Proton nuclear magnetic resonance-based metabonomics for rapid diagnosis of meningitis and ventriculitis

Metabolomics approach to risk assessment: methoxyclor exposure in rats

The primary objective of this study was to develop exposure biomarkers that "correlate with the endocrine-disrupting effects induced by methoxyclor (MTC), an organochlorine pesticide, using" urinary (1)H nuclear magnetic resonance (NMR) spectral data. Exposure biomarkers play an important role in risk assessment. MTC is an environmental endocrine disruptor with estrogenic, anti-estrogenic, and anti-androgenic properties. A new approach of proton nuclear magnetic resonance ((1)H NMR) urinalysis using pattern recognition was proposed for exposure biomarkers of MTC in female rats. The endocrine disruptor was expected to induce estrogenic effects in a dose dependent manner which, was confirmed by the uterotrophic assay. MTC [50, 100, or 200 m g/kg/d, orally (p.o.) or subcutaneously (s.c.)] was administered to ovariectomized female Sprague-Dawley (SD) rats for 3 d consecutively and urine was collected every 24 h. The animals were sacrificed 24 h after the last dose. All animals treated orally with MTC showed a significant increase in uterine and vaginal weight at all doses. However, in the s.c. route, only a high dose of 200 mg MTC/kg induced a significant increase in uterine and vaginal weight. (1)H NMR spectroscopy revealed evident separate clustering between pre- and post-treatment groups using global metabolic profiling through principal component analysis (PCA) and partial least square (PLS) discrimination analysis (DA) after different exposure routes. With targeted profiling, the endogenous metabolites of acetate, alanine, benzoate, lactate, and glycine were selected as putative exposure biomarkers for MTC. Data suggest that the proposed putative exposure biomarkers may be useful in a risk assessment of the endocrine-disrupting effects produced by MTC.

New strategies to identify molecular markers predicting chemotherapy activity and toxicity in breast cancer

Despite significant improvements in the treatment and outcomes of early-stage breast cancer, the quest continues to find biological and molecular markers that would enable earlier diagnosis or better prediction of treatment efficacy and toxicity. Metabolomics--the latest and one of the most exciting of the 'omic' sciences--has shown early promise as a non-invasive diagnostic aid in ovarian cancer, and may allow the detection of subtle metabolic changes that could have diagnostic, prognostic or predictive value in breast cancer. Routine monitoring of circulating tumour cells (CTCs) has also been advocated as a novel means of detecting breast cancer progression earlier, and identifying alterations in tumour cells that might signal the need for therapy changes. Ongoing studies should help to answer important questions relating to the use of metabolomics and CTC evaluation as new strategies to monitor cancer progression and identify markers of chemotherapy activity and toxicity.

NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology

We have reviewed the main contributions to the development of NMR-based metabonomic and metabolic profiling approaches for toxicological assessment, biomarker discovery, and studies on toxic mechanisms. The metabonomic approach, (defined as the quantitative measurement of the multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification) was originally developed to assist interpretation in NMR-based toxicological studies. However, in recent years there has been extensive fusion with metabolomic and other metabolic profiling approaches developed in plant biology, and there is much wider coverage of the biomedical and environmental fields. Specifically, metabonomics involves the use of spectroscopic techniques with statistical and mathematical tools to elucidate dominant patterns and trends directly correlated with time-related metabolic fluctuations within spectral data sets usually derived from biofluids or tissue samples. Temporal multivariate metabolic signatures can be used to discover biomarkers of toxic effect, as general toxicity screening aids, or to provide novel mechanistic information. This approach is complementary to proteomics and genomics and is applicable to a wide range of problems, including disease diagnosis, evaluation of xenobiotic toxicity, functional genomics, and nutritional studies. The use of biological fluids as a source of whole organism metabolic information enhances the use of this approach in minimally invasive longitudinal studies.

Metabolomic investigation of CLN6 neuronal ceroid lipofuscinosis in affected South Hampshire sheep

The neuronal ceroid lipofuscinoses (NCLs; Batten disease) are a group of fatal inherited neurodegenerative diseases in humans and animals distinguished by a common clinical pathology, characteristic storage body accumulation in cells, and gross brain atrophy. An (1)H NMR spectroscopy- and GC-MS-based metabolomic investigation of changes in the cerebellum, frontal and occipital lobes, and cerebrospinal fluid (CSF) of CLN6 NCL affected South Hampshire sheep charted changes from the preclinical state to advanced disease. Glutamine and succinate concentrations increased in all brain regions in affected sheep relative to controls, whereas concentrations of aspartate, acetate, glutamate, N-acetyl aspartate (NAA), and gamma-aminobutyric acid (GABA) decreased. Changes in the concentrations of inositols, NAA, and GABA were consistent with glial cell activation and neurodegeneration beginning in the frontal and occipital lobes, in agreement with previous histopathological data. Further metabolic deficits were defined in all regions at earlier time points, including the cerebellum, where very little neurological degeneration has been reported. Biochemical abnormalities in the CSF of affected sheep at 18-31 months include relative increases in lactate, acetate, tyrosine, and creatine/creatinine concentrations and decreases in myo- and scyllo-inositol and citrate concentrations. The changes detected in the CSF and brain tissue mirrored those previously apparent in NCL mouse models, suggesting that they are common to all NCLs. However, the changes in glutamate and glutamine concentrations in CSF occurred after clinical disease, indicating that any changes in glutamate/glutamine cycling occur as a consequence of the primary deficits associated with the NCLs.

GC/MS analysis of the rat urine for metabonomic research

In this paper, an optimized protocol was established and validated for the metabonomic profiling in rat urine using GC/MS. The urine samples were extracted by methanol after treatment with urease to remove excessive urea, then the resulted supernatant was dried, methoximated, trimethylsilylated, and analyzed by GC/MS. Forty-nine endogenous metabolites were separated and identified in GC/MS chromatogram, of which 26 identified compounds were selected for quantitative analysis to evaluate the linearity, precision, and sensitivity of the method. It showed good linearity between mass spectrometry responses and relative concentrations of the 26 endogenous compounds over the range from 0.063 to 1.000 (v/v, urine/urine+water) and satisfactory reproducibility with intra-day and inter-days precision values all below 15%. The metabonomic profiling method based on GC/MS was successfully applied to urine samples from hyperlipidemia model rats. Obviously, separated clustering of model rats and the control rats were shown by principal components analysis (PCA); time-dependent metabonomic modification was detected as well. It was suggested that metabonomic profiling based on GC/MS be a robust method for urine samples.

Metabonomics in pharmaceutical R&D

This minireview is based on a lecture given at the First Maga Circe Conference on metabolomics held at Sabaudia, Italy, in March 2006 in which the analytical and statistical techniques used in metabonomics, efforts at standardization and some of the major applications to pharmaceutical research and development are reviewed. Metabonomics involves the determination of multiple metabolites simultaneously in biofluids, tissues and tissue extracts. Applications to preclinical drug safety studies are illustrated by the Consortium for Metabonomic Toxicology, a collaboration involving several major pharmaceutical companies. This consortium was able, through the measurement of a dataset of NMR spectra of rodent urine and serum samples, to build a predictive expert system for liver and kidney toxicity. A secondary benefit was the elucidation of the endogenous biochemicals responsible for the classification. The use of metabonomics in disease diagnosis and therapy monitoring is discussed with an exemplification from coronary artery disease, and the concept of pharmaco-metabonomics as a way of predicting an individual's response to treatment is exemplified. Finally, some advantages and perceived difficulties of the metabonomics approach are summarized.

Metabonomics in pharmaceutical discovery and development

Metabonomics has emerged as a key technology in pharmaceutical discovery and development, evolving as the small molecule counterpart of transcriptomics and proteomics. In drug discovery laboratories, metabonomics aids in target identification, phenotyping, and the understanding of the biochemical basis of disease and toxicity. This review focuses on three areas where metabonomics is used in the industry: (1) analytical considerations, (2) chemometric and statistical concerns, and (3) biological aspects and applications.

Metabolomics applied to exhaled breath condensate in childhood asthma

RATIONALE

Metabolomic analysis provides biochemical profiles of low-molecular-weight endogenous metabolites in biological fluids.

OBJECTIVES

The aim of this study was to assess the feasibility of nuclear magnetic resonance (NMR)-based metabolomic analysis applied to exhaled breath condensate ("breathomics"). Information coming from NMR spectra was analyzed with a view to establish the NMR variables that best discriminate between children with asthma and healthy children.

METHODS

Twenty-five children with asthma (17 with persistent asthma treated with inhaled corticosteroids, 8 with intermittent asthma inhaled corticosteroid naive; age, 7-15 yr) and 11 healthy age-matched control subjects were enrolled. Every child performed exhaled nitric oxide measurement, spirometry, and condensate collection. Condensate samples were analyzed by means of NMR spectroscopy. Linear and partial least squares discriminant analyses were applied to data obtained from the NMR spectra.

MEASUREMENTS AND MAIN RESULTS

The combination of exhaled nitric oxide and FEV(1) discriminates children with asthma and healthy children with a success rate of approximately 81%, whereas selected signals from NMR spectra offer a slightly better discrimination (approximately 86%). The selected NMR variables derive from the region of 3.2 to 3.4 ppm, indicative of oxidized compounds, and from the region of 1.7 to 2.2 ppm, indicative of acetylated compounds.

CONCLUSIONS

Metabolomics can be applied to exhaled breath condensate, leading to the characterization of airway biochemical fingerprints. The presence of acetylated compounds suggests new metabolic pathways that may have a role in asthma pathophysiology.

Metabolomic biomarkers: their role in the critical path

Global metabolic profiling is being applied to identify biomarkers of health. Some small molecules are exquisitely sensitive indicators of health status. Metabolic profiling analyses are being used to determine biomarkers of drug safety and effectiveness as well as disease diagnosis and prognosis including organ transplant rejection. To understand the mechanism(s) of drug toxicity and disease, a systems biology approach that considers the information generated from metabolic profiling, genetics, transcriptomics and proteomics research paradigms is necessary. This will allow for a better understanding of the mechanism(s) of drug interactions and disease while possibly identifying susceptible populations, an important goal in the move toward personalized medicine.:

Diagnosing diabetic nephropathy by 1H NMR metabonomics of serum

OBJECT

The most severe complication of type 1 diabetes (T1DM) is diabetic nephropathy. It is associated with a high risk of cardiovascular complications and premature death and requires early detection to be efficiently treated. The clinical practice to diagnose diabetic nephropathy is also a non-optimal and tedious set up based on albumin excretion rate in multiple overnight or 24h urine samples. Conversely, in this study, these independent diagnostic data are used to provide a realistic testing case for applying (1)H NMR metabonomics of serum in a diagnostic fashion.

MATERIALS AND METHODS

182 T1DM and 21 non-diabetic (non-T1DM) individuals were studied. The (1)H NMR of serum at 500 MHz was targeted at two molecular windows: lipoprotein lipids and low-molecular-weight metabolites.

RESULTS

T1DM and non-T1DM individuals were exclusively separated by (1)H NMR. For diabetic nephropathy diagnosis in the T1DM patients, (1)H NMR data (and clinical biochemistry data) gave a sensitivity of 87.1% (83.9%) and a specificity of 87.7% (95.9%). The predictive values of positive and negative tests were 89.0% (95.5%) and 83.6% (79.2%), respectively.

CONCLUSIONS

(1)H NMR metabonomics clearly distinguishes metabolic characteristics of T1DM and appears approximately as good a means to diagnose diabetic nephropathy from serum as an advanced set of biochemical variables.

Monitoring the health to disease continuum with global metabolic profiling and systems biology

Global metabolic profiling, which includes both metabolomics and metabonomics studies, is the latest ‘omics’ research platform that is being applied to understand the health and disease continuum. Metabolic profiling analyses have been demonstrated for the investigation of inborn errors of metabolism, organ transplant rejection, drug toxicity, disease diagnosis and prognosis, drug efficacy and nutritional status. Combining information generated from a metabolic profiling platform with that obtained based on genetics, transcriptomics and proteomics research paradigms will pave the way for a better understanding of the mechanisms of disease and toxicity. Metabolomics and nutrition will lay the groundwork for the application of personalized medicine in the 21st century.

Application of proton nuclear magnetic resonance spectroscopy to the study of Cryptococcus and cryptococcosis

Proton nuclear magnetic resonance spectroscopy is a nondestructive technique that identifies chemicals in solution and in living cells. It has been used in cryptococcal research to identify the primary structure of capsular glucuronoxylomannans, link cellular apoptosis susceptibility (CAS) genes to positioning of residues on the mannose backbone of glucuronoxylomannan, and verify that the cryptococcal virulence determinant, phospholipase B, is elaborated in vivo. Promising clinical applications include speciation (Cryptococcus neoformans and Cryptococcus gattii), with preliminary evidence that varieties neoformans and grubii can also be distinguished, non-invasive diagnosis of cerebral cryptococcomas, and, in cases of meningitis, monitoring therapeutic response by analysis of cerebrospinal fluid.

The application of NMR-based metabonomics in neurological disorders

Advances in postgenomic technologies have radically changed the information output from complex biological systems, generating vast amounts of high complexity data that can be interpreted by means of chemometric and bioinformatic methods to achieve disease diagnosis and prognosis. High-resolution nuclear magnetic resonance (NMR) spectroscopy of biofluids such as plasma, cerebrospinal fluid (CSF), and urine can generate robust, interpretable metabolic fingerprints that contain latent information relating to physiological or pathological status. This technology has been successfully applied to both preclinical and clinical studies of neurodegenerative diseases such as Huntington's disease, muscular dystrophy, and cerebellar ataxia. An extension of this technology, (1)H magic-angle-spinning (HRMAS) NMR spectroscopy, can be used to generate metabolic information on small intact tissue samples, providing a metabolic link between metabolic profiling of biofluids and histology. In this review we provide a summary of high-resolution NMR studies in neurodegenerative disease and explore the potential of metabonomics in evaluating disease progression with respect to therapeutic intervention.

Metabonomics techniques and applications to pharmaceutical research & development

In this review, the background to the approach known as metabonomics is provided, giving a brief historical perspective and summarizing the analytical and statistical techniques used. Some of the major applications of metabonomics relevant to pharmaceutical Research & Development are then reviewed including the study of various influences on metabolism, such as diet, lifestyle, and other environmental factors. The applications of metabonomics in drug safety studies are explained with special reference to the aims and achievements of the Consortium for Metabonomic Toxicology. Next, the role that metabonomics might have in disease diagnosis and therapy monitoring is provided with some examples, and the concept of pharmacometabonomics as a way of predicting an individual's response to treatment is highlighted. Some discussion is given on the strengths and weaknesses, opportunities of, and threats to metabonomics.