusion and water-referenced concentrations of mobile lipids showed clearly increasing and interconnected trends during treatment. Of the accumulating (1)H MRS-visible lipids, the fatty acid --CH==CH-- groups and cholesterol compounds showed the strongest associations with water diffusion (r(2) = 0.30; P < 0.05 and r(2) = 0.48; P < 0.01, respectively). These results indicate that the tumour histopathology and apoptotic processes during tumour shrinkage can be interrelated in vivo by DWI of tissue water and (1)H MRS of mobile lipids, respectively. However, there is considerable individual variation in the associations, particularly at the end of the treatment period, and in the relative compositions of the accumulating NMR-visible lipids. The findings suggest that the assessment of individual treatment response in vivo may benefit from combining DWI and (1)H MRS. Absolute and relative changes in mobile lipids may indicate initiation of tumour shrinkage even when changes in tissue water diffusion are still small. Conversely, greatly increased water diffusion probably indicates that substantial cell decomposition has taken place in the tumour tissue when the (1)H MRS resonances of mobile lipids alone can no longer give a reliable estimate of tissue conditions.

Plasma amino acid analysis for diagnosis and amino acid-based metabolic networks

PURPOSE OF REVIEW

To highlight the usefulness of amino acid profiling in clinical diagnosis and current developments in analysis revealing underlying metabolic relationships.

RECENT FINDINGS

Recent innovations in metabolomics and systems biology enable high throughput measurement of diverse amino acids and the subsequent data mining for various uses. Recent studies show new possibilities of using plasma amino acid analysis as biomarker discovery tools by generating diagnostic indices through systematic computation. Such studies show that amino acid-based clinical diagnostic indices for hepatic fibrosis in type C hepatitis patients can be generated. In addition, several studies show the potential of treating amino acid profile data as a metabolomic subset, which can be integrated through the analysis of correlation with different types of 'omics' data for describing metabolite-to-metabolite or metabolite-to-gene interaction networks.

CONCLUSION

Amino acid profiling of biological samples could be used to generate indices that could be used for clinical diagnosis and is a useful tool for understanding metabolic implications under various physiological conditions. Although further improvements in analytical methods are needed, amino acids could be useful indicators for facilitating nutritional management of specific physiological and pathological states.

Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy

The toxicological effects of realgar after intragastrical administration (1 g/kg body weight) were investigated over a 21 day period in male Wistar rats using metabonomic analysis of (1)H NMR spectra of urine, serum and liver tissue aqueous extracts. Liver and kidney histopathology examination and serum clinical chemistry analyses were also performed. (1)H NMR spectra and pattern recognition analyses from realgar treated animals showed increased excretion of urinary Kreb's cycle intermediates, increased levels of ketone bodies in urine and serum, and decreased levels of hepatic glucose and glycogen, as well as hypoglycemia and hyperlipoidemia, suggesting the perturbation of energy metabolism. Elevated levels of choline containing metabolites and betaine in serum and liver tissue aqueous extracts and increased serum creatine indicated altered transmethylation. Decreased urinary levels of trimethylamine-N-oxide, phenylacetylglycine and hippurate suggested the effects on the gut microflora environment by realgar. Signs of impairment of amino acid metabolism were supported by increased hepatic glutamate levels, increased methionine and decreased alanine levels in serum, and hypertaurinuria. The observed increase in glutathione in liver tissue aqueous extracts could be a biomarker of realgar induced oxidative injury. Serum clinical chemistry analyses showed increased levels of lactate dehydrogenase, aspartate aminotransferase, and alkaline phosphatase as well as increased levels of blood urea nitrogen and creatinine, indicating slight liver and kidney injury. The time-dependent biochemical variations induced by realgar were achieved using pattern recognition methods. This work illustrated the high reliability of NMR-based metabonomic approach on the study of the biochemical effects induced by traditional Chinese medicine.

Metabolic changes in temporal lobe structures measured by HR-MAS NMR at early stage of electrogenic rat epilepsy

The purpose of this study was to determine cerebral metabolic profile changes in response to electric stimulation to the right dorsal hippocampus (HPC) for the establishment of an epileptic rat model. Electroencephalogram measurements and behavioral results indicated that the experimental rats were in an early stage of epilepsy. Metabolites were determined by high-resolution magic-angle-spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy of the following intact brain tissue: bilateral hippocampi, entorhinal cortices (ECs), and temporal lobes (TLs). The NMR data was statistically analyzed using principal component analysis (PCA). Results demonstrated that metabolic profiles were significantly different between the experimental and sham rats in the bilateral hippocampi and the ipsilateral EC. Significant increases in total creatine in the ipsilateral HPC and alanine in the ipsilateral TL were measured (p<0.05). Some metabolite levels were disturbed in the bilateral HPC-EC loops. In the sham group, glutamate and choline concentrations were significantly higher or lower in the ipsilateral EC than bilateral hippocampi, respectively (p<0.01). However, such differences were not observed in the experimental group. In addition, N-acetylaspartate levels in the experimental group were significantly less in the ipsilateral HPC than in bilateral ECs (p<0.05). The level of myo-inositol in the ipsilateral EC significantly increased in the experimental group, compared to the contralateral EC (p<0.05). These results may provide metabolic information about temporal lobe structures to provide more knowledge about epileptic abnormalities at the early stage.

Metabolomics in biomarker discovery: future uses for cancer prevention

Metabolomics is the systematic study of small-molecular-weight substances in cells, tissues and/or whole organisms as influenced by multiple factors including genetics, diet, lifestyle and pharmaceutical interventions. These substances may directly or indirectly interact with molecular targets and thereby influence the risk and complications associated with various diseases, including cancer. Since the interaction between metabolites and specific targets is dynamic, knowledge regarding genetics, susceptibility factors, timing, and degree of exposure to an agent (drug or food component) is fundamental to understanding the metabolome and its potential use for predicting and preventing early phenotypic changes. The future of metabolomics rests with its ability to monitor subtle changes in the metabolome that occur prior to the detection of a gross phenotypic change reflecting disease. The integrated analysis of metabolomics and other 'omics' may provide more sensitive ways to detect changes related to disease and discover novel biomarkers. Knowledge regarding these multivariant characteristics is critical for establishing validated and predictive metabolomic models for cancer prevention. Understanding the metabolome will not only provide insights into the critical sites of regulation in health promotion, but will also assist in identifying intermediate or surrogate cancer biomarkers for establishing preemptive/preventative or therapeutic approaches for health. While unraveling the metabolome will not be simple, the societal implications are enormous.

New inserts and low temperature--two strategies to overcome the bottleneck in MAS NMR on wet gels

MAS NMR experiments on wet and dry aluminium alkoxide fluoride gels are presented here for the first time. For the MAS studies on wet jelly like gels special inserts were developed which fit perfectly a 4mm rotor and allow rotation frequencies up to 12 kHz. Six different insert materials were tested concerning their suitability including different organic polymers ((poly(methyl methacrylate) (PMMA), poly(ether ether ketone) (PEEK), poly(vinylchloride) (PVC) and poly(tetrafluorethylene) (PTFE)), glass as well as pure quartz (SiO(2)). Alternatively, low-temperature MAS NMR experiments taken at 150K with the wet gel frozen directly in the rotor led to comparable results. (27)Al, (19)F, (13)C, (1)H were used as nuclear spin probes to identify local structures in the wet as well as in the dry xerogels. Both wet and dry gels consist of a network structure of AlF(6-x)OiPr(x) species (x: 0-3). The main structural units of the dried gel are already preformed in the jelly like gel and change only little at aging and drying processes.

Metabolic mapping by use of high-resolution magic angle spinning 1H MR spectroscopy for assessment of apoptosis in cervical carcinomas

Background

High-resolution magic angle proton magnetic resonance spectroscopy (HR ¹H MAS MRS) provides a broad metabolic mapping of intact tumor samples and allows for microscopy investigations of the samples after spectra acquisition. Experimental studies have suggested that the method can be used for detection of apoptosis, but this has not been investigated in a clinical setting so far. We have explored this hypothesis in cervical cancers by searching for metabolites associated with apoptosis that were not influenced by other histopathological parameters like tumor load and tumor cell density.

Methods

Biopsies (n = 44) taken before and during radiotherapy in 23 patients were subjected to HR MAS MRS. A standard pulse-acquire spectrum provided information about lipids, and a spin-echo spectrum enabled detection of non-lipid metabolites in the lipid region of the spectra. Apoptotic cell density, tumor cell fraction, and tumor cell density were determined by histopathological analysis after spectra acquisition.

Results

The apoptotic cell density correlated with the standard pulse-acquire spectra (p < 0.001), but not with the spin-echo spectra, showing that the lipid metabolites were most important. The combined information of all lipids contributed to the correlation, with a major contribution from the ratio of fatty acid -CH₂ to CH₃ (p = 0.02). In contrast, the spin-echo spectra contained the main information on tumor cell fraction and tumor cell density (p < 0.001), for which cholines, creatine, taurine, glucose, and lactate were most important. Significant correlations were found between tumor cell fraction and glucose concentration (p = 0.001) and between tumor cell density and glycerophosphocholine (GPC) concentration (p = 0.024) and ratio of GPC to choline (p < 0.001).

Conclusion

Our findings indicate that the apoptotic activity of cervical cancers can be assessed from the lipid metabolites in HR MAS MR spectra and that the HR MAS data may reveal novel information on the metabolic changes characteristic of apoptosis. These changes differed from those associated with tumor load and tumor cell density, suggesting an application of the method to explore the role of apoptosis in the course of the disease.

Metabolic Profiling of Liver from Hypercholesterolemic Pigs Fed Rye or Wheat Fiber and from Normal Pigs. High-Resolution Magic Angle Spinning1H NMR Spectroscopic Study

This study presents the first application of a high-resolution magic angle spinning 1H NMR approach to elucidate the metabolic effects of a hypercholesterolemic condition and two high-fiber diets based on rye and wheat bread, respectively, in intact pig liver biopsy samples. Standard 1D and spin-echo 1H spectra were acquired on a total of 20 biopsy samples, and 2D total correlation spectroscopy experiments were carried out on selected samples for assignment of the observed resonances. Principal component analyses and partial least-squares regression discriminant analysis revealed differences in the hepatic lipid content and choline-containing compounds between normal and hypercholesterolemic pigs. In addition, the results demonstrated that the liver metabolite profile of hypercholesterolemic pigs fed a high-fiber rye bread differed from that of pigs fed high-fiber wheat bread with respect to both the lipoprotein fractions and the choline-containing compounds. These findings suggest that earlier reports on high-fiber rye diet-induced effects on plasma HDL/LDL content partially can be ascribed to effects on liver cholesterol metabolism and that the hepatic phospholipase pathways of phosphatidylcholine breakdown are affected by the high-fiber rye diet.

Identification of mobile cholesterol compounds in experimental gliomas by (1)H MRS in vivo: effects of ganciclovir-induced apoptosis on lipids

This letter presents a novel identification and analysis of mobile cholesterol compounds in an experimental glioma model by (1)H MRS in vivo. The cholesterol compounds turned out to comprise as much as 17 mol% of MRS visible total lipids. The results also imply partly associated accumulation of (1)H MRS detectable cholesterol compounds and unsaturated lipids during gene therapy-induced apoptosis, and indicate that the contribution of cholesterol compounds cannot be bypassed in spectral lipid analysis. The introduced (1)H MRS approach facilitates a non-invasive follow-up of mobile cholesterol compounds, paving way for studies of tumour cholesterol metabolism in vivo.