PubMed

A Comparative Metabolomic Evaluation of Behcet's Disease with Arthritis and Seronegative Arthritis Using Synovial Fluid. PLoS One. 2015;10(8):e0135856 Authors: Ahn JK, Kim S, Kim J, Hwang J, Kim KH, Cha HS Abstract Behcet's disease (BD) with arthritis is often confused with seronegative arthritis (SNA) because of shared clinical symptoms and the lack of definitive biomarkers for BD. To investigate possible metabolic patterns and potential biomarkers of BD with arthritis, metabolomic profiling of synovial fluid (SF) from 6 patients with BD with arthritis and 18 patients with SNA was performed using gas chromatography/time-of-flight mass spectrometry in conjunction with univariate and multivariate statistical analyses. A total of 123 metabolites were identified from samples. Orthogonal partial least square-discriminant analysis showed clear discrimination between BD with arthritis and SNA. A set of 11 metabolites were identified as potential biomarkers for BD using variable importance for projection values and the Wilcoxon-Mann-Whitney test. Compared with SNA, BD with arthritis exhibited relatively high levels of glutamate, valine, citramalate, leucine, methionine sulfoxide, glycerate, phosphate, lysine, isoleucine, urea, and citrulline. There were two markers identified, elevated methionine sulfoxide and citrulline, that were associated with increased oxidative stress, providing a potential link to BD-associated neutrophil hyperactivity. Glutamate, citramalate, and valine were selected and validated as putative biomarkers for BD with arthritis (sensitivity, 100%; specificity, 61.1%). This is the first report to present potential biomarkers from SF for discriminating BD with arthritis from SNA. The metabolomics of SF may be helpful in searching for potential biomarkers and elucidating the clinicopathogenesis of BD with arthritis. PMID: 26270538 [PubMed - as supplied by publisher]

Related Articles Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli. Appl Microbiol Biotechnol. 2014 Jun;98(11):5131-43 Authors: Peebo K, Valgepea K, Nahku R, Riis G, Oun M, Adamberg K, Vilu R Abstract Elimination of acetate overflow in aerobic cultivation of Escherichia coli would improve many bioprocesses as acetate accumulation in the growth environment leads to numerous negative effects, e.g. loss of carbon, inhibition of growth, target product synthesis, etc. Despite many years of studies, the mechanism and regulation of acetate overflow are still not completely understood. Therefore, we studied the growth of E. coli K-12 BW25113 and several of its mutant strains affecting acetate-related pathways using the continuous culture method accelerostat (A-stat) at various specific glucose consumption rates with the aim of diminishing acetate overflow. Absolute quantitative exo-metabolome and proteome analyses coupled to metabolic flux analysis enabled us to demonstrate that onset of acetate overflow can be postponed and acetate excretion strongly reduced in E. coli by coordinated activation of phosphotransacetylase-acetyl-CoA synthetase (PTA-ACS) and tricarboxylic acid (TCA) cycles. Fourfold reduction of acetate excretion (2 vs. 8 % from total carbon) at fastest growth compared to wild type was achieved by deleting the genes responsible for inactivation of acetyl-CoA synthetase protein (pka) and TCA cycle regulator arcA. The Δpka ΔarcA strain did not accumulate any other detrimental by-product besides acetate and showed identical μ max and only ~5 % lower biomass yield compared to wild type. We conclude that a fine-tuned coordination between increasing the recycling capabilities of acetate in the PTA-ACS node through a higher concentration of active acetate scavenging Acs protein and downstream metabolism throughput in the TCA cycle is necessary for diminishing overflow metabolism of acetate in E. coli and achieving higher target product production in bioprocesses. PMID: 24633370 [PubMed - indexed for MEDLINE]

Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects Book. 2015 Authors: Kobeissy FH Abstract There are four biochemical components that control biological systems by serving as building blocks and as information databases: genes, transcripts, proteins, and metabolites. The study of these four components have become entire fields of biological study and have often been referred to collectively as the omics, including genomics, transcriptomics, proteomics, and metabolomics. The ability to study each of these biological components in great detail and to study the relationship between them has led to significant advances in medical discovery and understanding. The goal of medical systems biology is to integrate all biological information to understand mechanistic information about cellular events and functions that may contribute to disease propensity, development, progression, diagnosis, and/or treatment. Having a systems perspective on human biology is desirable, where details of various system components can be integrated with increasing complexity to better understand properties of the entire system. The systems-oriented approach requires extensive and complex datasets; reliable analytical techniques; thoughtful data integration across platforms; and advanced biostatistical methods. Medical systems biology necessitates an unbiased and comprehensive approach when interpreting experimental results and biological interpretations need to be carefully explained, justified by the data, and tested on larger data sets. Traumatic brain injury (TBI) patients would benefit from a medical systems biology understanding of the systemic dysregulation and cellular changes that follow an insult to the head. A subspecialty in the critical care environment, neurocritical care, evolved from the acceptance that recovery from the primary injury to the brain tissue is affected by systemic alterations that can result in secondary injuries to the brain. The neurological intensive care unit (ICU) has realized significant improvements in patient outcomes due to protocols to address and prevent secondary injuries and due to neurointensivist-led teamwork, both aided by modern technological advances in multimodality neuromonitoring (Elf et al., 2002, Le Roux et al., 2012, Varelas et al., 2006). Considering the notable advances achieved through incorporating a systems-level approach to treating head injury and improving outcomes, in this review we discuss metabolomics applied to TBI. First, we will introduce metabolomics for readers not familiar with the field. Second, we summarize research on the metabolic changes following TBI to highlight what information has been translated to the clinic and what treatments exist. Finally, we discuss metabolomics techniques applied to TBI metabolism, reviewing the examples in the literature, and offering the authors’ suggestions for using NMR spectroscopy to study biofluids from head injured patients. As researchers and clinicians report and validate metabolomics findings, building a medical systems biology perspective on post-TBI metabolic dysfunction is likely to aid in informing physicians’ decisions and in integrating treatments into daily practice. Metabolomics refers to the study of the metabolome, which has been defined as “the quantitative complement of metabolites in a biological system” (Dunn et al., 2011). A metabolome, estimated to contain thousands of compounds, is organism-specific and sample type–specific. The human serum metabolome has been reported to contain 4,229 unique compounds, detection of which involved the use of several analytic techniques, and is still not considered exhaustive (Psychogios et al., 2011). Metabolomics studies aim to discriminate pathological metabolic profiles from that of a normal physiological state and to predict class assignment based on this set of metabolite biomarkers (Baker, 2011; Holmes et al., 2008; Nicholson et al., 2012). The field of metabolomics research consists of several investigative methods. First, there is a distinction to be made between targeted and exploratory metabolomics studies (Lenz and Wilson, 2007). In the latter, the goal is to generate a metabolomic fingerprint for each case and to use multivariate analysis to probe class-specific patterns. Generally, the focus of such studies is not to identify and quantify metabolites nor to propose mechanistic explanations of the results, but rather to predict class assignment based on the metabolomic fingerprint. Targeted metabolomics studies aim to identify and quantify specific metabolites. These metabolites may be hypothesized to be biomarkers of disease progression or may be considered an indicator of the severity of a physiological state. Targeted metabolomics studies may use the same multivariate statistical techniques as the metabolome fingerprint-type studies, but also typically include more traditional univariate and multivariate analyses on the metabolite concentrations. Targeted studies can be targeted to a set of endogenous metabolites or can be targeted to study an exogenous substance, including labeled tracer metabolites or a pharmaceutical. Blood plasma, blood serum, urine, and cerebrospinal fluid (CSF) have been extensively investigated in the metabolomics literature. These biofluids are readily available and are interpreted as an average representation of the surrounding tissue. Researchers working with animal models have access to tissue after sacrifice, which is considerably rarer in human studies. As the field has grown, online metabolite databases containing biological, structural, and experimental information have been developed and are a key tool for metabolomics researchers (Ulrich et al., 2008; Wishart et al., 2007). The term metabolomics resulted from research in the 1980s and 1990s (Nicholson et al., 1999), yet the concept behind metabolomics was a focus of research for several decades prior. What distinguishes contemporary metabolomics studies from past studies on metabolic changes is the technology available for analyzing such biofluid samples and, therefore, the extent and accuracy of the metabolome quantified. In addition to the larger data set, there have also been computational and statistical advances that make the prospect of drawing meaningful conclusions from thousands of metabolites and the changes that occur between classes possible. With improvements in technology, metabolomics research has reached a level of complexity requiring a multidisciplinary team and has made providing biological rationale for the findings challenging because of data set complexity. The Institute of Medicine of the National Academies published a report on translational omics that issued recommendations for improving the overall quality of the metabolomics research and for translating these findings to the clinical setting (Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials, 2012). The use of mass spectrometry (MS)-based and nuclear magnetic resonance (NMR)-based quantification are the most common in the metabolomics literature. Both of these analytical instruments are reliable, accurate, and widely available. There are advantages and disadvantages associated with each, some of which will be briefly mentioned, and the reader is referred to a number of excellent metabolomics review articles (Dunn et al., 2011; Lenz and Wilson, 2007; Nicholson et al., 1999). Because an individual’s metabolome is highly influenced by environment and diet, population studies require a large number of subjects, and the reliability and reproducibility of these analytical techniques is key. The focus of this review is NMR-based metabolomics applied to TBI, but both analytical methods will be described. The reader is referred to extensive review articles focused on the application of MS and/or NMR to metabolomics (Dettmer et al., 2007; Zhang et al., 2010). MS detects compounds in the picomolar concentration range that become ionized after injection into the mass spectrometer; the readout is the mass-to-charge ratio of the detectable compounds in solution. MS-based metabolomics have used gas chromatography MS and liquid chromatography MS. Preparing samples for MS analysis requires extraction of metabolites and may require derivitization, which can be a labor-intensive process. Metabolite extraction involves a series of experimental steps in which metabolite loss can occur and where additional sample-to-sample variability may be introduced. The high sensitivity of MS-based quantification makes it a powerful tool in targeted metabolomics studies. In metabolome fingerprinting studies, it is challenging to measure all compounds with the same efficiency and accuracy for technical reasons. NMR spectroscopy is used to identify and quantify compounds in solution containing elements that are magnetic resonance–detectable (i.e., elemental isotopes that will absorb photons when placed in a magnetic field). NMR is considerably less sensitive than MS and is able to detect concentrations in the micromolar concentration range, but does not destroy the sample in the process of measurement. Application of a radiofrequency field at a known frequency and power excites the spin of the magnetic resonance–detectable isotopes. Spin is a fundamental property of elements akin to mass and charge and both the absorption and emission of radiofrequency photons is nondestructive and noninvasive. Each unique chemical structure in a molecule will resonate in the magnetic field at a specific frequency as the spins relax to equilibrium alignment with the magnetic field. The signal collected by the NMR spectrometer is then Fourier transformed into a NMR spectrum with spectral peaks at specific frequencies corresponding to the molecular structure of the compound being measured. The integrated area of the spectral peaks is proportional to the concentration of the compound. All compounds in solution above a certain concentration will be detected, unlike the variable efficiency of MS-based quantification. There is minimal sample preparation required when compared with MS. There are a number of biologically relevant isotopes that can be measured, including (1)H, (13)C, (31)P, and (15)N. (1)H is the most abundant isotope of hydrogen (99.99%) and, because biologically relevant molecules contain hydrogen, (1)H NMR is widely used. NMR spectrometers are standard equipment in research environments and increased spectral resolution is possible due to the prevalence of high-field spectrometers with field strengths ≥400 MHz (9.4 T). High-resolution magic angle spinning spectroscopy is able to quantify metabolites in intact tissue using solid-state NMR spectrometers (Beckonert et al., 2010). Another aspect of modern metabolomics research is application of multivariate statistical approaches. Unsupervised multivariate techniques such as principal component analysis (PCA) reduce the number of variables to a few principal components. Principal components are orthogonal to one another, are linear combinations of the original data, and can reduce hundreds of input variables to three or four. There are many NMR-based metabolomics fingerprint-type studies that use the complete NMR spectrum as the set of variables. Some metabolomics studies are designed to build a prediction model with supervised multivariate techniques, for example partial least squares (PLS) or PLS-discriminant analysis (PLS-DA) among others (Bylesjo et al., 2006). Most metabolomics studies generate a PCA model of the data to test whether the groups can be reasonably separated based on metabolic information. To build a predictive model, validation is vital and the data set is randomly separated into a larger training set and a smaller test set; the model generated from the training set is then tested on the test set. In reality, metabolomics studies generally quantify fewer than 100 metabolites per sample. Several advances are required to achieve high-throughput quantification of the entire metabolome and to translate metabolomics to the clinical setting. The steps following data collection, including processing and statistical analyses, will be discussed later in this chapter within the context of metabolomics of TBI. PMID: 26269925

The Metabolome in Finnish Carriers of the MYBPC3-Q1061X Mutation for Hypertrophic Cardiomyopathy. PLoS One. 2015;10(8):e0134184 Authors: Jørgenrud B, Jalanko M, Heliö T, Jääskeläinen P, Laine M, Hilvo M, Nieminen MS, Laakso M, Hyötyläinen T, Orešič M, Kuusisto J Abstract AIMS: Mutations in the cardiac myosin-binding protein C gene (MYBPC3) are the most common genetic cause of hypertrophic cardiomyopathy (HCM) worldwide. The molecular mechanisms leading to HCM are poorly understood. We investigated the metabolic profiles of mutation carriers with the HCM-causing MYBPC3-Q1061X mutation with and without left ventricular hypertrophy (LVH) and non-affected relatives, and the association of the metabolome to the echocardiographic parameters. METHODS AND RESULTS: 34 hypertrophic subjects carrying the MYBPC3-Q1061X mutation, 19 non-hypertrophic mutation carriers and 20 relatives with neither mutation nor hypertrophy were examined using comprehensive echocardiography. Plasma was analyzed for molecular lipids and polar metabolites using two metabolomics platforms. Concentrations of branched chain amino acids, triglycerides and ether phospholipids were increased in mutation carriers with hypertrophy as compared to controls and non-hypertrophic mutation carriers, and correlated with echocardiographic LVH and signs of diastolic and systolic dysfunction in subjects with the MYBPC3-Q1061X mutation. CONCLUSIONS: Our study implicates the potential role of branched chain amino acids, triglycerides and ether phospholipids in HCM, as well as suggests an association of these metabolites with remodeling and dysfunction of the left ventricle. PMID: 26267065 [PubMed - as supplied by publisher]

Analytical Bias in the Measurement of Serum 25-Hydroxyvitamin D Concentrations Impairs Assessment of Vitamin D Status in Clinical and Research Settings. PLoS One. 2015;10(8):e0135478 Authors: Black LJ, Anderson D, Clarke MW, Ponsonby AL, Lucas RM, Ausimmune Investigator Group Abstract Measured serum 25-hydroxyvitamin D concentrations vary depending on the type of assay used and the specific laboratory undertaking the analysis, impairing the accurate assessment of vitamin D status. We investigated differences in serum 25-hydroxyvitamin D concentrations measured at three laboratories (laboratories A and B using an assay based on liquid chromatography-tandem mass spectrometry and laboratory C using a DiaSorin Liaison assay), against a laboratory using an assay based on liquid chromatography-tandem mass spectrometry that is certified to the standard reference method developed by the National Institute of Standards and Technology and Ghent University (referred to as the 'certified laboratory'). Separate aliquots from the same original serum sample for a subset of 50 participants from the Ausimmune Study were analysed at the four laboratories. Bland-Altman plots were used to visually check agreement between each laboratory against the certified laboratory. Compared with the certified laboratory, serum 25-hydroxyvitamin D concentrations were on average 12.4 nmol/L higher at laboratory A (95% limits of agreement: -17.8,42.6); 12.8 nmol/L higher at laboratory B (95% limits of agreement: 0.8,24.8); and 10.6 nmol/L lower at laboratory C (95% limits of agreement: -48.4,27.1). The prevalence of vitamin D deficiency (defined here as 25-hydroxyvitamin D <50 nmol/L) was 24%, 16%, 12% and 41% at the certified laboratory, and laboratories A, B, and C, respectively. Our results demonstrate considerable differences in the measurement of 25-hydroxyvitamin D concentrations compared with a certified laboratory, even between laboratories using assays based on liquid chromatography-tandem mass spectrometry, which is often considered the gold-standard assay. To ensure accurate and reliable measurement of serum 25-hydroxyvitamin D concentrations, all laboratories should use an accuracy-based quality assurance system and, ideally, comply with international standardisation efforts. PMID: 26266807 [PubMed - as supplied by publisher]

Evidence for Chronic Kidney Disease-Mineral and Bone Disorder Associated With Metabolic Pathway Changes. Medicine (Baltimore). 2015 Aug;94(32):e1273 Authors: Wu Q, Lai X, Zhu Z, Hong Z, Dong X, Wang T, Wang H, Lou Z, Lin Q, Guo Z, Chai Y Abstract Abnormalities in the levels of calcium, phosphorus, and parathyroid hormone (PTH) in serum are typical for patients with chronic kidney disease (CKD). They are used routinely to predict the onset of CKD-mineral and bone disorder (MBD). However, CKD-MBD associated with metabolic pathway imbalance is not well understood.The objective of the study was to identify endogenous metabolic signatures in patients with intact PTH using mass spectrometry-based metabolomics. This study was a cross-sectional study. Ultra performance liquid chromatography-Quadrupole Time-of-Flight/mass spectrometry-based metabolic profiling was employed to analyze serum samples from 19 disease controls (DCs) (intact parathyroid hormone [iPTH] 150-300 pg/mL) and 19 secondary hyperparathyroidism (SHPT) patients (iPTH >300 pg/mL) (the training data set) to identify metabolic biomarkers for CKD-MBD. Then, another set of samples including 19 DCs (iPTH 150-300 pg/mL) and 19 SHPT patients (iPTH >300 pg/mL) (the test data set) were used to validate the potential biomarkers identified.Metabolic profiling analyses revealed different patterns of endogenous metabolites between the SHPT and the DC groups. A total of 32 unique metabolites were identified and 30 metabolites were elevated in the iPTH compared with control serum pools. Cytidine and L-phenylalanine were downregulated in the SHPT patients. The metabolic signatures identified were assessed respectively by an internal 10-fold cross validation with an accuracy of 91.4% and an external validation with an accuracy of 71.1%, a sensitivity of 73.7%, and a specificity of 68.4%.Mass spectrometry-based metabolomic analyses for SHPT patients promises immense potential for early diagnosis and therapy monitoring. Our results indicated that the onset of CKD-MBD is associated with pathway changes of protein synthesis and metabolism, amino acid metabolism, energy metabolism, and steroid hormone metabolism, with obvious promise for better understanding the pathogenesis of this disease. Several metabolic biomarkers were identified, which warrant further development. PMID: 26266360 [PubMed - as supplied by publisher]

A metabolomics strategy to explore urinary biomarkers and metabolic pathways for assessment of interaction between Danhong injection and low-dose aspirin during their synergistic treatment. J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Jul 26; Authors: Li J, Guo J, Shang E, Zhu Z, Zhu KY, Li S, Zhao B, Jia L, Zhao J, Tang Z, Duan J Abstract The drug combination of Danhong injection (DHI) and low-dose aspirin (ASA) was frequently applied for the treatment of cardiovascular and cerebrovascular diseases. Due to the drug interactions, a lot of potential benefits and risks might exist side by side in the course of combination therapy. However, there had been no studies of interaction between DHI and ASA. Metabolomics was a powerful tool to explore endogenous biomarkers and metabolic pathways. In present study, metabolic profiling with ultra-high-performance liquid chromatography coupled to quadrupole time of flight mass spectrometry (UHPLC-QTOF/MS) coupled with multivariate statistical analysis was performed to provide insight into understanding the interaction between DHI and low-dose ASA. Eleven potential biomarkers of three types were identified and seven metabolic pathways were constructed. The results showed that the interaction between DHI and low-dose ASA during synergistic treatment indeed affected some key endogenous biomarkers and metabolic pathways, which could not happen when DHI or low-dose ASA was used alone. The quality and quantity of endogenous metabolite were both influenced by interaction between DHI and low-dose ASA. In details, the amount of flavin mononucleotide, L-2, 4-diaminobutyric acid (DABA) and 4-aminohippuric acid were significantly increased. On the contrary, the amount of 3-methyluridine, 4, 6-dihydroxyquinoline, cortolone-3-glucuronide, and serotonin were significantly decreased. Furthermore, O-phosphotyrosine, 3-methyl-2-butenal, indoxyl sulfate and dolichyl diphosphate were disappeared in urine. As to metabolic pathways, riboflavin metabolism, pentose and glucuronate interconversions, and tryptophan metabolism were all significantly influenced. The emerging alterations of biomarkers and metabolic pathways were associated with a lot of drugs and diseases based on literature researches, which might influence the co-administration of other drugs or the treatments of relevant diseases. Our paper presented some hints to uncover the mechanism of interaction between DHI and low-dose ASA, which would provide some references for application of DHI and low-dose ASA combination. PMID: 26265434 [PubMed - as supplied by publisher]

Profiling the metabolome changes caused by cranberry procyanidins in plasma of female rats using H NMR and UHPLC-Q-Orbitrap-HRMS global metabolomics approaches. Mol Nutr Food Res. 2015 Aug 12; Authors: Liu H, Garrett TJ, Tayyari F, Gu L Abstract SCOPE: The objective was to investigate the metabolome changes in female rats gavaged with partially purified cranberry procyanidins (PPCP) using (1) H NMR and UHPLC-Q-Orbitrap-HRMS metabolomics approaches, and to identify the contributing metabolites. METHODS AND RESULTS: Twenty four female Sprague-Dawley rats were randomly separated into two groups and administered PPCP or partially purified apple procyanidins (PPAP) for 3 times using a 250 mg extracts/extracts body weight dose. Plasma were collected six hours after the last gavage and analyzed using (1) H NMR and UHPLC-Q-Orbitrap-HRMS. No metabolome difference was observed using (1) H NMR metabolomics approach. However, LC-HRMS metabolomics data show that metabolome in plasma of female rats administered PPCP differed from those gavaged with PPAP. Eleven metabolites were tentatively identified from a total of 36 discriminant metabolic features based on accurate masses and/and product ion spectra. PPCP caused a greater increase of exogenous metabolites including p-hydroxybenzoic acid, phenol, phenol-sulfate, catechol sulphate, 3, 4-dihydroxyphenylvaleric acid, and 4'-O-methyl-(-)-epicatechin-3'-O-beta-glucuronide in rat plasma. Furthermore, the plasma level of O-methyl-(-)-epicatechin-O-glucuronide, 4-hydroxy-5-(hydroxyphenyl)-valeric acid-O-sulphate, 5-(hydroxyphenyl)-ϒ-valerolactone-O-sulphate, 4-hydroxydiphenylamine, and peonidin-3-O-hexose were higher in female rats administered with PPAP. CONCLUSION: The metabolome changes caused by cranberry procyanidins were revealed using an UHPLC-Q-Orbitrap-HRMS global metabolomics approach. Exogenous and microbial metabolites were the major identified discriminate biomarkers. This article is protected by copyright. All rights reserved. PMID: 26264887 [PubMed - as supplied by publisher]

Discovery of urinary biomarkers of whole grain rye intake in free-living subjects using non-targeted LC-MS metabolite profiling (1-9). Mol Nutr Food Res. 2015 Aug 12; Authors: Hanhineva K, Brunius C, Andersson A, Marklund M, Juvonen R, Keski-Rahkonen P, Auriola S, Landberg R Abstract SCOPE: Whole grain (WG) intake is associated with decreased risk of developing colorectal cancer, type 2 diabetes and cardiovascular disease and its comorbidities. However, the role of specific grains is unclear. Moreover, intake of specific WG is challenging to measure accurately with traditional dietary assessment methods. Our aim was to use non-targeted metabolite profiling to discover specific urinary biomarkers for WG rye to objectively reflect intake under free-living conditions. METHODS AND RESULTS: WG rye intake was estimated by weighed food records, and 24 h urine collections were analyzed by LC-MS. Multivariate modelling was undertaken by repeated double cross-validated partial least squares regression against reported WG rye intake, which correlated well with multivariate prediction estimates (r = 0.67-0.80, p<0.001), but not with intakes of WG wheat or oats. Hydroxyhydroxyphenyl acetamide (HHPA) sulfate, 3,5-dihydroxyphenylpropionic acid (DHPPA) sulfate, caffeic acid sulfate and hydroxyphenyl acetamide (HPAA) sulfate were among the 20 features which had the greatest potential as intake biomarkers of WG. In addition, three compounds exhibited MS/MS fragmentation of carnitine structures. CONCLUSION: With this non-targeted approach, we confirmed the specificity of alkylresorcinol metabolites as biomarkers for WG rye intake, but also discovered other compounds that should be evaluated as putative biomarkers in future studies. This article is protected by copyright. All rights reserved. PMID: 26264776 [PubMed - as supplied by publisher]

Related Articles Sampling and analysis of metabolomes in biological fluids. Analyst. 2014 Aug 7;139(15):3683-94 Authors: Nunes de Paiva MJ, Menezes HC, de Lourdes Cardeal Z Abstract Metabolome analysis involves the study of small molecules that are involved in the metabolic responses that occur through patho-physiological changes caused by genetic stimuli or chemical agents. Qualitative and quantitative metabolome analyses are used for the diagnosis of various diseases or chemical exposure. This article presents an overview of the different analytical methods available for performing the determination of the metabolome, including sampling, sample preparation and processing and interpretation of data. Critical comments are aimed at emphasizing the extraction methods as well as the biological samples used for metabolome analysis and data processing. PMID: 24941103 [PubMed - indexed for MEDLINE]

Related Articles Metabolic signatures associated with environmental pollution by metals in Doñana National Park using P. clarkii as bioindicator. Environ Sci Pollut Res Int. 2014 Dec;21(23):13315-23 Authors: Gago-Tinoco A, González-Domínguez R, García-Barrera T, Blasco-Moreno J, Bebianno MJ, Gómez-Ariza JL Abstract Bioindicators can reflect the effects of pollutants on their metabolism, being widely used to assess environmental stress. In this sense, the crab Procambarus clarkii has been previously proposed to monitor the contamination in Doñana National Park (southwest Spain) using conventional biomarkers. In this work, a metabolomic approach based on direct infusion mass spectrometry, which allows an easy and quick study of a large number of metabolites in a single run, was used for pollution assessment of this area, considering the biological response of this organism to contamination. In addition, metal accumulation in crab tissues was determined. Thus, the integrated analysis of metabolomic and metallomic data enabled the study of metabolic response of the organism against pollution. Several metabolites were discovered as potential biomarkers of pollution, such as decreased levels of carnosine, alanine, niacinamide, acetoacetate, pantothenic acid, ascorbate, glucose-6-phosphate, arginine, glucose, lactate, phospholipids, and tryglicerides, as well as elevated levels of acetyl carnitine, phosphocholine, choline, and uric acid. In this way, metal-induced toxicity could be related to metabolic impairments, principally oxidative stress, metabolic dysfunction, and dyslipidemia. PMID: 24756666 [PubMed - indexed for MEDLINE]

Novel Approach to Identify Potential Bioactive Plant Metabolites: Pharmacological and Metabolomics Analyses of Ethanol and Hot Water Extracts of Several Canadian Medicinal Plants of the Cree of Eeyou Istchee. PLoS One. 2015;10(8):e0135721 Authors: Shang N, Saleem A, Musallam L, Walshe-Roussel B, Badawi A, Cuerrier A, Arnason JT, Haddad PS Abstract We evaluated and compared the antidiabetic potential and molecular mechanisms of 17 Cree plants' ethanol extracts (EE) and hot water extracts (HWE) on glucose homeostasis in vitro and used metabolomics to seek links with the content of specific phytochemicals. Several EE of medical plants stimulated muscle glucose uptake and inhibited hepatic G6Pase activity. Some HWE partially or completely lost these antidiabetic activities in comparison to EE. Only R. groenlandicum retained similar potential between EE and HWE in both assays. In C2C12 muscle cells, EE of R. groenlandicum, A. incana and S. purpurea stimulated glucose uptake by activating AMP-activated protein kinase (AMPK) pathway and increasing glucose transporter type 4 (GLUT4) expression. In comparison to EE, HWE of R. groenlandicum exhibited similar activities; HWE of A. incana completely lost its effect on all parameters; interestingly, HWE of S. purpurea activated insulin pathway instead of AMPK pathway to increase glucose uptake. In the liver, for a subset of 5 plants, HWE and EE activated AMPK pathway whereas the EE and HWE of S. purpurea and K. angustifolia also activated insulin pathways. Quercetin-3-O-galactoside and quercetin 3-O-α-L-arabinopyranoside, were successfully identified by discriminant analysis as biomarkers of HWE plant extracts that stimulate glucose uptake in vitro. More importantly, the latter compound was not identified by previous bioassay-guided fractionation. PMID: 26263160 [PubMed - as supplied by publisher]

Strategy for NMR metabolomic analysis of urine in mouse models of obesity- from sample collection to interpretation of acquired data. J Pharm Biomed Anal. 2015 Jul 17;115:225-235 Authors: Pelantová H, Bugáňová M, Anýž J, Železná B, Maletínská L, Novák D, Haluzík M, Kuzma M Abstract The mouse model of monosodium glutamate induced obesity was used to examine and consequently optimize the strategy for analysis of urine samples by NMR spectroscopy. A set of nineteen easily detectable metabolites typical in obesity-related studies was selected. The impact of urine collection protocol, choice of (1)H NMR pulse sequence, and finally the impact of the normalization method on the detected concentration of selected metabolites were investigated. We demonstrated the crucial effect of food intake and diurnal rhythms resulting in the choice of a 24-hour fasting collection protocol as the most convenient for tracking obesity-induced increased sensitivity to fasting. It was shown that the Carr-Purcell-Meiboom-Gill (CPMG) experiment is a better alternative to one-dimensional nuclear Overhauser enhancement spectroscopy (1D-NOESY) for NMR analysis of mouse urine due to its ability to filter undesirable signals of proteins naturally present in rodent urine. Normalization to total spectral area provided comparable outcomes as did normalization to creatinine or probabilistic quotient normalization in the CPMG-based model. The optimized approach was found to be beneficial mainly for low abundant metabolites rarely monitored due to their overlap by strong protein signals. PMID: 26263053 [PubMed - as supplied by publisher]

Mass spectrometry-based serum metabolomics of a C57BL/6J mouse model of high-fat diet induced nonalcoholic fatty liver disease development. J Agric Food Chem. 2015 Aug 11; Authors: Lai YS, Chen WC, Kuo TC, Ho CT, Kuo CH, Tseng YJ, Lu KH, Lin SH, Panyod S, Sheen LY Abstract Obesity, dyslipidemia, insulin resistance, oxidative stress, and inflammation are key clinical risk factors for the progression of nonalcoholic fatty liver disease (NAFLD). Currently there is no comprehensive metabolic profile of a well-established animal model that effectively mimics the etiology and pathogenesis of NAFLD in humans. Here, we report the pathophysiological and metabolomic changes associated with NAFLD development in a C57BL/6J mouse model in which NAFLD was induced by feeding high-fat diet (HFD) for 4, 8, 12, and 16 weeks. Serum metabolomic analysis was conducted using UHPLC-QTOF-MS and GC/MS to establish a metabolomic profile. Analysis of the metabolomics profile in combination with principal components analysis revealed marked differences in metabolites between the control and HFD group depending on NAFLD severity. Thirty potential biomarkers were strongly associated with the development of NAFLD. Among these, 11 metabolites were mainly related to carbohydrate metabolism, hepatic biotransformation, collagen synthesis, and gut microbial metabolism, which are characteristics of obesity, as well as significantly increased serum glucose, total cholesterol, and hepatic triglycerides levels during the onset of NAFLD (4 weeks). At 8 weeks, 5 additional metabolites that are chiefly involved in perturbation of lipid metabolism and insulin secretion were found to be associated with hyperinsulinemia, hyperlipidemia, and hepatic steatosis in the mid-term of NAFLD progression. At the end of 12 and 16 weeks, 14 additional metabolites were predominantly correlated to abnormal bile acid synthesis, oxidative stress, and inflammation, representing hepatic inflammatory infiltration during NAFLD development. These results provide potential biomarkers for early risk assessment of NAFLD and further insights into NAFLD development. PMID: 26262841 [PubMed - as supplied by publisher]

Related Articles Proteomic analysis of lymphoblastoid cells from Nasu-Hakola patients: a step forward in our understanding of this neurodegenerative disorder. PLoS One. 2014;9(12):e110073 Authors: Giuliano S, Agresta AM, De Palma A, Viglio S, Mauri P, Fumagalli M, Iadarola P, Montalbetti L, Salvini R, Bardoni A Abstract Nasu-Hakola disease (NHD) is a recessively inherited rare disorder characterized by a combination of neuropsychiatric and bone symptoms which, while being unique to this disease, do not provide a rationale for the unambiguous identification of patients. These individuals, in fact, are likely to go unrecognized either because they are considered to be affected by other kinds of dementia or by fibrous dysplasia of bone. Given that dementia in NHD has much in common with Alzheimer's disease and other neurodegenerative disorders, it cannot be expected to achieve the differential diagnosis of this disease without performing a genetic analysis. Under this scenario, the availability of protein biomarkers would indeed provide a novel context to facilitate interpretation of symptoms and to make the precise identification of this disease possible. The work here reported was designed to generate, for the first time, protein profiles of lymphoblastoid cells from NHD patients. Two-dimensional electrophoresis (2-DE) and nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) have been applied to all components of an Italian family (seven subjects) and to five healthy subjects included as controls. Comparative analyses revealed differences in the expression profile of 21 proteins involved in glucose metabolism and information pathways as well as in stress responses. PMID: 25470616 [PubMed - indexed for MEDLINE]

Related Articles Inhibition of monocarboxylate transporter-1 (MCT1) by AZD3965 enhances radiosensitivity by reducing lactate transport. Mol Cancer Ther. 2014 Dec;13(12):2805-16 Authors: Bola BM, Chadwick AL, Michopoulos F, Blount KG, Telfer BA, Williams KJ, Smith PD, Critchlow SE, Stratford IJ Abstract Inhibition of the monocarboxylate transporter MCT1 by AZD3965 results in an increase in glycolysis in human tumor cell lines and xenografts. This is indicated by changes in the levels of specific glycolytic metabolites and in changes in glycolytic enzyme kinetics. These drug-induced metabolic changes translate into an inhibition of tumor growth in vivo. Thus, we combined AZD3965 with fractionated radiation to treat small cell lung cancer (SCLC) xenografts and showed that the combination provided a significantly greater therapeutic effect than the use of either modality alone. These results strongly support the notion of combining MCT1 inhibition with radiotherapy in the treatment of SCLC and other solid tumors. PMID: 25281618 [PubMed - indexed for MEDLINE]

[The Austrian LEAD (Lung hEart sociAL boDy) Study]. Pneumologie. 2015 Aug;69(8):459-462 Authors: Breyer-Kohansal R, Breyer MK, Hartl S, Burghuber OC Abstract More research is needed to elucidate natural history and underlying pathomechanisms of the most common airway diseases, Asthma and COPD. In the last decade risk factors affecting the natural history of lung function, defined by the decline of lung function over time, have been evaluated. Moreover, scientific methods have been extended and novel biomarkers, genetics, metabolomics, and epidemiology are dominant tools for investigating the natural history of lung function and potential risk factors. Evidence shows that lung function in childhood is a predictor for lung function in adulthood and risk factors starting in utero contribute to lung function decline during life. Therefore, recently it has been hypothesized that COPD begins in childhood. Thus, prospective investigation of lung function changes including novel scientific methodology has been advocated. The Austrian LEAD study has been initiated in the general population 2012 to investigate the natural history of obstructive airway diseases. PMID: 26258419 [PubMed - as supplied by publisher]

Alteration in Metabolic Signature and Lipid Metabolism in Patients with Angina Pectoris and Myocardial Infarction. PLoS One. 2015;10(8):e0135228 Authors: Park JY, Lee SH, Shin MJ, Hwang GS Abstract Lipid metabolites are indispensable regulators of physiological and pathological processes, including atherosclerosis and coronary artery disease (CAD). However, the complex changes in lipid metabolites and metabolism that occur in patients with these conditions are incompletely understood. We performed lipid profiling to identify alterations in lipid metabolism in patients with angina and myocardial infarction (MI). Global lipid profiling was applied to serum samples from patients with CAD (angina and MI) and age-, sex-, and body mass index-matched healthy subjects using ultra-performance liquid chromatography/quadruple time-of-flight mass spectrometry and multivariate statistical analysis. A multivariate analysis showed a clear separation between the patients with CAD and normal controls. Lysophosphatidylcholine (lysoPC) and lysophosphatidylethanolamine (lysoPE) species containing unsaturated fatty acids and free fatty acids were associated with an increased risk of CAD, whereas species of lysoPC and lyso-alkyl PC containing saturated fatty acids were associated with a decreased risk. Additionally, PC species containing palmitic acid, diacylglycerol, sphingomyelin, and ceramide were associated with an increased risk of MI, whereas PE-plasmalogen and phosphatidylinositol species were associated with a decreased risk. In MI patients, we found strong positive correlation between lipid metabolites related to the sphingolipid pathway, sphingomyelin, and ceramide and acute inflammatory markers (high-sensitivity C-reactive protein). The results of this study demonstrate altered signatures in lipid metabolism in patients with angina or MI. Lipidomic profiling could provide the information to identity the specific lipid metabolites under the presence of disturbed metabolic pathways in patients with CAD. PMID: 26258408 [PubMed - as supplied by publisher]

Related Articles Coping with drought: stress and adaptive responses in potato and perspectives for improvement. Front Plant Sci. 2015;6:542 Authors: Obidiegwu JE, Bryan GJ, Jones HG, Prashar A Abstract Potato (Solanum tuberosum L.) is often considered as a drought sensitive crop and its sustainable production is threatened due to frequent drought episodes. There has been much research aiming to understand the physiological, biochemical, and genetic basis of drought tolerance in potato as a basis for improving production under drought conditions. The complex phenotypic response of potato plants to drought is conditioned by the interactive effects of the plant's genotypic potential, developmental stage, and environment. Effective crop improvement for drought tolerance will require the pyramiding of many disparate characters, with different combinations being appropriate for different growing environments. An understanding of the interaction between below ground water uptake by the roots and above ground water loss from the shoot system is essential. The development of high throughput precision phenotyping platforms is providing an exciting new tool for precision screening, which, with the incorporation of innovative screening strategies, can aid the selection and pyramiding of drought-related genes appropriate for specific environments. Outcomes from genomics, proteomics, metabolomics, and bioengineering advances will undoubtedly compliment conventional breeding strategies and presents an alternative route toward development of drought tolerant potatoes. This review presents an overview of past research activity, highlighting recent advances with examples from other crops and suggesting future research directions. PMID: 26257752 [PubMed]

Related Articles Evolution of a thienopyrimidine antitubercular relying on medicinal chemistry and metabolomics insights. Tetrahedron Lett. 2015 Jun 3;56(23):3246-3250 Authors: Li SG, Vilchèze C, Chakraborty S, Wang X, Kim H, Anisetti M, Ekins S, Rhee KY, Jacobs WR, Freundlich JS Abstract The metabolic instability of an antitubercular small molecule CD117 was addressed through iterative alteration of a key sulfide substituent and interrogation of the effect on growth inhibition of cultured Mycobacterium tuberculosis. This process was informed by studies of the intramycobacterial metabolism of CD117 and its inactive carboxylic acid derivative. Isoxazole 4e and thiazole 4m demonstrated significant gains in mouse liver microsomal stability with slight losses in whole-cell activity. This work illustrates the challenges of antitubercular hit evolution, requiring a balance of chemical and biological insights. PMID: 26257441 [PubMed - as supplied by publisher]