D-Serine-induced nephrotoxicity: a HPLC-TOF/MS-based metabonomics approach

Dietary restriction and medical therapy drives PPARα-regulated improvements in early diabetic kidney disease in male rats

The attenuation of diabetic kidney disease (DKD) by metabolic surgery is enhanced by pharmacotherapy promoting renal fatty acid oxidation (FAO). Using the Zucker Diabetic Fatty and Zucker Diabetic Sprague Dawley rat models of DKD, we conducted studies to determine if these effects could be replicated with a non-invasive bariatric mimetic intervention. Metabolic control and renal injury were compared in rats undergoing a dietary restriction plus medical therapy protocol (DMT; fenofibrate, liraglutide, metformin, ramipril, and rosuvastatin) and ad libitum-fed controls. The global renal cortical transcriptome and urinary 1H-NMR metabolomic profiles were also compared. Kidney cell type-specific and medication-specific transcriptomic responses were explored through in silico deconvolution. Transcriptomic and metabolomic correlates of improvements in kidney structure were defined using a molecular morphometric approach. The DMT protocol led to ∼20% weight loss, normalized metabolic parameters and was associated with reductions in indices of glomerular and proximal tubular injury. The transcriptomic response to DMT was dominated by changes in fenofibrate- and peroxisome proliferator-activated receptor-α (PPARα)-governed peroxisomal and mitochondrial FAO transcripts localizing to the proximal tubule. DMT induced urinary excretion of PPARα-regulated metabolites involved in nicotinamide metabolism and reversed DKD-associated changes in the urinary excretion of tricarboxylic acid (TCA) cycle intermediates. FAO transcripts and urinary nicotinamide and TCA cycle metabolites were moderately to strongly correlated with improvements in glomerular and proximal tubular injury. Weight loss plus pharmacological PPARα agonism is a promising means of attenuating DKD.

Intestinal microbiome and metabolome analyses reveal metabolic disorders in the early stage of renal transplantation

Renal transplantation is the most effective treatment for end-stage renal disease, but the long-term prognosis of organs after transplantation is not ideal. In recent years, the importance of gut microbes and metabolites in the study of disease mechanisms has gradually received attention. However, the coordination between gut microbes and the metabolism of renal transplant patients needs further study. We integrated 16s sequencing and metabolomics data to describe the changes in the serum and fecal metabolites of renal transplant patients. Our data revealed that the gut microbial diversity decreased and the relative abundance of many bacteria, such as Enterococcus and Streptococcus, significantly changed after transplantation. In addition, a large number of amino acids and peptides in serum and feces significantly changed, suggesting an abnormal amino acid metabolism after transplantation. Spearman's correlation analysis revealed the changes in the co-metabolism pattern between gut microbes and the host metabolism after transplantation. Furthermore, Enterococcus was found to be correlated with renal functions and metabolites reflecting renal damage. This study provides potential gut microbes and metabolites impacting renal health, which helps in understanding the renal damage in patients with kidney transplantation.

Metabolomics analysis of serum in pediatric nephrotic syndrome based on targeted and non-targeted platforms

BACKGROUND AND AIMS

Nephrotic syndrome (NS) is a common pediatric urinary system disease. The aim in this work was to investigate the changes in pediatric NS-related metabolites through serum metabolomics, and explore the new potential metabolites and differential metabolic pathways.

METHODS

Serum samples from 40 pediatric patients with nephrotic syndrome and 40 healthy controls were collected. The targeted and non-targeted metabolomics analyses were performed to determine the metabolic changes in pediatric NS. Based on multivariate statistical analysis and the regression model, the serum potential metabolites were screened and different metabolic pathways were explored.

RESULTS

39 differential metabolites in pediatric NS were obtained based on the metabolomics analysis. 12 differential metabolites (serine, C18: 2 (EFA), C18: 2 (FFA), Isonuatigenin 3- [rhamnosyl- (1- > 2) -glucoside], C18: 4 (EFA), C18: 4 (FFA), caprylic acid, citric acid, methylmalonic acid, caproic acid, canavalioside and uroporphyrin were identified to establish the diagnostic model for pediatric NS. Five metabolic pathways including TCA cycle, amino acid metabolism, bile acid biosynthesis, linoleate metabolism and glyoxylate and dicarboxylate metabolism were the key differential metabolic pathways.

CONCLUSION

These data elucidated the metabolic alterations associated with pediatric NS and suggested a new diagnosis model for monitoring pediatric NS. The current study provides the useful information to bridge the gaps in our understanding of the metabolic alterations associated with pediatric NS and might facilitate the characterization of pediatric NS patients by performing serum metabolomics.

Application of omics technologies in dermatological research and skin management

BACKGROUND

"Omics" are usually based on the use of high-throughput analysis methods for global analysis of biological samples and the discovery of biomarkers, and may provide new insights into biological phenomena. Over the last few years, the development of omics technologies has considerably accelerated the pace of dermatological research.

AIMS

The purpose of this article was to review the development of omics in recent decades and their application in dermatological research.

METHODS

An extensive literature search was conducted on omics technologies since the first research on omics.

RESULTS

This article summarizes the history and main research methods of the six omics technologies, including genomics, transcriptomics, proteomics, metabolomics, lipidomics, and microbiomics. Their application in certain skin diseases and cosmetics research and development are also summarized.

CONCLUSIONS

This information will help to understand the mechanism of some skin diseases and the discovery of potential biomarkers, and provide new insights for skin health management and cosmetics research and development.

Urine Metabolomics Study on Potential Hepatoxic Biomarkers Identification in Rats Induced by Aurantio-Obtusin

Previous studies revealed the hepatotoxic effect of aurantio-obtusin on rats. The aim of this study was to identify potential biomarkers of urine caused by aurantio-obtusin. Sprague–Dawley (SD) rats with body weight of 0, 4, 40, and 200 mg/kg were orally given aurantio-obtusin for 28 days, and urine was collected for 24 h after the last administration. The urine metabolites in the aurantio-obtusin group and the control group were analyzed by ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). Twenty-three metabolites were identified as potential biomarkers, and 10 of them were up-regulated, including xanthosine, hippuric acid, 5-L-glutamyl-taurine, etc. The other 13 biomarkers were down-regulated, including thymidine, 3-methyldioxyindole, cholic acid, etc. The significant changes of these biomarkers indicated that purine metabolism, taurine and hypotaurine metabolism, primary bile acid biosynthesis, pyrimidine metabolism, and tryptophan metabolism played an important role in the hepatotoxicity of aurantio-obtusin in rats. In this paper, the safety and potential risk of aurantio-obtusin were studied for the first time by combining the toxicity of aurantio-obtusin with the results of urine metabolomics, which provided information for the mechanism of liver injury induced by aurantio-obtusin.

Metabolomics in pharmacology - a delve into the novel field of pharmacometabolomics

Introduction: Pharmacometabolomics is an emerging science pursuing the application of precision medicine. Combining both genetic and environmental factors, the so-called pharmacometabolomic approach guides patient selection and stratification in clinical trials and optimizes personalized drug dosage, improving efficacy and safety.Areas covered: This review illustrates the progressive introduction of pharmacometabolomics as an innovative solution for enhancing the discovery of novel drugs and improving research and development (R&D) productivity of the pharmaceutical industry. An extended analysis on published pharmacometabolomics studies both in animal models and humans includes results obtained in several areas such as hepatology, gastroenterology, nephrology, neuropsychiatry, oncology, drug addiction, embryonic cells, neonatology, and microbiomics.Expert opinion: a tailored, individualized therapy based on the optimization of pharmacokinetics and pharmacodynamics, the improvement of drug efficacy, and the abolition of drug toxicity and adverse drug reactions is a key issue in precision medicine. Genetics alone has become insufficient for deciphring intra- and inter-individual variations in drug-response, since they originate both from genetic and environmental factors, including human microbiota composition. The association between pharmacogenomics and pharmacometabolomics may be considered the new strategy for an in-deep knowledge on changes and alterations in human and microbial metabolic pathways due to the action of a drug.

Urinary metabolomics reveals the therapeutic effect of HuangQi Injections in cisplatin-induced nephrotoxic rats

The side effects of cisplatin (CDDP), notably nephrotoxicity, greatly limited its use in clinical chemotherapy. HuangQi Injections (HI), a commonly used preparation of the well-known Chinese herbal medicine Astragali radix, appeared to be promising treatment for nephrotoxicity without compromising the anti-tumor activity of CDDP. In this study, the urinary metabolomics approach using liquid chromatography time of flight mass spectrometry (LC-TOF/MS) was developed to assess the toxicity-attenuation effects and corresponding mechanisms of HI on CDDP-exposed rats. As a result, successive administration of HI significantly recovered the decline of body weight and downregulated the abnormal increase of serum creatinine and urea. HI partly restored the CDDP-induced alteration of metabolic profiling back into normal condition. Totally 43 toxicity-attenuation potential biomarkers were screened and tentatively identified, which were involved in important metabolic pathways such as amino acid metabolism, TCA cycle, fatty acid metabolism, vitamin B6 metabolism and purine metabolism. The results clearly revealed that HI could alleviate CDDP-induced nephrotoxicity and improve the disturbed metabolic balance induced by repeated CDDP exposure. The present study provided reliable evidence for the protective effect of HI on CDDP-induced toxicity with the multi-target pharmacological characteristics.

Multipathway Integrated Adjustment Mechanism of Glycyrrhiza Triterpenes Curing Gastric Ulcer in Rats

Background:

Gastric ulcer is a common chronic disease in human digestive system, which is difficult to cure, easy to relapse, and endangers human health seriously. Compared with western medicine, traditional Chinese medicine has a unique advantage in improving the general situation, stablizing medical condition, and with little side effects. Glycyrrhiza known as “king of all the medicine”, has a range of pharmacological activities and is commonly used in a variety of proprietary Chinese medicines and formulations.

Objective:

On the basis of explicit antiulcer effect of Glycyrrhiza triterpenes, the molecular mechanisms of its therapeutic effect on acetic acid induced gastric ulcer in rats were explored.

Materials and Methods:

Acetic acid induced gastric ulcer model in rats was established to evaluate the curing effect of G. triterpenes and all of the rats were randomised into six groups: Control group, model group, omeprazole group (0.8 mg/mL), triterpenes high dose group (378.0 mg/mL), triterpenes middle dose group (126.0 mg/mL), and triterpenes low dose group (42.0 mg/mL). All rats in groups were orally administered the active group solution 1.5 mL once daily (model and control groups with saline) for 7 days. HPLC-TOF-MS analysis method was performed to obtain the plasma metabolites spectrums of control group, model group, triterpenes high, middle and low dose groups.

Results:

A total of 11 differential endogenous metabolites related to the therapeutic effect of G. triterpenes were identified, including tryptophan, phingosine-1-phosphate, pantothenic acid, and so on, among which tryptophan and phingosine-1-phosphate are related with the calcium signaling pathway and arachidonic acid (AA) metabolism. At the same time, in order to verify the above results, quantitative real time polymerase chain reaction were performed to evaluate the expression of H⁺-K⁺-ATPase alpha mRNA and phospholipase a 2 mRNA in relational signaling pathways. Combined with statistical analysis of plasma metabolic spectrum and gene expression in tissue, it is suggested that G. triterpenes has antiulcer effect on gastric ulcer in rats.

Conclusion:

G. triterpenes has a certain regulating effect on the metabolism of tryptophan, AA, sphingosine, and other endogenous metabolites, and we speculated that the antiulcer potential of G. triterpenes can be primarily attributed to its inhibiting gastric acid secretion, reducing the release of inflammatory mediators, and protecting gastric mucosa effects to prevent the further development of gastric ulcer.

SUMMARY

G. triterpenes can obviously relieve the symptoms of gastric ulcer, especially the low dose group.

G. triterpenes can effectively regulate the amount of small molecule metablism in gastric ulcer rats in vivo, including tryptophan, phingosine-1-phosphate, etc.

G. triterpenes resisting gastric ulcer is probably by regulating arachidonic acid metabolism, sphingosine metabolism, etc.

Down-regulation of H+-K+-ATPase alpha subunit mRNA and up-regulation of PLA₂ mRNA in gastric tissue of dose group validated the possible mechanisms of G. triterpenes for the treatment of gastric ulcer

Abbreviations used: HP: Helicobacter pylori, ECL: enterochromaffinlike, TCM: Traditional Chinese medicine; HPLC: High Performance Liquid Chromatography, HPLC/MS: High Performance Liquid chromatography Mass Spectrometry, HPLC-TOF-MS: High Performance Liquid Chromatography and Tof Mass Spectrometry, SD: Sprague Dawley, PCDL: Personal Compound Database and Library, MPP: Mass Profiler Professiona; PCA: principal component analysis, RT-PCR: real time polymerase chain reaction, PGE 2: Prostaglandin E2, COX1: cyclooxygenase 1 S1P: Sphingosine-1-phosphate, AA: Arachidonic acid, 5-HT: 5- hydroxytryptamine.

QGQS Granule in SHR Serum Metabonomics Study Based on Tools of UPLC-Q-TOF and Renin-Angiotensin-Aldosterone System Form Protein Profilin-1

QGQS granule is effective for the therapeutic of hypertension in clinic. The aim of this research is to observe the antihypertension effect of QGQS granule on SHR and explain the mechanism of its lowering blood pressure. 30 SHR were selected as model group, captopril group, and QGQS group, 10 WKYr were used as control group, and RBP were measured on tail artery consciously. And all the serum sample analysis was carried out on UPLC-TOF-MS system to determine endogenous metabolites and to find the metabonomics pathways. Meanwhile, ELISA kits for the determination pharmacological indexes of PRA, AngI, AngII, and ALD were used for pathway confirmatory; WB for determination of profilin-1 protein expression was conducted for Ang II pathway analysis as well. It is demonstrated that QGQS granule has an excellent therapeutic effect on antihypertension, which exerts effect mainly on metabonomics pathway by regulating glycerophospholipid, sphingolipid, and arachidonic acid metabolism, and it could inhibit the overexpression of the profilin-1 protein. We can come to a conclusion that RAAS should be responsible mainly for the metabonomics pathway of QGQS granule on antihypertension, and it plays a very important role in protein of profilin-1 inhibition.

Enhancing NMDA Receptor Function: Recent Progress on Allosteric Modulators

The N-methyl-D-aspartate receptors (NMDARs) are subtype glutamate receptors that play important roles in excitatory neurotransmission and synaptic plasticity. Their hypo- or hyperactivation are proposed to contribute to the genesis or progression of various brain diseases, including stroke, schizophrenia, depression, and Alzheimer's disease. Past efforts in targeting NMDARs for therapeutic intervention have largely been on inhibitors of NMDARs. In light of the discovery of NMDAR hypofunction in psychiatric disorders and perhaps Alzheimer's disease, efforts in boosting NMDAR activity/functions have surged in recent years. In this review, we will focus on enhancing NMDAR functions, especially on the recent progress in the generation of subunit-selective, allosteric positive modulators (PAMs) of NMDARs. We shall also discuss the usefulness of these newly developed NMDAR-PAMs.

Potential urinary biomarkers of nephrotoxicity in cyclophosphamide-treated rats investigated by NMR-based metabolic profiling

The anticancer-drug cyclophosphamide (CP) is known to have nephrotoxicity. The aim of this study was to identify urinary biomarkers indicating CP-induced nephrotoxicity. We investigated the urine metabolic profiles using nuclear magnetic resonance spectrometry of rats administered with single high-doses of CP (0, 30, and 100 mg/kg body weight) and daily low-doses over a 4-week period (0, 1, 3, and 10 mg/kg body weight). Among 18 identified urinary metabolites, 2-oxoglutarate, citrate, hippurate, formate, valine, and alanine for short-term and 2-oxoglutarate, citrate, hippurate, isoleucine, leucine, allantoin, valine, and lysine for long-term were selected as potential biomarkers. Pathway-enrichment analysis suggested that the urinary metabolism of CP is related to valine, leucine, and isoleucine biosynthesis; taurine and hypotaurine metabolism; glyoxylate and dicarboxylate metabolism; citrate cycle; and alanine, aspartate, and glutamate metabolism, with high pathway impact. The potential biomarkers obtained in this study could be used to monitor CP-induced nephrotoxicity relative to dose and treatment time.

Metabolomics in nephrotoxicity

Nephrotoxicity or renal toxicity can be a result of hemodynamic changes, direct injury to cells and tissue, inflammatory tissue injury, and/or obstruction of renal excretion. Nephrotoxicity is frequently induced by a wide spectrum of therapeutic drugs and environ mental pollutants. Knowledge of the complex molecular and pathophysiologic mechanisms leading to nephrotoxicity remains limited, in part, by research that historically focused on single or relatively few risk markers. As such, current kidney injury biomarkers are inadequate in terms of sensitivity and specificity. In contrast, metabolomics enables screening of a vast array of metabolites simultaneously using NMR and MS to assess their role in nephrotoxicity development and progression. A more comprehensive understanding of these biochemical pathways would also provide valuable insight to disease mechanisms critical for drug development and treatment.

UHPLC UHD Q-TOF MS/MS analysis of the impact of sulfur fumigation on the chemical profile of Codonopsis Radix (Dangshen)

Over recent decades sulfur fumigation has been becoming abused in processing some freshly harvested Chinese medicinal herbs, although it is questioned whether sulfur fumigation can result in changes in efficacy and safety of the herbs. One of the herbs commonly processed by sulfur fumigation is Codonopsis Radix (Dangshen). A report showed that lobetyolin content in sulfur-fumigated Dangshen was lower than in air-dried Dangshen. Whereas there is no investigation designed to compare the chemical profiles of the sulfur-fumigated Dangshen and the air-dried Dangshen. In the present study, a rapid and versatile ultra-high-performance liquid chromatography coupled with ultra-high resolution quadrupole time-of-flight mass spectrometry (UHPLC UHD Q-TOF MS/MS) method was developed for comprehensive analysis of the chemical profiles of sulfur-fumigated and air-dried Dangshen samples. Principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) demonstrated that there were significant chemical differences between sulfur-fumigated and air-dried Dangshen samples. Among the changed components, 57 compounds were identified, in which 15 sulfur-containing compounds were detected only in sulfur-fumigated samples. The established methods were successfully applied to discriminate sulfur-fumigated Dangshen among commercial samples. Whether the chemical changes caused by sulfur fumigation affect the clinical efficacy and safety of Dangshen needs to be further investigated.

Potential of metabolomics in preclinical and clinical drug development

Metabolomics is an upcoming technology system which involves detailed experimental analysis of metabolic profiles. Due to its diverse applications in preclinical and clinical research, it became an useful tool for the drug discovery and drug development process. This review covers the brief outline about the instrumentation and interpretation of metabolic profiles. The applications of metabolomics have a considerable scope in the pharmaceutical industry, almost at each step from drug discovery to clinical development. These include finding drug target, potential safety and efficacy biomarkers and mechanisms of drug action, the validation of preclinical experimental models against human disease profiles, and the discovery of clinical safety and efficacy biomarkers. As we all know, nowadays the drug discovery and development process is a very expensive, and risky business. Failures at any stage of drug discovery and development process cost millions of dollars to the companies. Some of these failures or the associated risks could be prevented or minimized if there were better ways of drug screening, drug toxicity profiling and monitoring adverse drug reactions. Metabolomics potentially offers an effective route to address all the issues associated with the drug discovery and development.

Uremic solutes and risk of end-stage renal disease in type 2 diabetes: metabolomic study

Here we studied plasma metabolomic profiles as determinants of progression to ESRD in patients with Type 2 diabetes (T2D). This nested case-control study evaluated 40 cases who progressed to ESRD during 8-12 years of follow-up and 40 controls who remained alive without ESRD from the Joslin Kidney Study cohort. Controls were matched with cases for baseline clinical characteristics; although controls had slightly higher eGFR and lower levels of urinary albumin excretion than T2D cases. Plasma metabolites at baseline were measured by mass spectrometry-based global metabolomic profiling. Of the named metabolites in the library, 262 were detected in at least 80% of the study patients. The metabolomic platform recognized 78 metabolites previously reported to be elevated in ESRD (uremic solutes). Sixteen were already elevated in the baseline plasma of our cases years before ESRD developed. Other uremic solutes were either not different or not commonly detectable. Essential amino acids and their derivatives were significantly depleted in the cases, whereas certain amino acid-derived acylcarnitines were increased. All findings remained statistically significant after adjustment for differences between study groups in albumin excretion rate, eGFR or HbA1c. Uremic solute differences were confirmed by quantitative measurements. Thus, abnormal plasma concentrations of putative uremic solutes and essential amino acids either contribute to progression to ESRD or are a manifestation of an early stage(s) of the disease process that leads to ESRD in T2D.

A urinary metabonomics study on biochemical changes in yeast-induced pyrexia rats: a new approach to elucidating the biochemical basis of the febrile response

Fever is a prominent feature of many diseases, such as infection, inflammation and trauma. In the clinic, fever can be easily judged by measuring the body temperature; however, the pathogenesis of fever is still not fully understood. A febrile response is a systemic pathological process that can cause metabolic disorders. Metabonomics can provide powerful tools to reveal the pathological mechanisms for such a systemic disease. Thus, to reveal subtle metabolic changes under the condition of fever and to explore its mechanism, an ultra performance liquid chromatography coupled with a quadrupole time-of-flight mass spectrometry metabonomics approach was employed to investigate the urine biochemical characteristics of yeast-induced pyrexia rats. The acquired data were subjected to principal component analysis for differentiating the pyrexia rats from the control rats. Potential biomarkers were screened by using orthogonal partial least-squares-discriminant analysis and were identified by accurate mass, database, and MS/MS fragment information obtained from the MS(E) technique. Sixteen metabolites in rat urine were identified as potential biomarkers. The relative intensities of the 15 potential biomarkers were calculated. The thermoregulatory circuitry of "endogenous pyrogen (EP) ↑-hypothalamus Na⁺/Ca²⁺-cAMP↑" was partially confirmed in this study. The results suggested that UPLC/MS-based metabolic profiling of rat urine identifies impaired tryptophan metabolism as the mechanism of yeast-induced fever. This research provided informative data that the impaired tryptophan metabolism might be one of the important reasons in elucidating the biochemical basis of the febrile response.

Nutritional and medicinal aspects of D-amino acids

This paper reviews and interprets a method for determining the nutritional value of D-amino acids, D-peptides, and amino acid derivatives using a growth assay in mice fed a synthetic all-amino acid diet. A large number of experiments were carried out in which a molar equivalent of the test compound replaced a nutritionally essential amino acid such as L-lysine (L-Lys), L-methionine (L-Met), L-phenylalanine (L-Phe), and L-tryptophan (L-Trp) as well as the semi-essential amino acids L-cysteine (L-Cys) and L-tyrosine (L-Tyr). The results show wide-ranging variations in the biological utilization of test substances. The method is generally applicable to the determination of the biological utilization and safety of any amino acid derivative as a potential nutritional source of the corresponding L-amino acid. Because the organism is forced to use the D-amino acid or amino acid derivative as the sole source of the essential or semi-essential amino acid being replaced, and because a free amino acid diet allows better control of composition, the use of all-amino-acid diets for such determinations may be preferable to protein-based diets. Also covered are brief summaries of the widely scattered literature on dietary and pharmacological aspects of 27 individual D-amino acids, D-peptides, and isomeric amino acid derivatives and suggested research needs in each of these areas. The described results provide a valuable record and resource for further progress on the multifaceted aspects of D-amino acids in food and biological samples.

Untargeted metabolomics identifies enterobiome metabolites and putative uremic toxins as substrates of organic anion transporter 1 (Oat1)

Untargeted metabolomics on the plasma and urine from wild-type and organic anion transporter-1 (Oat1/Slc22a6) knockout mice identified a number of physiologically important metabolites, including several not previously linked to Oat1-mediated transport. Several, such as indoxyl sulfate, derive from Phase II metabolism of enteric gut precursors and accumulate in chronic kidney disease (CKD). Other compounds included vitamins (pantothenic acid, 4-pyridoxic acid), urate, and metabolites in the tryptophan and nucleoside pathways. Three metabolites, indoxyl sulfate, kynurenine, and xanthurenic acid, were elevated in the plasma and interacted strongly and directly with Oat1 in vitro with IC50 of 18, 12, and 50 μM, respectively. A pharmacophore model based on several identified Oat1 substrates was used to screen the NCI database and candidate compounds interacting with Oat1 were validated in an in vitro assay. Together, the data suggest a complex, previously unidentified remote communication between the gut microbiome, Phase II metabolism in the liver, and elimination via Oats of the kidney, as well as indicating the importance of Oat1 in the handling of endogenous toxins associated with renal failure and uremia. The possibility that some of the compounds identified may be part of a larger remote sensing and signaling pathway is also discussed.

The neurobiology of D-amino acid oxidase and its involvement in schizophrenia

D-amino acid oxidase (DAO) is a flavoenzyme that metabolizes certain D-amino acids, notably the endogenous N-methyl D-aspartate receptor (NMDAR) co-agonist, D-serine. As such, it has the potential to modulate the function of NMDAR and to contribute to the widely hypothesized involvement of NMDAR signalling in schizophrenia. Three lines of evidence now provide support for this possibility: DAO shows genetic associations with the disorder in several, although not all, studies; the expression and activity of DAO are increased in schizophrenia; and DAO inactivation in rodents produces behavioural and biochemical effects, suggestive of potential therapeutic benefits. However, several key issues remain unclear. These include the regional, cellular and subcellular localization of DAO, the physiological importance of DAO and its substrates other than D-serine, as well as the causes and consequences of elevated DAO in schizophrenia. Herein, we critically review the neurobiology of DAO, its involvement in schizophrenia, and the therapeutic value of DAO inhibition. This review also highlights issues that have a broader relevance beyond DAO itself: how should we weigh up convergent and cumulatively impressive, but individually inconclusive, pieces of evidence regarding the role that a given gene may have in the aetiology, pathophysiology and pharmacotherapy of schizophrenia?

Systems toxicology study of doxorubicin on rats using ultra performance liquid chromatography coupled with mass spectrometry based metabolomics

A metabolomics-based systems toxicology approach was used to profile the urinary metabolites for the toxicity related processes and pathogenesis induced by doxorubicin (DOX) to rats. Endogenous metabolite profiles were obtained with ultra performance liquid chromatography-mass spectrometry (UPLC-MS) for rats receiving different single dosages of DOX (5, 10 or 20 mg/kg) prior and at three time points after dosage. Principal components analysis (PCA) allowed detection of two major systemic metabolic changes with the time due to the induced toxicity. Furthermore, Analysis of variance (ANOVA) Simultaneous Component Analysis (ASCA) was applied to reveal the variation caused by time and dose, and their interaction in a multivariate way. Finally, various metabolites involved in the toxic processes could be identified using their accurate mass and MS(n) experiments, and possible mechanisms of the toxicity of DOX were postulated. In conclusion, metabolomics as a systems toxicology approach was able to provide comprehensive information on the dynamic process of drug induced toxicity. In addition, detection of the systemic toxic effects could be obtained with metabolomics at an earlier stage compared to the clinical chemistry and histopathological assessment.

Response and recovery in the plasma metabolome tracks the acute LCMV-induced immune response

Lymphocytic choriomeningitis virus (LCMV) infection of mice is noncytopathic, producing well-characterized changes reflecting the host immune response. Untargeted metabolomics using mass spectrometry identified endogenous small molecule changes in blood from mice inoculated with LCMV, sampled at days 1, 3, 7, and 14 post infection. These time points correspond to well characterized events during acute LCMV infection and the immune response. Diverse pathways were altered, including TCA cycle intermediates, gamma-glutamyl dipeptides, lysophosphatidyl cholines, and fatty acids. The kynurenine pathway was activated, surprising because it is stimulated by IFN-gamma, which LCMV suppresses, thus, suggesting alternative activators. In contrast, biopterin/neopterin, another IFN-gamma stimulated pathway, was not activated. Many metabolites followed "response and recovery" kinetics, decreasing after infection to a minimum at days 3-7, and returning to normal by day 14. The TCA pathway followed this pattern, including citrate, cis-aconitate and alpha-ketoglutarate, intriguing because succinate has been shown to mediate cellular immunity. This response and recovery dynamic tracks the immune response, including the rise and fall of natural killer cell populations, serum TNF receptor concentration, and viral clearance. Metabolomics can provide target pathways for molecular diagnostics or therapeutics of viral infection and immunity.

Analytical and statistical approaches to metabolomics research

Metabolomics, the global profiling of metabolites in different living systems, has experienced a rekindling of interest partially due to the improved detection capabilities of the instrumental techniques currently being used in this area of biomedical research. The analytical methods of choice for the analysis of metabolites in search of disease biomarkers in biological specimens, and for the study of various low molecular weight metabolic pathways include NMR spectroscopy, GC/MS, CE/MS, and HPLC/MS. Global metabolite analysis and profiling of two different sets of data results in a plethora of data that is difficult to manage or interpret manually because of their subtle differences. Multivariate statistical methods and pattern-recognition programs were developed to handle the acquired data and to search for the discriminating features between data acquired from two sample sets, healthy and diseased. Metabolomics have been used in toxicology, plant physiology, and biomedical research. In this paper, we discuss various aspects of metabolomic research including sample collection, handling, storage, requirements for sample analysis, peak alignment, data interpretation using statistical approaches, metabolite identification, and finally recommendations for successful analysis.

Applications of metabolomics in drug discovery and development

Metabolomics is a relatively new field of 'omics' technology that is primarily concerned with the global or system-wide characterization of small molecule metabolites using technologies such as nuclear magnetic resonance, liquid chromatography and/or mass spectrometry. Its unique focus on small molecules and the physiological effects of small molecules aligns the field of metabolomics very closely with the aims and interests of many researchers in the pharmaceutical industry. Because of its conceptual and technical overlap with many aspects of pharmaceutical research, metabolomics is now finding applications that span almost the full length of the drug discovery and development pipeline, from lead compound discovery to post-approval drug surveillance. This review explores some of the most interesting or significant applications of metabolomics as they relate to pharmaceutical research and development. Specific examples are given that show how metabolomics can be used to facilitate lead compound discovery, to improve biomarker identification (for monitoring disease status and drug efficacy) and to monitor drug metabolism and toxicity. Other applications are also discussed, including the use of metabolomics to facilitate clinical trial testing and to improve post-approval drug monitoring. These examples show that metabolomics potentially offer drug researchers and drug regulators an effective, inexpensive route to addressing many of the riskier or more expensive issues associated with the discovery, development and monitoring of drug products.

Propiverine-induced accumulation of nuclear and cytosolic protein in F344 rat kidneys: isolation and identification of the accumulating protein

Male and female F344 rats but not B6C3F1 mice exposed for 104 weeks to propiverine hydrochloride (1-methylpiperid-4-yl 2,2-diphenyl-2-(1-propoxy)acetate hydrochloride), used for treatment of patients with neurogenic detrusor overactivity (NDO) and overactive bladder (OAB), presented with an accumulation of proteins in the cytosol and nuclei of renal proximal tubule epithelial cells, yet despite this, no increased renal tumor incidence was observed. In order to provide an improved interpretation of these findings and a better basis for human health risk assessment, male and female F344 rats were exposed for 16 weeks to 1000 ppm propiverine in the diet, the accumulating protein was isolated from the kidneys via cytosolic and nuclear preparations or laser-capture microdissection and analyzed using molecular weight determination and mass spectrometry. The accumulating protein was found to be d-amino acid oxidase (DAAO), an enzyme involved in amino and fatty acid metabolism. Subsequent reanalysis of kidney homogenate and nuclear samples as well as tissue sections using western blot and DAAO-immunohistochemistry, confirmed the presence and localization of DAAO in propiverine-treated male and female F344 rats. The accumulation of DAAO only in rats, and the limited similarity of rat DAAO with other species, including humans, suggests a rat-specific mechanism underlying the drug-induced renal DAAO accumulation with little relevance for patients chronically treated with propiverine.

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.

Current applications of liquid chromatography/mass spectrometry in pharmaceutical discovery after a decade of innovation

Current drug discovery involves a highly iterative process pertaining to three core disciplines: biology, chemistry, and drug disposition. For most pharmaceutical companies the path to a drug candidate comprises similar stages: target identification, biological screening, lead generation, lead optimization, and candidate selection. Over the past decade, the overall efficiency of drug discovery has been greatly improved by a single instrumental technique, liquid chromatography/mass spectrometry (LC/MS). Transformed by the commercial introduction of the atmospheric pressure ionization interface in the mid-1990s, LC/MS has expanded into almost every area of drug discovery. In many cases, drug discovery workflow has been changed owing to vastly improved efficiency. This review examines recent trends for these three core disciplines and presents seminal examples where LC/MS has altered the current approach to drug discovery.

LC-MS-based metabonomics analysis

Metabonomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. It has shown particular promise in the areas of toxicology and drug development, functional genomics, systems biology, and clinical diagnosis. Comprehensive metabonomics investigations are primarily a challenge for analytical chemistry. High-performance liquid chromatography-mass spectrometry (HPLC-MS) is an established technology in drug metabolite analysis and is now expanding into endogenous metabolite research. Its main advantages include wide dynamic range, reproducible quantitative analysis, and the ability to analyze biofluids with extreme molecular complexity. The aims of developing HPLC-MS for metabonomics range from understanding basic biochemistry to biomarker discovery and the structural characterization of physiologically important metabolites. In this review, the strategy and application of HPLC-MS-based metabonomics are reviewed.

Why is d-serine nephrotoxic and α-aminoisobutyric acid protective?

d-Serine selectively causes necrosis of S3 segments of proximal tubules in rats. This leads to aminoaciduria and glucosuria. Coinjection of the nonmetabolizable amino acid α-aminoisobutyric acid (AIB) prevents the tubulopathy. d-serine is selectively reabsorbed in S3, thereby gaining access to peroxisomal d-amino acid oxidase (d-AAO). d-AAO-mediated metabolism produces reactive oxygen species. We determined the fractional excretion of amino acids and glucose in rats after intraperitoneal injection of d-serine alone or together with reduced glutathione (GSH) or AIB. Both compounds prevented the hyperaminoaciduria. We measured GSH concentrations in renal tissue before (control) and after d-serine injection and found that GSH levels decreased to ∼30% of control. This decrease was prevented when equimolar GSH was coinjected with d-serine. To find out why AIB protected the tubule from d-serine toxicity, we microinfused d-[14C]serine or [14C]AIB (0.36 mmol/l) together with [3H]inulin in late proximal tubules in vivo and measured the radioactivity in the final urine. Fractional reabsorption of d-[14C]serine and [14C]AIB amounted to 55 and 70%, respectively, and 80 mmol/l of AIB or d-serine mutually prevented reabsorption to a great extent. d-AAO activity measured in vitro (using d-serine as substrate) was not influenced by a 10-fold higher AIB concentration. We conclude from these results that 1) d-AAO-mediated d-serine metabolism lowers renal GSH concentrations and thereby provokes tubular damage because reduction of reactive oxygen species by GSH is diminished and 2) AIB prevents d-serine-induced tubulopathy by inhibition of d-serine uptake in S3 segments rather than by interfering with intracellular d-AAO-mediated d-serine metabolism.

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 in monitoring kidney transplants

PURPOSE OF REVIEW

The success of any given kidney transplant is closely tied to the ability to monitor patients and responsively change their medications. Transplant monitoring is still, however, dependent on relatively old technologies: serum creatinine levels, urine output, blood pressure, blood glucose and histopathology of biopsy samples. These older technologies do not offer sufficient specificity, sensitivity, or accuracy to allow appropriate and timely interventions. Using the tools of genomics, proteomics and metabolomics new biomarkers are being found that may greatly improve transplant monitoring and significantly enhance graft survival. This review describes the basic principles of metabolomics and summarizes a number of recent developments in the use of metabolite biomarkers and metabolomics to monitor kidney transplants.

RECENT FINDINGS

Changes in the concentration profiles of a number of small molecule metabolites found in either blood or urine can be used to localize organ damage, identify organs at risk of rejection, assess organs suffering from ischemia-repurfusion injury or identify organs that have been damaged by immunosuppressive drugs.

SUMMARY

The application of metabolomics to kidney transplant monitoring is still very much in its infancy. Nevertheless, there are a number of easily measured metabolites in both urine and serum that can provide reliable indications of organ function, organ injury, and immunosuppressive drug toxicity. As the field matures, metabolomics may eventually lead to the development of rapid, inexpensive and noninvasive approaches to assist clinicians in monitoring kidney transplants.

A metabonomic study of strain- and age-related differences in the Zucker rat

Ultra-performance liquid chromatography (UPLC) coupled to orthogonal acceleration time-of-flight mass spectrometry (oa-TOFMS) in positive electrospray ionization mode was used to obtain metabolite profiles for urine obtained from three strains of Zucker rat. These were the Zucker lean, the Zucker (fa/fa) obese and the Zucker lean/(fa) cross. Clear age- and strain-related differences were noted with the leptin-deficient (fa/fa) obese animal showing significant differences from both the other Zucker rat strains with respect to metabolite profiles.