Optimization of Sample Preparation for Metabolomics Exploration of Urine, Feces, Blood and Saliva in Humans Using Combined NMR and UHPLC-HRMS Platforms.

Currently, most clinical studies in metabolomics only consider a single type of sample such as urine, plasma, or feces and use a single analytical platform, either NMR or MS. Although some studies have already investigated metabolomics data from multiple fluids, the information is limited to a unique analytical platform. On the other hand, clinical studies investigating the human metabolome that combine multi-analytical platforms have focused on a single biofluid. Combining data from multiple sample types for one patient using a multimodal analytical approach (NMR and MS) should extend the metabolome coverage. Pre-analytical and analytical phases are time consuming. These steps need to be improved in order to move into clinical studies that deal with a large number of patient samples. Our study describes a standard operating procedure for biological specimens (urine, blood, saliva, and feces) using multiple platforms (1H-NMR, RP-UHPLC-MS, and HILIC-UHPLC-MS). Each sample type follows a unique sample preparation procedure for analysis on a multi-platform basis. Our method was evaluated for its robustness and was able to generate a representative metabolic map.

Endogenous metabolites that are substrates of organic anion transporter's (OATs) predict methotrexate clearance.

Variable pharmacokinetics of high-dose-methotrexate (MTX) is responsible for severe toxicities. Unpredictable overexposure still occurs during some courses despite having controlled the main factors known to play a role in its elimination. The aim of our study was to evaluate whether the urine metabolomic profile measured at the time of MTX administration is predictive of the drug's clearance and/or of treatment-related toxicity. We analyzed the urine content of endogenous metabolites before MTX administration in a cohort of adult patients treated for lymphoid malignancies. Individual MTX clearance (MTXCL) was estimated from population pharmacokinetic analyses of therapeutic drug monitoring data. We determined the urine metabolite content by gas chromatography-mass spectrometry (GC-MS) and applied Partial Least Square (PLS) analysis to assess the relationship between the urine metabolome and MTXCL. External validation was applied to evaluate the performances of the PLS model. We used orthogonal partial least squares discriminant analysis (OPLS-DA) to distinguish patients with normal or delayed elimination, and patients with or without toxicity. Sixty-two patients were studied. We obtained a very good prediction of individual MTX clearance using a set of 28 metabolites present in patient urine at baseline. The mean prediction error and precision were -0.36% and 21.4%, respectively, for patients not included in the model. The model included a set of endogenous organic anions, of which the tubular secretion depends on organic anion transporter (OAT) function. Our analyses did not allow us to discriminate between patients with or without delayed elimination or those who did or did not experience toxicity. Urinary metabolomics can be informative about an individual's ability to clear MTX. More broadly, it paves the way for the development of a biomarker of tubular secretion, easily measurable from endogenous substances.

Analytical methodology for metabolomics study of adherent mammalian cells using NMR, GC-MS and LC-HRMS.

We developed a methodology for the analysis of intracellular metabolites using nuclear magnetic resonance spectrometry (NMR), gas-chromatography coupled with mass spectrometry (GC-MS), and liquid chromatography coupled with high resolution mass spectrometry (LC-HRMS). The main steps for analysis of adherent cells in order to recover the widest possible range of intracellular compounds are blocking metabolic activity by quenching and extraction of intracellular metabolites. We explored three protocols to quench NSC-34 cell metabolism and four different extraction methods, analyzed by NMR. On the basis of the number of metabolites extracted and their relative standard deviation (RSD) analyzed by NMR, the most reproducible protocol [quenching by MeOH at -40 °C and extraction with CH2Cl2/MeOH/H2O (3:3:2)] was used to obtain intracellular media to be analyzed by GC-MS and LC-HRMS. GC-MS analysis was optimized by three oximation procedures followed by silylation derivatization and these were compared to silylation alone. Using reversed-phase liquid chromatography (C18), four different gradients for LC-MS were compared. The analytical protocols were determined to establish the reliability and suitability of sample treatments required to achieve the correct biological analysis of untargeted mammalian cell metabolomics.

GC-MS-based urine metabolic profiling of autism spectrum disorders.

Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders resulting from multiple factors. Diagnosis is based on behavioural and developmental signs detected before 3 years of age, and there is no reliable biological marker. The purpose of this study was to evaluate the value of gas chromatography combined with mass spectroscopy (GC-MS) associated with multivariate statistical modeling to capture the global biochemical signature of autistic individuals. GC-MS urinary metabolic profiles of 26 autistic and 24 healthy children were obtained by liq/liq extraction, and were or were not subjected to an oximation step, and then were subjected to a persilylation step. These metabolic profiles were then processed by multivariate analysis, in particular orthogonal partial least-squares discriminant analysis (OPLS-DA, R(2)Y(cum) = 0.97, Q(2)(cum) = 0.88). Discriminating metabolites were identified. The relative concentrations of the succinate and glycolate were higher for autistic than healthy children, whereas those of hippurate, 3-hydroxyphenylacetate, vanillylhydracrylate, 3-hydroxyhippurate, 4-hydroxyphenyl-2-hydroxyacetate, 1H-indole-3-acetate, phosphate, palmitate, stearate, and 3-methyladipate were lower. Eight other metabolites, which were not identified but characterized by a retention time plus a quantifier and its qualifier ion masses, were found to differ between the two groups. Comparison of statistical models leads to the conclusion that the combination of data obtained from both derivatization techniques leads to the model best discriminating between autistic and healthy groups of children.

Deciphering the Role of Klf10 in the Cerebellum.

Recent studies have demonstrated a new role for Klf10, a Krüppel-like transcription factor, in skeletal muscle, specifically relating to mitochondrial function. Thus, it was of interest to analyze additional tissues that are highly reliant on optimal mitochondrial function such as the cerebellum and to decipher the role of Klf10 in the functional and structural properties of this brain region. In vivo (magnetic resonance imaging and localized spectroscopy, behavior analysis) and in vitro (histology, spectroscopy analysis, enzymatic activity) techniques were applied to comprehensively assess the cerebellum of wild type (WT) and Klf10 knockout (KO) mice. Histology analysis and assessment of locomotion revealed no significant difference in Klf10 KO mice. Diffusion and texture results obtained using MRI revealed structural changes in KO mice characterized as defects in the organization of axons. These modifications may be explained by differences in the levels of specific metabolites (myo-inositol, lactate) within the KO cerebellum. Loss of Klf10 expression also led to changes in mitochondrial activity as reflected by a significant increase in the activity of citrate synthase, complexes I and IV. In summary, this study has provided evidence that Klf10 plays an important role in energy production and mitochondrial function in the cerebellum.

Analytical Methodology for a Metabolome Atlas of Goat's Plasma, Milk and Feces Using 1H-NMR and UHPLC-HRMS.

Metabolomics has been increasingly used in animal and food sciences. Animal health is one of the most important factor that can also alter animal integrity and welfare. Some studies have already investigated the link between health and metabolic profile of dairy animals. These studies in metabolomics often consider a single type of sample using a single analytical platform (nuclear magnetic resonance or mass spectrometry). Only few studies with multi-platform approaches are also used with a single or a multi type of sample, but they mainly consider dairy cows' metabolome although dairy goats present similar diseases, that it could be interesting to detect early to preserve animal health and milk production. This study aims to create a metabolic atlas of goat plasma, milk and feces, based on healthy animals. Our study describes a standard operating procedure for three goat matrices: blood plasma, milk, and feces using multiple platforms (NMR (1H), UHPLC (RP)-MS and UHPLC (HILIC)-MS) that follows a unique sample preparation procedure for each sample type to be analyzed on multi-platforms basis. Our method was evaluated for its robustness and allowed a better characterization of goat metabolic profile in healthy conditions.

Chiral oxorhenium(V) complexes as candidates for the experimental observation of molecular parity violation: a structural, synthetic and theoretical study.

We report the synthesis and resolution of a series of new chiral "3 + 1" oxorhenium(V) complexes, designed for high-resolution laser spectroscopy experiments probing molecular parity-violation (PV) effects in the Re=O stretching mode frequency. These complexes display a particularly simple chemical structure, with the rhenium atom as the stereogenic center, and show large PV energy differences according to our calculations. They were obtained in the racemic and enantioenriched forms, in the latter case by using either semi-preparative chiral HPLC resolution or enantioselective synthesis. The vibrational transition frequency differences between the enantiomeric pairs due to PV have been calculated with two- and four-component relativistic Hamiltonians using Hartree-Fock (HF) and density functional theory (DFT). For three complexes, including one synthesized in enantioenriched form, our HF calculations predict frequency differences above the present resolution limit of 1 Hz. These results confirm the order of magnitude for the calculated HF PV vibrational frequency differences reported earlier for this class of compounds [P. Schwerdtfeger and R. Bast, J. Am. Chem. Soc., 2004, 126, 1652]. However, at the DFT level the PV vibrational frequency differences are in some cases reduced by an order of magnitude, but are still within the sensitivity of 0.01 Hz, which is the anticipated sensitivity in a new proposed experiment. We therefore believe that the present study represents an important step towards the experimental observation of PV in molecular systems, and emphasizes the extreme sensitivity of the PV vibrational frequency difference to the chemical environment around the rhenium center.

A multiplatform metabolomic approach to characterize fecal signatures of negative postnatal events in chicks: a pilot study.

BACKGROUND: Negative experiences in early life can induce long-lasting effects on the welfare, health, and performance of farm animals. A delayed placement of chicks in rearing houses has negative effects on their performance, and results in fecal-specific odors detectable by rats. Based on this observation, the volatile organic compounds (VOCs) and metabolites from the feces of 12-day-old chickens were screened for early markers of response to negative events using gas-chromatography and liquid-chromatography coupled with mass spectrometry (GC-MS, LC-HRMS). RESULTS: The low reproducibility of solid-phase micro-extraction of the VOCs followed by GC-MS was not suitable for marker discovery, in contrast to liquid extraction of metabolites from freeze-dried feces followed by GC-MS or LC-HRMS analysis. Therefore, the fecal metabolome from 12-day-old chicks having experienced a normal or delayed placement were recorded by GC-MS and LC-HRMS in two genotypes from two experiments. From both experiments, 25 and 35 metabolites, respectively explaining 81% and 45% of the difference between delayed and control chickens, were identified by orthogonal partial least-squares discriminant analysis from LC-HRMS and GC-MS profiling. CONCLUSION: The sets of molecules identified will be useful to better understand the chicks' response to negative events over time and will contribute to define stress or welfare biomarkers. .

Single nucleotide polymorphisms of ABCC2 modulate renal secretion of endogenous organic anions.

The ATP-binding cassette family transporter MRP2 (multidrug resistance-associated protein 2), encoded by the ABCC2 gene, is involved in the renal excretion of numerous xenobiotics and it is likely that it also transports many endogenous molecules arising from not only normal essential metabolic processes but also from environmental toxins or food intake. We used a targeted gas chromatography-mass spectrometry metabolomics analysis to study whether endogenous organic anions are differentially excreted in urines of healthy volunteers according to their genotype for three functional single nucleotide polymorphisms (SNPs) in ABCC2. This was the case for 35 of the 108 metabolites analyzed. Eight of them are most likely substrates of MRP2 since they are the most contributive to the difference between carriers of a decreasing function allele vs those carrying an increasing function one. Seven out of 8 metabolites are fatty acids (dodecanoic acid; 3-hydroxypropanoic acid) or metabolites of polyphenols (caffeine; resorcinol; caffeic acid; 2-(3,4-dihydroxyphenyl) acetic acid; and 4-hydroxyhippuric acid). Most of them were structurally similar to a series of substances previously shown to interact with MRP2 function in vitro. Interestingly, coproporphyrin isomer I, a prototypical substrate of MRP2, also belonged to our final list although it was not significantly discriminant on its own. This suggests that the simultaneous measurement of a set of endogenous metabolites in urine, rather than that of unique metabolites, has the potential to provide a phenotypic measure of MRP2 function in vivo. This would represent an innovative tool to study the variability of the transport activity of MRP2 under a physiological or pathological condition, especially in pharmacokinetic studies of its substrates.

Workflow methodology for rat brain metabolome exploration using NMR, LC-MS and GC-MS analytical platforms.

We developed a multi-platform approach for the metabolome exploration of rat brain tissue, using liquid chromatography coupled with mass spectrometry (LC-MS), nuclear magnetic resonance spectroscopy (NMR) and gas-chromatography coupled with mass spectrometry (GC-MS). The critical steps for metabolite exploration of cerebral tissues are tissue lysis and metabolites extraction. We first evaluated the impact of freeze-drying compared to wet tissue metabolites extraction using NMR and LC-MS with a reversed phase liquid chromatography. Then, we compared four metabolite extraction methods Based on the number of metabolites extracted, their intensity and their coefficient of variation (%CV), the most reproducible protocol (one-step extraction with acetonitrile on lyophilized material) was chosen to further evaluate the impact of sample mass on method performance (3, 6, and 9mg were essayed). GC-MS analysis was also investigated by analyzing four different methoximation/silylation derivatization combinations. The optimal analytical protocols were proposed to establish the reliability required to realize untargeted brain tissue metabolomics exploration. The most reliable workflow was then exemplified by analyzing three rat brain regions (cerebellum, frontal and parietal cortices, n=12) by 1H NMR, LC-MS and GC-MS, allowing their clustering based on their metabolic profiles. We present here an example of development of methodology that should be done before running analysis campaigns.

1H-13C NMR-based urine metabolic profiling in autism spectrum disorders.

Autism Spectrum Disorders (ASD) are a group of developmental disorders caused by environmental and genetic factors. Diagnosis is based on behavioral and developmental signs detected before 3 years of age with no reliable biological marker. The purpose of this study was to evaluate the potential use of a 2D NMR-based approach to express the global biochemical signature of autistic individuals compared to normal controls. This technique has greater spectral resolution than to 1D (1)H NMR spectroscopy, which is limited by overlapping signals. The urinary metabolic profiles of 30 autistic and 28 matched healthy children were obtained using a (1)H-(13)C NMR-based approach. The data acquired were processed by multivariate orthogonal partial least-squares discriminant analysis (OPLS-DA). Some discriminating metabolites were identified: ß-alanine, glycine, taurine and succinate concentrations were significatively higher, and creatine and 3-methylhistidine concentrations were lower in autistic children than in controls. We also noted differences in several other metabolites that were unidentified but characterized by a cross peak correlation in (1)H-(13)C HSQC. Statistical models of (1)H and (1)H-(13)C analyses were compared and only 2D spectra allowed the characterization of statistically relevant changes [R(2)Y(cum)=0.78 and Q(2)(cum)=0.60] in the low abundance metabolites. This method has the potential to contribute to the diagnosis of neurodevelopment disorders but needs to be validated on larger cohorts and on other developmental disorders to define its specificity.

Ant cuticles: a trap for atmospheric phthalate contaminants.

Phthalates are universal contaminants. We show that they are trapped by the ant cuticles and maintained permanently at a low level, generally less than 1% of cuticular components. They are found throughout the interior of the insect, predominately in the fat body, which suggests that they are adsorbed by the cuticle. In open plastic boxes free of phthalates the ants became more contaminated with phthalates over a period of time, whereas in closed glass jars they did not. This finding suggests that the main source of pollutants is the atmosphere. Different ant species collected from multiple places showed similar levels of contamination. It appeared that in some pristine places the contamination was lower, but this needs to be confirmed. Ants can be considered as bio-indicators of phthalate pollution.

Tandem synthesis of alternating polyesters from renewable resources.

The vast majority of commodity materials are obtained from petrochemical feedstocks. These resources will plausibly be depleted within the next 100 years, and the peak in global oil production is estimated to occur within the next few decades. In this regard, biomass represents an abundant carbon-neutral renewable resource for the production of polymers. Here we report a new strategy, based on tandem catalysis, to obtain renewable materials. Commercially available complexes are found to be efficient catalysts for alternating polyesters from the cyclization of dicarboxylic acids followed by alternating copolymerization of the resulting anhydrides with epoxides. This operationally simple method is an attractive strategy for the production of new biodegradable polyesters.

(Eta6-arene) ruthenium(II) complexes and metallo-papain hybrid as Lewis acid catalysts of Diels-Alder reaction in water.

Covalent embedding of a (eta(6)-arene) ruthenium(II) complex into the protein papain gives rise to a metalloenzyme displaying a catalytic efficiency for a Lewis acid-mediated catalysed Diels-Alder reaction enhanced by two orders of magnitude in water.

Synthesis, cytotoxicity, and COMPARE analysis of ferrocene and [3]ferrocenophane tetrasubstituted olefin derivatives against human cancer cells.

Herein we report the antiproliferative effects of a series of 28 compounds against the MDA-MB-231 breast cancer cell line, including the synthesis of seven new [3]ferrocenophanyl and four new ferrocenyl compounds. For each p-R-phenyl substitution pattern investigated, the [3]ferrocenophanyl derivatives were more cytotoxic than the corresponding ferrocenyl derivative, with the highest activity found for compounds with protic substituents. Theoretical calculations of the HOMO-LUMO gap for the molecules in the Fe³(+) oxidation state suggest a higher reactivity for the [3]ferrocenophanyl derivatives. A lead compound from each series, a [3]ferrocenophanyl and a ferrocenyl compound, possessing two phenol groups, were screened against the NCI/DTP 60-cell-line panel. The mean activity over all cell lines was better than cisplatin for both compounds, and both compounds showed subpanel selectivity for leukemia, CNS cancer, and renal cancer. Low systemic toxicity and lack of interaction with DNA (when in the reduced form), suggest that the compounds may act as prodrugs.

Subtle chirality in oxo- and sulfidorhenium(v) complexes.

Enantioenriched square-pyramidal oxo- and sulfidorhenium(v) complexes have been prepared and their stereochemistry studied by vibrational circular dichroism (VCD) spectroscopy.

Metallaborane reactivity. A stoichiometric mechanism for the insertion of two alkynes into an iridaborane framework via a disposable molybdenum chaperone.

Building on earlier work that showed the formation of [1-Cp*-2,2,2-(CO)3-2-THF-nido-1,2-IrMoB(4)H(8)], 2, from the reaction of [1-Cp*-arachno-1-IrB(4)H(10)], 1, with (arene)Mo(CO)3, the stoichiometric mechanism for the generation of [1-Cp*-5,6,7,8-(R)4-nido-1,5,6,7,8-IrC(4)B(3)H(3)], 8, from the reaction of 2 with RCCR, R = Me, Ph, has been identified. For R = Me, the major product in solution is [1-Cp*-5,6,7,8-(CH3)4-closo-1,5,6,7,8-IrC(4)B(3)H(3)Mo(CO)3], 7, which is in equilibrium with 8. The equilibrium 8 + Mo(THF)3(CO)3 <==> 7 + 3THF is characterized by DeltaH = 8 kcal/mol and DeltaS = 34 cal/mol K. Density functional theory calculations carried out on 7 indicate that the Mo(CO)3 moiety is weakly bound to the cluster mainly through Mo-C rather than Mo-B interactions. Under alkyne deficient conditions, the product [1-Cp*-2,2,2-(CO)3(mu-CO)-3,4-(CH3)2-closo-1,2,3,4-IrMoC(2)B(3)H(3)], 6, can be isolated. Solid-state structures of 1 and 2 have been reported previously, and those of 6, 7, and 8, R = Me, Ph, are reported here. The evolution of products with time was monitored by 1H and 11B NMR and showed the formation and decay of two additional species which have been identified as the structural isomers [1-Cp*-7,7,7-(CO)3-7-THF-2,3-(CH3)2-nido-1,7,2,3-IrMoC(2)B(3)H(5)], 4, and [5-Cp*-7,7,7-(CO)3-7-THF-2,3-(CH3)2-nido-5,7,2,3-IrMoC(2)B(3)H(5)], 5, with the metals nonadjacent in 4 and adjacent in 5. Circumstantial evidence suggests that 4 is the precursor to 5 and 5 is the precursor to both 6 and 7. Cluster 2 also is a catalyst or catalyst precursor for the isomerization of olefins, namely, hex-1-ene to cis-hex-2-ene and tetramethyl allene to 2,4-dimethylpenta-1,3-diene. These novel results also establish that [1-Cp*-2,2,2-(CO)3-2-(alkyne)-nido-1,2-IrMoB(4)H(8)], 3, forms from 2 and constitutes a logical precursor to 4. The entire process, 1 + 2alkyne = 8 + BH3 + 2H2, which is promoted by (arene)Mo(CO)3, constitutes an explicit example of a transition-metal-facilitated process analogous to metal-facilitated organic transformations observed in organometallic chemistry.