Automatic data reduction and pattern recognition methods for analysis of 1H nuclear magnetic resonance spectra of human urine from normal and pathological states

Ethyl glucoside in human urine following dietary exposure: detection by 1H NMR spectroscopy as a result of metabonomic screening of humans

Metabonomic screening of human urine samples using 1H NMR spectroscopy has revealed the presence of signals resulting from the excretion of ethyl glucoside. Experiments in volunteers have demonstrated that this ethyl glucoside results from dietary exposure to the compound, which is present in beverages such as rice wine and sake, rather than representing a new route for the metabolism of ethanol by humans. The limited studies undertaken in volunteers indicate that ethyl glucoside has a longer biological half life than ethanol itself. The potential problems associated with using this glucoside metabolite as a marker of ethanol consumption are considered.

INTERMAP: background, aims, design, methods, and descriptive statistics (nondietary)

Blood pressure (BP) above optimal (< or =120/< or =80 mmHg) is established as a major cardiovascular disease (CVD) risk factor. Prevalence of adverse BP is high in most adult populations; until recently research has been sparse on reasons for this. Since the 1980s, epidemiologic studies confirmed that salt, alcohol intake, and body mass relate directly to BP; dietary potassium, inversely. Several other nutrients also probably influence BP. The DASH feeding trials demonstrated that with the multiple modifications in the DASH combination diet, SBP/DBP (SBP: systolic blood pressure, DBP: diastolic blood pressure) was sizably reduced, independent of calorie balance, alcohol intake, and BP reduction with decreased dietary salt. A key challenge for research is to elucidate specific nutrients accounting for this effect. The general aim of the study was to clarify influences of multiple nutrients on SBP/DBP of individuals over and above effects of Na, K, alcohol, and body mass. Specific aims were, in a cross-sectional epidemiologic study of 4680 men and women aged 40-59 years from 17 diverse population samples in China, Japan, UK, and USA, test 10 prior hypotheses on relations of macronutrients to SBP/DBP and on role of dietary factors in inverse associations of education with BP; test four related subgroup hypotheses; explore associations with SBP/DBP of multiple other nutrients, urinary metabolites, and foods. For these purposes, for all 4680 participants, with standardized high-quality methods, assess individual intake of 76 nutrients from four 24-h dietary recalls/person; measure in two timed 24-h urine collections/person 24-h excretion of Na, K, Ca, Mg, creatinine, amino acids; microalbuminuria; multiple nutrients and metabolites by nuclear magnetic resonance and high-pressure liquid chromatography. Based on eight SBP/DBP measurements/person, and data on multiple possible confounders, utilize mainly multiple linear regression and quantile analyses to test prior hypotheses and explore relations of multiple dietary and urinary variables to SBP/DBP of individuals. The 4680 INTERMAP participants are equally divided across four age/gender strata: diverse in ethnicity, education, occupation, physical activity; use of cigarettes, alcohol; diagnosed high BP, CVD, diabetes; CVD family history; women vary in parity, use of contraceptive medication and hormone replacement therapy.

The safety testing of amino acids

The risk assessment of compounds added to foods or taken as supplements is usually based on hazard characterization studies performed in animal test species. A large default uncertainty factor, or margin or exposure, is usually required to allow for possible species differences and human variability in the toxicokinetics and toxicodynamics of the compound. The development of biomarkers offers the potential to rationalize the risk assessment of amino acids, and to refine the extrapolation of data from animals to humans. The use of high resolution nuclear magnetic resonance spectroscopy applied to readily accessible biological fluids, such as urine and plasma, offers great potential for the identification of toxicologically relevant biomarkers in animal studies that can then be applied to studies in humans.

Metabolite profiling in rat urine by liquid chromatography/electrospray ion trap mass spectrometry. Application to the study of heavy metal toxicity

This work reports the use of reverse-phase liquid chromatography coupled to electrospray ion trap (QIT) mass spectrometry for the analysis of the metabolome in rat urine. An injection of 20 microL of urine into the chromatographic system is followed by a slow gradient elution and mass spectrometric detection in the scanning mode from m/z 100-1000 in both positive and negative modes. Over a time scale of 90 min, 30 and 20 resolved peaks were observed in the positive and the negative modes, respectively, corresponding to the presence of a few hundred m/z ratios. By using a QIT analyzer, data-dependent tandem mass spectrometry of selected m/z ratios identified several compounds in rat urine and characterized various chemical families, including carboxylic acids, amines, sulfated compounds, glucuronides and glycosides, by the observation of characteristic fragment ions or neutral losses. The method has been applied to the investigation of the chronic toxicity of heavy metals in rat urine. A few tens of m/z ratios, differing in intensity more than threefold from control values, were observed in both positive and negative modes. The time variations for some selected ions suggest that LC/ESI-MS could allow selective characterization of biomarkers in response to specific toxic compounds.

Physiological variation in metabolic phenotyping and functional genomic studies: use of orthogonal signal correction and PLS-DA

Metabolic phenotyping, or metabotyping, is increasingly being used as a probe in functional genomics studies. However, such profiling is subject to intrinsic physiological variation found in all animal populations. Using a nuclear magnetic resonance-based metabonomic approach, we show that diurnal variations in metabolism can obscure the interpretation of strain-related metabolic differences in two phenotypically normal mouse strains (C57BL10J and Alpk:ApfCD). To overcome this problem, diurnal-related metabolic variation was removed from these spectral data by application of orthogonal signal correction (OSC), a data filtering method. Interpretation of the removed orthogonal variation indicated that diurnal-related variation had been removed and that the AM samples contained higher levels of creatine, hippurate, trimethylamine, succinate, citrate and 2-oxo-glutarate and lower levels of taurine, trimethylamine-N-oxide, spermine and 3-hydroxy-iso-valerate relative to the PM samples. We propose OSC will have great potential removing confounding variation obscuring subtle changes in metabolism in functional genomic studies and will be of benefit to optimising interpretation of proteomic and genomic datasets.

Pathology of hepatocellular carcinoma and its precursors using proton magnetic resonance spectroscopy and a statistical classification strategy

AIM

Apply the statistical classification strategy (SCS) to magnetic resonance spectroscopy (MRS) data from liver biopsies and test its potential to discriminate between normal liver, cirrhotic nodules and nodules of hepatocellular carcinoma with a high degree of accuracy.

METHODS

Liver tissue specimens from 54 patients undergoing either partial (hemi) or total hepatectomy were analysed by one-dimensional proton MRS at 8.5 Tesla. Histologically, these specimens were confirmed as normal (n=31), cirrhotic (n=59), and hepatocellular carcinoma (HCC, n=32). Diagnostic correlation was performed between the MR spectra and histopathology. An SCS was applied consisting of pre-processing MR magnitude spectra to identify spectral regions of maximal discriminatory value, and cross-validated linear discriminant analysis.

RESULTS

SCS applied to MRS data distinguished normal liver tissue from HCC with an accuracy of 100%. Normal liver tissue was distinguished from cirrhotic liver with an accuracy of 92% and cirrhotic liver was distinguished from HCC with an accuracy of 98%.

CONCLUSIONS

SCS applied to proton MRS of liver biopsies provides a robust method to distinguish, with a high degree of accuracy, HCC from both cirrhotic and normal liver.

NMR and pattern recognition studies on liver extracts and intact livers from rats treated with alpha-naphthylisothiocyanate

The metabolite profiles from livers of toxin-treated rats were investigated using high resolution 1H NMR spectroscopy of aqueous (acetonitrile/water), lipidic (chloroform/methanol) extracts and magic angle spinning (MAS)-NMR spectroscopy of intact tissue. Rats were treated with the model cholestatic hepatotoxin, alpha-naphthylisothiocyanate (ANIT, 150 mg/kg) and NMR spectra of liver were analysed using principal components analysis (PCA) to extract novel toxicity biomarker information. 1H NMR spectra of control aqueous extracts showed signals from a range of organic acids and bases, amino acids, sugars, and glycogen. Chloroform/methanol extracts showed signals from a range of saturated and unsaturated triglycerides, phospholipids and cholesterol. The MAS 1H NMR spectra of livers showed a composite of signals found in both aqueous and lipophilic extracts. Following ANIT treatment, 1H NMR-PCA of aqueous extracts indicated a progressive reduction in glucose and glycogen, together with increases in bile acid, choline, and phosphocholine signals. 1H NMR-PCA of chloroform/methanol extracts showed elevated triglyceride levels. The 1H MAS-NMR-PCA analysis allowed direct detection of all of the ANIT-induced tissue perturbations revealed by 1H NMR of extracts, enabling metabolic characterisation of the lesion, which included steatosis, bile duct obstruction and altered glucose/glycogen metabolism. MAS-NMR spectroscopy requires minimal sample preparation and, unlike 1H NMR spectroscopy of tissue extracts, does not discriminate metabolites based on their solubility in a particular solvent and so this is a particularly useful exploratory tool in biochemical toxicology.

Metabonomics: a platform for studying drug toxicity and gene function

The later that a molecule or molecular class is lost from the drug development pipeline, the higher the financial cost. Minimizing attrition is therefore one of the most important aims of a pharmaceutical discovery programme. Novel technologies that increase the probability of making the right choice early save resources, and promote safety, efficacy and profitability. Metabonomics is a systems approach for studying in vivo metabolic profiles, which promises to provide information on drug toxicity, disease processes and gene function at several stages in the discovery-and-development process.

Investigations into biochemical changes due to diurnal variation and estrus cycle in female rats using high-resolution (1)H NMR spectroscopy of urine and pattern recognition

Metabonomic methods utilizing (1)H NMR spectroscopy and pattern recognition analysis (NMR-PR) have been applied to investigate biochemical variation in a control population of female rats over time in relation to diurnal and estrus cycle fluctuations. Urine samples were collected twice daily (6 AM-6 PM and 6 PM-6 AM) from female rats (n = 10) for a period of 10 days. (1)H NMR spectroscopic analysis and PR were performed on each sample. Subtle differences in the endogenous metabolite excretion profiles of urine samples at the various stages of the estrus cycle were observed. The main inherent metabolic clustering in the principal components analysis (PCA) maps was related to interrat variation and was observed in the first two principal components (PCs), accounting for 66% of the variance in these data. Separation of urinary data according to time of sampling (day and night) was achieved in the lower PCs. Some of the differences in the urinary profiles of day and night samples causing this separation were attributed to the increase in metabolic activity of the rat during the night. Individual rat data were also mapped as a function of time, using PCA, to produce a metabolic trajectory, which in a number of cases facilitated separation of one or more stages of the estrus cycle. Several of the fluctuations observed between urine samples collected during the different stages of the estrus cycle may be related to hormone levels. Although variation in metabolite profiles relating to both diurnal and hormonal variation could be detected these perturbations were minor compared with the effects observed due to interrat variation. This is the first time that a hormonal cycle has been described for individuals based on NMR spectroscopic and multivariate analysis of metabolic data and shows the value of metabonomic methods in the investigation of physiological variation and rhythms.

Automated mode-of-action detection by metabolic profiling

Rapid classification and identification of the mode-of-action of bioactive compounds applied to plants can be achieved by a robust and easy-to-use metabolic-profiling method. This method uses artificial neural network analysis of one-dimensional proton NMR spectra of aqueous plant extracts to rapidly classify changes in the total metabolic profile caused by application of crop protection chemicals.

Directly coupled high-performance liquid chromatography and nuclear magnetic resonance spectroscopic with chemometric studies on metabolic variation in Sprague--Dawley rats

We report here the first combined use of NMR-PR (pattern recognition) analysis and directly coupled HPLC--NMR analysis to identify metabolic subpopulations in normal laboratory animals and their discriminating endogenous urinary biomarkers. Urine samples obtained from control Sprague-Dawley rats (n = 68) were analyzed using (1)H NMR spectroscopy and principal components (PC) analysis to investigate physiological variability. Two distinct subpopulations of animals were classified based on metabolite excretion profiles. Analysis of the PC loadings established the spectral regions that were responsible for classification of the subpopulations and was used to direct the identification of biomarkers using a directly coupled HPLC--NMR analysis. One population had low urinary hippurate levels together with an increased concentration of 3-(3-hydroxyphenyl)propionic acid (3-HPPA)and 3-hydroxycinnamic acid (3-HCA). The other subpopulation excreted high levels of hippurate. Thus, we report the bimodal occurrence of hippuric acid and chlorogenic acid metabolites in a genetically homogeneous population of rats maintained under identical conditions, which may have significance in relation to the understanding of the consequences of biochemical variation in animals used for drug toxicity testing.

Investigation of the metabolite variation in control rat urine using (1)H NMR spectroscopy

An exploratory statistical analysis has been undertaken of 640 (1)H NMR spectra of rat urine, obtained from predose and control animals during the course of eight separate toxicology studies. The aim was to determine the degree and type of variation between (1)H NMR spectra from such control animals and to investigate the variations in the spectral descriptors based on averaged peak intensities. The results showed that many of the spectral descriptors had skew and/or multimodal distributions, and that it was possible to distinguish between samples of urine collected at different times of day with a success rate of (89%) and to classify 90% of the predose spectra into their correct study group using principal component and linear discriminant analyses. The results show that successful classification can be achieved of NMR spectra of control rat urine, which exhibit more subtle changes than those previously reported when treated and control animals were compared. The results presented here suggest that it will be possible to identify very subtle toxicological changes if care is taken to standardize the experimental conditions used during toxicity screens.

An NMR-based metabonomic approach to investigate the biochemical consequences of genetic strain differences: application to the C57BL10J and Alpk:ApfCD mouse

As the human genome sequencing projects near completion, there is an active search for technologies that can provide insights into the genetic basis for physiological variation and interpreting gene expression in terms of phenotype at the whole organism level in order to understand the pathophysiology of disease. We present a novel metabonomic approach to the investigation of genetic influences on metabolic balance and metabolite excretion patterns in two phenotypically normal mouse models (C57BL10J and Alpk:ApfCD). Chemometric techniques were applied to optimise recovery of biochemical information from complex (1)H NMR urine spectra and to determine metabolic biomarker differences between the two strains. Differences were observed in tricarboxylic acid cycle intermediates and methylamine pathway activity. We suggest here a new 'metabotype' concept, which will be of value in relating quantitative physiological and biochemical data to both phenotypic and genetic variation in animals and man.

Pattern recognition analysis of endogenous cell metabolites for high throughput mode of action identification: removing the postscreening dilemma associated with whole-organism high throughput screening

Although whole-organism HTS can give clear indications of in vivo activity, typically few clues are given as to the mechanism of action (MOA), and determining the MOA for large numbers of active compounds can be costly and complex-an alternative approach is required. This report demonstrates that it is possible to conduct relatively high throughput MOA characterization of HTS hits utilizing a single sample preparation and analytical method. By monitoring a wide range of endogenous cellular metabolites via (1)H nuclear magnetic resonance spectroscopy, the MOA of herbicides can be predicted using computational methods to compare the metabolite perturbation patterns. Herbicides that induce a characteristic pattern of metabolic perturbation in maize include inhibitors of acetolactate synthase, acetyl co-enzyme A carboxylase, protoporphyrinogen oxidase, 5-enolpyruvylshikimate-3-phosphate synthase, and phytoene desaturase. In soya, photosystem II inhibitors can also be detected, further demonstrating that this method is not limited to inhibitors of enzymes that directly act upon endogenous metabolites, or a single species. The methods, including data analysis, can be readily automated, enabling relatively high throughput MOA elucidation of whole-organism screen hits. Additionally, for compounds with a novel MOA, this approach may lead to MOA identification faster than traditional methods. It is envisaged that application of these data analysis methods to other data types-for example, transcription (mRNA) or translation (protein) profiles-is likely to permit higher throughput with smaller sample requirements, along with ability to discriminate MOAs that are not adequately discriminated based upon endogenous metabolite profiles.

Distinction between normal and renal cell carcinoma kidney cortical biopsy samples using pattern recognition of (1)H magic angle spinning (MAS) NMR spectra

The technique of magic angle spinning (MAS) high resolution (1)H NMR spectroscopy applied to intact tissues provides excellent peak resolution and thus much biochemical information. The use of computer-based pattern recognition techniques to classify human renal cortex tissue samples as normal or tumour based on their (1)H MAS NMR spectra has been investigated. In this preliminary study of 22 paired control and tumour samples, exploratory data analysis using principal components based on NMR spectral intensities showed clear separation of the two classes. Furthermore, using the supervised method of linear discriminant analysis, based on individual data point intensities or on integrated spectral regions, it was possible to distinguish between the normal and tumour kidney cortex tissue with 100% accuracy, including a single example of a metastatic tumour from a primary lung carcinoma. A tumour sample from the collecting duct of the kidney showed a different NMR spectral profile, and pattern recognition indicated that this sample did not classify with the cortical tumours.

Heteronuclear NMR studies of metabolites produced by Cryptococcus neoformans in culture media: identification of possible virulence factors

The yeast, Cryptococcus neoformans var. neoformans is a major contributor to the morbidity and mortality experienced by the immunosuppressed population. With a view to providing better treatment, identification of cryptococcal virulence factors is an important goal, with most effort to date directed toward the significance of structural variations in the polysaccharide capsule. The present work describes the characterization of supernatants obtained from cryptococcal cultures. This was achieved by thorough identification of the spin systems of individual metabolites through both homonuclear and heteronuclear NMR experiments that circumvented the difficulties imposed by limited dispersion and a range of concentrations in different cultures covering more than 3 orders of magnitude. More than 30 metabolites, including amino acids, alditols, nucleosides, acetate, and ethanol, were identified by their (1)H and (13)C chemical shifts and observed long-range correlations. The possible contribution of some detected substances to the pathogenicity of Cryptococcus neoformans is discussed. Magn Reson Med 42:442-453, 1999.

High-resolution magic angle spinning 1H NMR spectroscopic studies on intact rat renal cortex and medulla

High-resolution magic angle spinning 1H NMR (MAS-NMR) spectroscopy was used to investigate the biochemical composition of normal renal cortex and renal papilla samples from rats, and results were compared with those from conventional 1H NMR analysis of protein-free tissue extracts. 1H MAS NMR spectra of samples obtained from inner and outer cortex were found to be broadly similar in terms of metabolite profile, and intra- and inter-animal variability was small. However, the MAS NMR spectra from renal papilla samples were qualitatively and quantitatively different from those obtained from cortex. High levels of free amino acids and several organic acids were detected in the cortex, together with choline, glucose, and trimethylamine-N-oxide. The dominant metabolite resonances observed in papillary tissue were from glycerophosphocholine (GPC), betaine, myo-inositol, and sorbitol. On increasing the magic angle spinning rate from 4,200 to 12,000 Hz, the lipid MAS 1H NMR signal profile remained largely unchanged in papillary tissue, whereas "new" resonances from triglycerides appeared in the spectra of cortical tissue, this effect being reversible on returning the spinning rate to 4,200 Hz. Further investigation into the behavior of the lipid components under different spinning rates suggested that the lipids in the cortex were present in more motionally constrained environments than those in the papilla. 1H MAS NMR spectra of tissues are of value both in interrogation of the biochemical composition of whole tissue, and in obtaining information on the mobility and compartmentalization of certain metabolites.

Paraquat-induced renal injury studied by 1H nuclear magnetic resonance spectroscopy of urine

The herbicide paraquat (1,1′-dimethyl-4,4′-bipyridylium dichloride; PQ), is a poison known to cause delayed mortality due to lung and kidney injuries. High-resolution proton nuclear magnetic resonance (1H NMR) spectroscopy has been extensively applied in evaluating nephrotoxicity by the characteristic perturbations in the excretion pattern of low molecular weight endogenous metabolites. The application of the method allows the rapid localization of the renal injury noninvasively. In this study, we report 1H NMR and conventional clinical chemistry urinalysis in two patients suffering from paraquat intoxication after overdose with suicidal intent. The alterations in the urine NMR spectrum suggest necrosis of the pars recta of the proximal renal tubules. The molecule of paraquat is also clearly detected in the same spectrum. In conclusion, the rapid screening of urine by NMR spectroscopy provides information about both the identity of the poison and the abnormal pattern of endogenous metabolites that characterize the location of the injury in renal tubules and reveals alterations in unusual metabolites that are not commonly measured.

Towards a method for automated classification of 1H MRS spectra from brain tumours

Recent studies have shown that MRS can substantially improve the non-invasive categorization of human brain tumours. However, in order for MRS to be used routinely by clinicians, it will be necessary to develop reliable automated classification methods that can be fully validated. This paper is in two parts: the first part reviews the progress that has been made towards this goal, together with the problems that are involved in the design of automated methods to process and classify the spectra. The second part describes the development of a simple prototype system for classifying 1H single voxel spectra, obtained at an echo time (TE) of 135 ms, of the four most common types of brain tumour (meningioma (MM), astrocytic (AST), oligodendroglioma (OD) and metastasis (ME)) and cysts. This system was developed in two stages: firstly, an initial database of spectra was used to develop a prototype classifier, based on a linear discriminant analysis (LDA) of selected data points. Secondly, this classifier was tested on an independent test set of 15 newly acquired spectra, and the system was refined on the basis of these results. The system correctly classified all the non-astrocytic tumours. However, the results for the the astrocytic group were poorer (between 55 and 100%, depending on the binary comparison). Approximately 50% of high grade astrocytoma (glioblastoma) spectra in our data base showed very little lipid signal, which may account for the poorer results for this class. Consequently, for the refined system, the astrocytomas were subdivided into two subgroups for comparison against other tumour classes: those with high lipid content and those without.

Development of a model for classification of toxin-induced lesions using 1H NMR spectroscopy of urine combined with pattern recognition

Pattern recognition approaches were developed and applied to the classification of 600 MHz 1H NMR spectra of urine from rats dosed with compounds that induced organ-specific damage in either the liver or kidney. Male rats were separated into groups (n = 5) and each treated with one of the following compounds; adriamycin, allyl alcohol, 2-bromoethanamine hydrobromide, hexachlorobutadiene, hydrazine, lead acetate, mercury II chloride, puromycin aminonucleoside, sodium chromate, thioacetamide, 1,1,2-trichloro-3,3,3-trifluoro-1-propene or dose vehicle. Urine samples were collected over a 7 day time-course and analysed using 600 MHz 1H NMR spectroscopy. Each NMR spectrum was data-reduced to provide 256 intensity-related descriptors of the spectra. Data corresponding to the periods 8-24 h, 24-32 h and 32-56 h post-dose were first analysed using principal components analysis (PCA). In addition, samples obtained 120-144 h following the administration of adriamycin and puromycin were included in the analysis in order to compensate for the late onset of glomerular toxicity. Having established that toxin-related clustering behaviour could be detected in the first three principal components (PCs), three-quarters of the data were used to construct a soft independent modelling of class analogy (SIMCA) model. The remainder of the data were used as a test set of the model. Only three out of 61 samples in the test set were misclassified. Finally as a further test of the model, data from the 1H NMR spectra of urine from rats that had been treated with uranyl nitrate were used. Successful prediction of the toxicity type of the compound was achieved based on NMR urinalysis data confirming the robust nature of the derived model.

Renal papillary necrosis--40 years on

Analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are well recognized as a major class of therapeutic agent that causes renal papillary necrosis (RPN). Over the last decade a broad spectrum of other therapeutic agents and many chemicals have also been reported that have the potential to cause this lesion in animals and man. There is consensus that RPN is the primary lesion that can progress to cortical degeneration; and it is only at this stage that the lesion is easily diagnosed. In the absence of sensitive and selective noninvasive biomarkers of RPN there is still no clear indication of which compound, under what circumstances, has the greatest potential to cause this lesion in man. Attempts to mimic RPN in rodents using analgesics and NSAIDs have not provided robust models of the lesion. Thus, much of the research has concentrated on those compounds that cause an acute or subacute RPN as the basis by which to study the pathogenesis of the lesion. Based on the mechanistic understanding gleaned from these model compounds it has been possible to transpose an understanding of the underlying processes to the analgesics and NSAIDs. The mechanism of RPN is still controversial. There are data that support microvascular changes and local ischemic injury as the underlying cause. Alternatively, several model papillotoxins, some analgesics, and NSAIDs target selectively for the medullary interstitial cells, which is the earliest reported aberration, after which there are a series of degenerative processes affecting other renal cell types. Many papillotoxins have the potential to undergo prostaglandin hydroperoxidase-mediated metabolic activation, specifically in the renal medullary interstitial cells. These reactive intermediates, in the presence of large quantities of polyunsaturated lipid droplets, result in localized and selective injury of the medullary interstitial cells. These highly differentiated cells do not repair, and it is generally accepted that continuing insult to these cells will result in their progressive erosion. The loss of these cells is thought to be central to the degenerative cascade that affects the cortex. There is still a need to understand better the primary mechanism and the secondary consequences of RPN so that the risk of chemical agents in use and novel molecules can be fully assessed.

Normal ultrastructure of the kidney and lower urinary tract

The mammalian urinary tract includes the kidneys, ureters, urinary bladder, and urethra. The renal parenchyma is composed of the glomeruli and a heterogeneous array of tubule segments that are specialized in both function and structure and are arranged in a specific spatial distribution. The ultrastructure of the glomeruli and renal tubule epithelia have been well characterized and the relationship between the cellular structure and the function of the various components of the kidney have been the subject of intense study by many investigators. The lower urinary tract, the ureters, urinary bladder, and urethra, which are histologically similar throughout, are composed of a mucosal layer lined by transitional epithelium, a tunica muscularis, and a tunica serosa or adventitia. The present manuscript reviews the normal ultrastructural morphology of the kidney and the lower urinary tract. The normal ultrastructure is illustrated using transmission electron microscopy of normal rat kidney and urinary bladder preserved by in vivo perfusion with glutaraldehyde fixative and processed in epoxy resin.

750 MHz 1H NMR spectroscopy characterisation of the complex metabolic pattern of urine from patients with inborn errors of metabolism: 2-hydroxyglutaric aciduria and maple syrup urine disease

750 MHz 1H NMR spectroscopy has been used to characterise in detail the abnormal low molecular weight metabolites of urine from two patients with inborn errors of metabolism. One case of the rare condition 2-hydroxyglutaric aciduria has been examined. There is at present no rapid routine method to detect this genetic defect, although NMR spectroscopy of urine is shown to provide a distinctive pattern of resonances. Assignment of a number of prominent urinary metabolites not normally seen in control urine could be made on the basis of their known NMR spectral parameters including the diagnostic marker 2-hydroxyglutaric acid, which served to confirm the condition. In addition, 750 MHz 1H NMR spectroscopy has been used to characterise further the abnormal metabolic profile of urine from a patient with maple syrup urine disease. This abnormality arises from a defect in branched chain keto-acid decarboxylase activity and results in a build up in the urine of high levels of branched chain oxo- and hydroxy-acids resulting from altered metabolism of the branched chain amino acids, valine, leucine and isoleucine. A number of previously undetected abnormal metabolites have been identified through the use of one-dimensional and two-dimensional J-resolved and COSY 750 MHz 1H NMR spectroscopy, including ethanol, 2-hydroxy-isovalerate, 2,3-dihydroxy-valerate, 2-oxo-3-methyl-n-valerate and 2-oxo-isocaproate. NMR spectroscopy of urine, particularly when combined with automatic data reduction and computer pattern recognition using a combination of biochemical markers, promises to provide an efficient alternative to other techniques for the diagnosis of inborn errors of metabolism.

High-resolution diffusion and relaxation edited one- and two-dimensional 1H NMR spectroscopy of biological fluids

A new approach to the characterization of biomolecules in whole biological fluids is presented based on simplification of 1H NMR spectra by utilizing differences in molecular diffusion coefficients alone and combinations of relaxation and diffusion parameters. New NMR pulse sequences incorporating both spectral editing features together with solvent water resonance elimination are presented. The methods are exemplified using whole human blood plasma, and it is shown that it is possible to obtain NMR spectra of the slowly diffusing species (generally large molecules) by diffusion editing, the slowly relaxing species (generally small molecules) by spin relaxation editing, or spectra showing any range of molecular mobility using a combination of the two methods. The diffusion-based editing methods are also applicable to the selection of resonances in two-dimensional NMR spectroscopy of biofluids, and we show this for the first time by the production of 1H-1H diffusion-edited TOCSY spectra of human blood plasma where the resonance intensities are weighted according to the molecular diffusion coefficient. In this case, by measuring a diffusion-edited 1H-1H TOCSY NMR spectrum of plasma, it is possible to obtain signals from only the macromolecular components, and this may be of benefit in the analysis of blood lipoproteins. In complex biofluids, the combination of diffusion and relaxation editing brings about considerable spectral simplification leading to an easier resonance assignment process. We also demonstrate the production of 1H NMR spectra with intensities corresponding to diffusion coefficient rather than number of protons, and this opens up new possibilities for pattern recognition classification of samples based on altered molecular mobility features of biofluid components.

Analysis of fetal and neonatal urine using proton nuclear magnetic resonance spectroscopy

AIM

To use high field proton nuclear magnetic resonance spectroscopy (1H NMR) to characterise the low molecular weight metabolite composition of neonatal and fetal urine in relation to gestational age and perinatal outcome.

METHODS

The first urine passed by two neonatal groups, six full term and five preterm infants with normal renal function, was analysed by 1H NMR and compared with fetal urine from 14 cases with obstructive uropathy.

RESULTS

The mean ratios of taurine, myo-inositol, and trimethylamine-N-oxide (TMAO) to creatinine were 4.3, 10.1, and 14.1 times higher, respectively, in the preterm group when compared with those of the full term group. Fetal obstructive uropathy was characterised by glycosuria, amino and organic aciduria, regardless of gestational age (13-30 weeks).

CONCLUSIONS

Samples of the first urine passed--that is, urine produced in fetal life--by normal preterm infants are useful controls for cases of obstructive uropathy detected in the third trimester. 1H NMR will become a clinically useful tool for monitoring renal development and abnormalities in utero.

Classification of toxin-induced changes in 1H NMR spectra of urine using an artificial neural network

NMR spectra of urine from rats treated with a range of liver, kidney and testicular toxins at various doses were measured and classified using neural network methods. Toxin-induced changes in the levels of 18 low molecular weight endogenous urinary metabolites were assessed using a simple semi-quantitative scoring system. These scores were used as input to an artificial neural network, the use of which has been explored as a means of predicting the class of toxin. With this limited data set, based only the level of the maximal changes of these 18 metabolites, the network was able to predict the class and hence target organ of the toxins. Renal cortical toxicity was well predicted as was liver toxicity. The few examples of renal medullary toxins in the data set resulted in relatively poor training of the network although correct classification was still possible.