Publications
383 results found
Castro C, Krumsiek J, Lehrbach NJ, et al., 2013, A study of Caenorhabditis elegans DAF-2 mutants by metabolomics and differential correlation networks., Mol Biosyst, Vol: 9, Pages: 1632-1642
daf-2 is one of the most studied mutants in C. elegans: it contains a deletion in the gene orthologue of the insulin/insulin-like growth factor (IGF) receptor. Using high resolution (1)H NMR spectroscopy, metabolomics has helped to dissect the metabolic consequences of altered daf-2 signalling. Here, we present a detailed metabolomic analysis of daf-2, using NMR spectroscopy, gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) to integrate information from different pathways. We have then used Pearson and partial correlation analysis to build networks to explore the central role of daf-2 in regulating fatty acid and amino acid metabolism. The results show the tight regulation between these two parts of the metabolome.
Pan X, Wilson M, McConville C, et al., 2013, Increased unsaturation of lipids in cytoplasmic lipid droplets in DAOY cancer cells in response to cisplatin treatment, Metabolomics, Vol: 9, Pages: 722-729, ISSN: 1573-3882
Increases in 1H nuclear magnetic resonance spectroscopy (NMR) visible lipids are a well-documented sign of treatment response in cancers. Lipids in cytoplasmic lipid droplets (LDs) are the main contributors to the NMR lipid signals. Two human primitive neuroectodermal tumour cell lines with different sensitivities to cisplatin treatment were studied. Increases in NMR visible saturated and unsaturated lipids in cisplatin treated DAOY cells were associated with the accumulation of LDs prior to DNA fragmentation due to apoptosis. An increase in unsaturated fatty acids (UFAs) was detected in isolated LDs from DAOY cells, in contrast to a slight decrease in UFAs in lipid extracts from whole cells. Oleic acid and linoleic acid were identified as the accumulating UFAs in LDs by heteronuclear single quantum coherence spectroscopy (HSQC). 1H NMR lipids in non-responding PFSK-1 cells were unchanged by exposure to 10 μM cisplatin. These findings support the potential of NMR detectable UFAs to serve as a non-invasive marker of tumour cell response to treatment. © 2012 The Author(s).
Catalán Ú, Rodríguez M-Á, Ras M-R, et al., 2013, Biomarkers of food intake and metabolite differences between plasma and red blood cell matrices; a human metabolomic profile approach., Mol Biosyst, Vol: 9, Pages: 1411-1422
Untargeted metabolomic analyses of plasma and red blood cells (RBCs) can provide complementary information on biomarkers of food consumption. To assess blood collection differences in biomarkers, fasting blood was drawn from 10 healthy individuals using sodium citrate and lithium heparin as anticoagulants. Plasma and RBCs were separated into aqueous and lipid fractions to be analyzed using 1D and 2D (1)H NMR spectroscopy. Fatty acids were analyzed using gas chromatography-mass spectrometry (GC-MS). Polyphenols were extracted from plasma and RBCs by micro-elution solid-phase extraction and analyzed by ultra performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS). (1)H NMR demonstrated higher aqueous metabolites such as glucose in plasma compared to RBCs, while RBCs contained higher ADP-ATP, creatine and acetone than plasma. Lipoproteins and their subclasses were higher in plasma than in RBCs. Percentages of saturated fatty acids (SFA) 16 : 0, 17 : 0, 20 : 0, 24 : 0 and polyunsaturated fatty acids (PUFA) 22 : 6 n-3 (docosahexaenoic acid) and 20 : 4 n-6 (arachidonic acid) were higher in RBCs than in plasma (p < 0.05), while SFA 14 : 0, monounsaturated fatty acids (MUFA) 14 : 1 n-5, 16 : 1 n-7, 17 : 1 n-7 and 18 : 1 n-9 and PUFA 18 : 3 n-3, 18 : 2 n-6, 18 : 3 n-6 and 20 : 3 n-6 were higher in plasma than in RBCs (p < 0.05). Polyphenols differed in plasma from those of RBCs. Biomarker concentrations were lower in sodium citrate compared to lithium heparin plasma. In conclusion, metabolomic profiles generated by NMR spectroscopy, GC-MS and UPLC-MS/MS analyses of RBCs versus plasma show complementary information on several specific molecular biomarkers that could be applied in nutritional assessment.
Heather LC, Wang X, West JA, et al., 2013, A practical guide to metabolomic profiling as a discovery tool for human heart disease., J Mol Cell Cardiol, Vol: 55, Pages: 2-11
Metabolomics has refreshed interest in metabolism across biology and medicine, particularly in the areas of functional genomics and biomarker discovery. In this review we will discuss the experimental techniques and challenges involved in metabolomic profiling and how these technologies have been applied to cardiovascular disease. Open profiling and targeted approaches to metabolomics are compared, focusing on high resolution NMR spectroscopy and mass spectrometry, as well as discussing how to analyse the large amounts of data generated using multivariate statistics. Finally, the current literature on metabolomic profiling in human cardiovascular disease is reviewed to illustrate the diversity of approaches, and discuss some of the key metabolites and pathways found to be perturbed in plasma, urine and tissue from patients with these diseases. This includes studies of coronary artery disease, myocardial infarction, and ischemic heart disease. These studies demonstrate the potential of the technology for biomarker discovery and elucidating metabolic mechanisms associated with given pathologies, but also in some cases provide a warning of the pitfalls of poor study design. This article is part of a Special Issue entitled "Focus on Cardiac Metabolism".
Jamers A, Blust R, De Coen W, et al., 2013, An omics based assessment of cadmium toxicity in the green alga Chlamydomonas reinhardtii., Aquat Toxicol, Vol: 126, Pages: 355-364
The effects of cadmium were assessed in the freshwater alga Chlamydomonas reinhardtii. Algae were exposed to concentrations of 0, 8.1 or 114.8 μM of cadmium and growth rates, gene transcription and metabolite profiles were examined after 48 and 72 h of exposure. In algae exposed to 8.1 μM Cd, several genes were differentially transcribed after 48 h but no adverse growth related effects were detected. A transient effect on both gene transcription patterns and metabolite profiles could be discerned after 48 h of exposure but the majority of these changes disappeared after 72 h. In contrast, all effects were more pronounced at the 114.8 μM cadmium exposure. Here growth was clearly reduced and transcription of a large number of genes involved in oxidative stress defense mechanisms was differentially increased. Metabolites involved in the glutathione synthesis pathway (an important antioxidant defense) were also affected but the effects of cadmium were found to be more pronounced at the transcript level than in the metabolome, suggesting that the former exhibits greater sensitivity toward cadmium exposure.
Haug K, Salek RM, Conesa P, et al., 2013, MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data., Nucleic Acids Research, Vol: 41, Pages: D781-D786, ISSN: 0305-1048
MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.
Virtue S, Feldmann H, Christian M, et al., 2012, A new role for lipocalin prostaglandin D synthase in the regulation of brown adipose tissue substrate utilization, Diabetes, Vol: 61, Pages: 3139-3147, ISSN: 0012-1797
In this study, we define a new role for lipocalin prostaglandin D synthase (L-PGDS) in the control of metabolic fuel utilization by brown adipose tissue (BAT). We demonstrate that L-PGDS expression in BAT is positively correlated with BAT activity, upregulated by peroxisome proliferator–activated receptor γ coactivator 1α or 1β and repressed by receptor-interacting protein 140. Under cold-acclimated conditions, mice lacking L-PGDS had elevated reliance on carbohydrate to provide fuel for thermogenesis and had increased expression of genes regulating glycolysis and de novo lipogenesis in BAT. These transcriptional differences were associated with increased lipid content in BAT and a BAT lipid composition enriched with de novo synthesized lipids. Consistent with the concept that lack of L-PGDS increases glucose utilization, mice lacking L-PGDS had improved glucose tolerance after high-fat feeding. The improved glucose tolerance appeared to be independent of changes in insulin sensitivity, as insulin levels during the glucose tolerance test and insulin, leptin, and adiponectin levels were unchanged. Moreover, L-PGDS knockout mice exhibited increased expression of genes involved in thermogenesis and increased norepinephrine-stimulated glucose uptake to BAT, suggesting that sympathetically mediated changes in glucose uptake may have improved glucose tolerance. Taken together, these results suggest that L-PGDS plays an important role in the regulation of glucose utilization in vivo.
Paschos GK, Ibrahim S, Song W-L, et al., 2012, Obesity in mice with adipocyte-specific deletion of clock component Arntl., Nat Med, Vol: 18, Pages: 1768-1777
Adipocytes store excess energy in the form of triglycerides and signal the levels of stored energy to the brain. Here we show that adipocyte-specific deletion of Arntl (also known as Bmal1), a gene encoding a core molecular clock component, results in obesity in mice with a shift in the diurnal rhythm of food intake, a result that is not seen when the gene is disrupted in hepatocytes or pancreatic islets. Changes in the expression of hypothalamic neuropeptides that regulate appetite are consistent with feedback from the adipocyte to the central nervous system to time feeding behavior. Ablation of the adipocyte clock is associated with a reduced number of polyunsaturated fatty acids in adipocyte triglycerides. This difference between mutant and wild-type mice is reflected in the circulating concentrations of polyunsaturated fatty acids and nonesterified polyunsaturated fatty acids in hypothalamic neurons that regulate food intake. Thus, this study reveals a role for the adipocyte clock in the temporal organization of energy regulation, highlights timing as a modulator of the adipocyte-hypothalamic axis and shows the impact of timing of food intake on body weight.
Lehrbach NJ, Castro C, Murfitt KJ, et al., 2012, Post-developmental microRNA expression is required for normal physiology, and regulates aging in parallel to insulin/IGF-1 signaling in C. elegans., RNA, Vol: 18, Pages: 2220-2235
Regulation of gene expression by microRNAs (miRNAs) is essential for normal development, but the roles of miRNAs in the physiology of adult animals are poorly understood. We have isolated a conditional allele of DGCR8/pash-1, which allows reversible and rapid inactivation of miRNA synthesis in vivo in Caenorhabditis elegans. This is a powerful new tool that allows dissection of post-developmental miRNA functions. We demonstrate that continuous synthesis of miRNAs is dispensable for cellular viability but critical for the physiology of adult animals. Loss of miRNA synthesis in the adult reduces lifespan and results in rapid aging. The insulin/IGF-1 signaling pathway is a critical determinant of lifespan, and is modulated by miRNAs. We find that although miRNA expression is required for some mechanisms of lifespan extension, it is not essential for the longevity of animals lacking insulin/IGF-1 signaling. Further, misregulated insulin/IGF-1 signaling cannot account for the reduced lifespan caused by disruption of miRNA synthesis. We show that miRNAs act in parallel with insulin/IGF-1 signaling to regulate a shared set of downstream genes important for physiological processes that determine lifespan. We conclude that coordinated transcriptional and post-transcriptional regulation of gene expression promotes longevity.
Howe PWA, Ament Z, Knowles K, et al., 2012, Combined use of filtered and edited 1 H NMR spectroscopy to detect 13 C-enriched compounds in complex mixtures., NMR Biomed, Vol: 25, Pages: 1217-1223
In conventional metabolism and pharmacokinetic studies, radioactive isotopes are used to identify and quantify the breakdown products of xenobiotics. However, the stable isotope (13) C provides a cheaper and less hazardous alternative. Metabolites of (13) C-enriched xenobiotics can be detected, quantified and identified by (13) C-filtered NMR spectroscopy. However, one obstacle to using (13) C is its 1.1% natural abundance that produces a background signal in (13) C-filtered NMR spectra of crude biological extracts. The signal makes it difficult to distinguish between (13) C-enriched xenobiotics resonances from endogenous metabolites unrelated to the xenobiotic. This study proposes that the (13) C background signal can be distinguished from resonances of (13) C-enriched xenobiotics by the absence of a (12) C component in the xenobiotic. This is detected by combined analysis of (13) C-filtered and -edited NMR spectra. The theory underlying the approach is described and the method is demonstrated by the detection of sub-microgram amounts of (13) C-enriched phenacetin in crude extracts of hepatocyte microsomes.
Ubhi BK, Cheng KK, Dong J, et al., 2012, Targeted metabolomics identifies perturbations in amino acid metabolism that sub-classify patients with COPD., Mol Biosyst, Vol: 8, Pages: 3125-3133
BACKGROUND: COPD, a leading cause of mortality is currently assessed by spirometry (forced expiratory volume in 1 second, FEV(1)). However FEV(1) does not correlate with patient mortality. ECLIPSE (Evaluation of Chronic obstructive pulmonary disease to Longitudinally Identify Predictive Surrogate Endpoints) aims to identify biomarkers that correlate with clinically relevant COPD subtypes, and to assess how these may predict disease progression. New methods were developed and validated to evaluate small molecules as potential diagnostic tools in patients with COPD, COPD related cachexia and cancer related cachexia. METHODS AND FINDINGS: quantitative LC-MS/MS was developed to measure 34 amino acids and dipeptides for stratification of patient groups. Subsets of the ECLIPSE patients were used to assess biomarkers of lung obstruction; GOLD IV (n = 30) versus control (n = 30); emphysema (n = 38) versus airways disease (n = 21) and cachexia (n = 30) versus normal body mass index (n = 30). Serum from cachexic (n = 7) and non-cachexic (n = 5) pancreatic cancer patients were included as controls. Targeted LC-MS/MS distinguished GOLD IV patients from controls, patients with and without emphysema and patients with and without cachexia. Glutamine, aspartate and arginine were significantly increased (p < 0.05; FDR adjustment α < 0.1) in cachexia, emphysema and GOLD IV patients and aminoadipate was decreased. Several amino acid concentrations were significantly altered in patients with COPD but not patients with pancreatic cancer (serine, sarcosine, tryptophan, BCAAs and 3-methylhistdine). Increased γ-aminobutyrate (GABA, p < 0.01) levels were specific to cachexia in patients with pancreatic cancer. β-aminoisobutyrate, 1-methylhistidine and asparagine (p < 0.05) were common across the patients with cachexia from both the COPD and pancreatic cancer cohorts. CONCLUSION: these results demonstrate that a metabolomic fingerprint has potential to stratify p
Steinbeck C, Conesa P, Haug K, et al., 2012, MetaboLights: Towards a new COSMOS of metabolomics data management, Metabolomics, Vol: 8, Pages: 757-760, ISSN: 1573-3882
Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www. ebi. ac. uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics. © 2012 The Author(s).
Deng L, Cheng KK, Dong J, et al., 2012, Non-negative principal component analysis for NMR-based metabolomic data analysis, Chemometrics and Intelligent Laboratory Systems, Vol: 118, Pages: 51-61, ISSN: 0169-7439
Proton nuclear magnetic resonance ( 1H-NMR) spectroscopy is one of the major analytical platforms used in metabolomics. The data acquired from NMR experiments are frequently processed using multivariate statistical methods such as principal component analysis (PCA) and partial least squares (PLS) to extract biologically meaningful information from complex spectra. Conventionally, these methods produce components with both positive and negative loadings, which contradict with the non-negativity of Fourier-transformed NMR spectra. In recent years, there is an increasing interest in incorporating non-negative constraints into multivariate methods. In the current study, a non-negative principal component analysis (NPCA) algorithm was introduced for the analysis of NMR-based metabolomic data. Using a simulated dataset, we showed that NPCA could reveal interesting local features in multivariate dataset, which are hidden in conventional PCA model. Notably, simulated peaks arising from a single compound were extracted by a same component in NPCA model. The current results also highlighted NPCA to be less susceptible to noise as compared to PCA. Furthermore, a supervised version of NPCA (sNPCA) was developed for class discrimination analysis, and it was used to identify urinary metabolites that distinguished hyperthyroid patients from healthy volunteers. Our results demonstrated that both NPCA and sNPCA could produce easily interpretable results and provide additional information to that of conventional projection methods. © 2012 Elsevier B.V.
Ubhi BK, Riley JH, Shaw PA, et al., 2012, Metabolic profiling detects biomarkers of protein degradation in COPD patients., Eur Respir J, Vol: 40, Pages: 345-355
There is a paucity of biomarkers for chronic obstructive pulmonary disease (COPD). Metabolomics were applied to a defined COPD patient cohort from the ECLIPSE study (Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points). Results were correlated with accepted biomarkers for the disease. Baseline control serum (n=66) and Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage II (n=70), III (n=64) and IV (n=44) COPD patients were analysed by proton nuclear magnetic resonance ((1)H NMR). Liquid chromatography with tandem mass spectrometry (LC-MS/MS) was used to confirm amino acid changes detected by (1)H NMR. Data were correlated with body composition, emphysema and systemic inflammation. (1)H NMR identified decreased lipoproteins, N,N-dimethylglycine, and increased glutamine, phenylalanine, 3-methylhistidine and ketone bodies in COPD patients with decreased branched-chain amino acids (BCAAs) observed in GOLD stage IV patients. BCAAs, their degradation products, 3-methylhistidine, ketone bodies, and triglycerides were correlated negatively with cachexia and positively with systemic inflammation. Emphysema patients also displayed decreased serum creatine, glycine and N,N-dimethylglycine. LC-MS/MS confirmed (1)H NMR findings relating to BCAAs, glutamine and 3-methylhistidine in GOLD stage IV patients. NMR-based metabolomics characterised COPD patients based on systemic effects and lung function parameters. Increased protein turnover occurred in all COPD patients with increased protein degradation in individuals with emphysema and cachexia.
Budczies J, Denkert C, Müller BM, et al., 2012, Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study, BMC Genomics, Vol: 13, ISSN: 1471-2164
BACKGROUND: Changes in energy metabolism of the cells are common to many kinds of tumors and are considered a hallmark of cancer. Gas chromatography followed by time-of-flight mass spectrometry (GC-TOFMS) is a well-suited technique to investigate the small molecules in the central metabolic pathways. However, the metabolic changes between invasive carcinoma and normal breast tissues were not investigated in a large cohort of breast cancer samples so far. RESULTS: A cohort of 271 breast cancer and 98 normal tissue samples was investigated using GC-TOFMS-based metabolomics. A total number of 468 metabolite peaks could be detected; out of these 368 (79%) were significantly changed between cancer and normal tissues (p<0.05 in training and validation set). Furthermore, 13 tumor and 7 normal tissue markers were identified that separated cancer from normal tissues with a sensitivity and a specificity of >80%. Two-metabolite classifiers, constructed as ratios of the tumor and normal tissues markers, separated cancer from normal tissues with high sensitivity and specificity. Specifically, the cytidine-5-monophosphate / pentadecanoic acid metabolic ratio was the most significant discriminator between cancer and normal tissues and allowed detection of cancer with a sensitivity of 94.8% and a specificity of 93.9%. CONCLUSIONS: For the first time, a comprehensive metabolic map of breast cancer was constructed by GC-TOF analysis of a large cohort of breast cancer and normal tissues. Furthermore, our results demonstrate that spectrometry-based approaches have the potential to contribute to the analysis of biopsies or clinical tissue samples complementary to histopathology.
Virtue S, Masoodi M, Velagapudi V, et al., 2012, Lipocalin prostaglandin D synthase and PPARγ2 coordinate to regulate carbohydrate and lipid metabolism in vivo, PLoS One, Vol: 7, ISSN: 1932-6203
Mice lacking Peroxisome Proliferator-Activated Receptor γ2 (PPARγ2) have unexpectedly normal glucose tolerance and mild insulin resistance. Mice lacking PPARγ2 were found to have elevated levels of Lipocalin prostaglandin D synthase (L-PGDS) expression in BAT and subcutaneous white adipose tissue (WAT). To determine if induction of L-PGDS was compensating for a lack of PPARγ2, we crossed L-PGDS KO mice to PPARγ2 KO mice to generate Double Knock Out mice (DKO). Using DKO mice we demonstrated a requirement of L-PGDS for maintenance of subcutaneous WAT (scWAT) function. In scWAT, DKO mice had reduced expression of thermogenic genes, the de novo lipogenic program and the lipases ATGL and HSL. Despite the reduction in markers of lipolysis in scWAT, DKO mice had a normal metabolic rate and elevated serum FFA levels compared to L-PGDS KO alone. Analysis of intra-abdominal white adipose tissue (epididymal WAT) showed elevated expression of mRNA and protein markers of lipolysis in DKO mice, suggesting that DKO mice may become more reliant on intra-abdominal WAT to supply lipid for oxidation. This switch in depot utilisation from subcutaneous to epididymal white adipose tissue was associated with a worsening of whole organism metabolic function, with DKO mice being glucose intolerant, and having elevated serum triglyceride levels compared to any other genotype. Overall, L-PGDS and PPARγ2 coordinate to regulate carbohydrate and lipid metabolism.
Baylay AJ, Spurgeon DJ, Svendsen C, et al., 2012, A metabolomics based test of independent action and concentration addition using the earthworm Lumbricus rubellus., Ecotoxicology, Vol: 21, Pages: 1436-1447
A major challenge in ecotoxicology is to understand the effects of multiple toxicants on organisms. Here we assess the effects on survival, weight change, cocoon production and metabolism caused by exposure to two similarly acting (imidacloprid/thiacloprid) and two dissimilarly acting (chlorpyrifos/Nickel) chemicals on the earthworm Lumbricus rubellus. We assessed the standard models of concentration addition (CA) and independent action (IA), in conjunction with a metabolomics based approach to elucidate mechanisms of effect. For imidacloprid and thiacloprid the reproductive effects indicated probable additivity. Although this suggests joint effects through a similar mechanism, metabolite changes for each pesticide actually indicated distinct effects. Further, earthworms exposed to a 0.5 toxic unit equitoxic mixture demonstrated metabolic effects intermediate between those for each pesticide, indicating a non-interactive, independent joint effect. For higher effect level mixtures (1 and 1.5 toxic units), metabolite changes associated with thiacloprid exposure began to dominate. The metabolomic effects of the two dissimilarly acting chemicals were distinct, confirming separate modes of action and both proved more toxic than anticipated from previous studies. In the mixtures, phenotypic effects were in accordance with IA estimates, while metabolite changes were dominated by Ni effects, even though chlorpyrifos contributed most to reproductive toxicity. This could be attributed to the greater systematic effect of Ni when compared to the more specifically acting chlorpyrifos.
McCombie G, Medina-Gomez G, Lelliott CJ, et al., 2012, Metabolomic and lipidomic analysis of the heart of peroxisome proliferator-activated receptor-γ coactivator 1-β knock out mice on a high fat diet, Metabolites, Vol: 2, Pages: 366-381
The peroxisome proliferator-activated receptor-γ coactivators (PGC-1) are transcriptional coactivators with an important role in mitochondrial biogenesis and regulation of genes involved in the electron transport chain and oxidative phosphorylation in oxidative tissues including cardiac tissue. These coactivators are thought to play a key role in the development of obesity, type 2 diabetes and the metabolic syndrome. In this study we have used a combined metabolomic and lipidomic analysis of cardiac tissue from the PGC-1β null mouse to examine the effects of a high fat diet on this organ. Multivariate statistics readily separated tissue from PGC-1β null mice from their wild type controls either in gender specific models or in combined datasets. This was associated with an increase in creatine and a decrease in taurine in the null mouse, and an increase in myristic acid and a reduction in long chain polyunsaturated fatty acids for both genders. The most profound changes were detected by liquid chromatography mass spectrometry analysis of intact lipids with the tissue from the null mouse having a profound increase in a number of triglycerides. The metabolomic and lipodomic changes indicate PGC-1β has a profound influence on cardiac metabolism. © 2012 by the authors; licensee MDPI, Basel, Switzerland.
Pan X, Wilson M, McConville C, et al., 2012, The lipid composition of isolated cytoplasmic lipid droplets from a human cancer cell line, BE(2)M17., Mol Biosyst, Vol: 8, Pages: 1694-1700
(1)H nuclear magnetic resonance spectroscopy (NMR) resonances from lipids in tumours are associated with tumour grade and treatment response. The origin of these NMR signals is mainly considered to be cytoplasmic lipid droplets (LDs). Techniques exist for isolating LDs but little is known about their composition and its relationship to NMR signals. In this work, density-gradient ultracentrifugation was performed on homogenised human cancer cells to isolate LDs. (1)H NMR was performed on whole cells, isolated LDs and their extracts. Heteronuclear single quantum coherence spectroscopy (HSQC) and liquid chromatography mass spectroscopy (LC-MS) were performed on lipid extracts of LDs. Staining and microscopy were used to characterize isolated LDs. An excellent agreement in chemical shift and relative signal intensity was observed between lipid resonances in cells and isolated LD spectra supporting that NMR-visible lipids originate primarily from LDs. Isolated LDs showed high concentrations of unsaturated lipids, a oleic-to-linoleic acid ratio greater than two and a cholesteryl ester (ChE)-to-cholesterol (Ch) ratio close to unity. These ratios were several-fold greater than respective ratios in whole cells, demonstrating isolation is important to characterize LD composition. LDs contain a specific group of lipid species that are likely to contribute to the (1)H NMR spectrum of cells.
Ament Z, Masoodi M, Griffin JL, 2012, Applications of metabolomics for understanding the action of peroxisome proliferator-activated receptors (PPARs) in diabetes, obesity and cancer, Genome Medicine, Vol: 4
The peroxisome proliferator-activated receptors (PPARs) are a set of three nuclear hormone receptors that together play a key role in regulating metabolism, particularly the switch between the fed and fasted state and the metabolic pathways involving fatty-acid oxidation and lipid metabolism. In addition, they have a number of important developmental and regulatory roles outside metabolism. The PPARs are also potent targets for treating type II diabetes, dyslipidemia and obesity, although a number of individual agonists have also been linked to unwanted side effects, and there is a complex relationship between the PPARs and the development of cancer. This review examines the part that metabolomics, including lipidomics, has played in elucidating the roles PPARs have in regulating systemic metabolism, as well as their role in aspects of drug-induced cancer and xenobiotic metabolism. These studies have defined the role PPARδ plays in regulating fatty-acid oxidation in adipose tissue and the interaction between aging and PPARα in the liver. The potential translational benefits of these approaches include widening the role of PPAR agonists and improved monitoring of drug efficacy. © 2012 BioMed Central Ltd.
Denkert C, Bucher E, Hilvo M, et al., 2012, Metabolomics of human breast cancer: New approaches for tumor typing and biomarker discovery, Genome Medicine, Vol: 4
Breast cancer is the most common cancer in women worldwide, and the development of new technologies for better understanding of the molecular changes involved in breast cancer progression is essential. Metabolic changes precede overt phenotypic changes, because cellular regulation ultimately affects the use of small-molecule substrates for cell division, growth or environmental changes such as hypoxia. Differences in metabolism between normal cells and cancer cells have been identified. Because small alterations in enzyme concentrations or activities can cause large changes in overall metabolite levels, the metabolome can be regarded as the amplified output of a biological system. The metabolome coverage in human breast cancer tissues can be maximized by combining different technologies for metabolic profiling. Researchers are investigating alterations in the steady state concentrations of metabolites that reflect amplified changes in genetic control of metabolism. Metabolomic results can be used to classify breast cancer on the basis of tumor biology, to identify new prognostic and predictive markers and to discover new targets for future therapeutic interventions. Here, we examine recent results, including those from the European FP7 project METAcancer consortium, that show that integrated metabolomic analyses can provide information on the stage, subtype and grade of breast tumors and give mechanistic insights. We predict an intensified use of metabolomic screens in clinical and preclinical studies focusing on the onset and progression of tumor development. © 2012 BioMed Central Ltd.
Mercer JR, Yu E, Figg N, et al., 2012, The mitochondria-targeted antioxidant MitoQ decreases features of the metabolic syndrome in ATM+/-/ApoE-/- mice., Free Radic Biol Med, Vol: 52, Pages: 841-849
A number of recent studies suggest that mitochondrial oxidative damage may be associated with atherosclerosis and the metabolic syndrome. However, much of the evidence linking mitochondrial oxidative damage and excess reactive oxygen species (ROS) with these pathologies is circumstantial. Consequently the importance of mitochondrial ROS in the etiology of these disorders is unclear. Furthermore, the potential of decreasing mitochondrial ROS as a therapy for these indications is not known. We assessed the impact of decreasing mitochondrial oxidative damage and ROS with the mitochondria-targeted antioxidant MitoQ in models of atherosclerosis and the metabolic syndrome (fat-fed ApoE(-/-) mice and ATM(+/-)/ApoE(-/-) mice, which are also haploinsufficient for the protein kinase, ataxia telangiectasia mutated (ATM). MitoQ administered orally for 14weeks prevented the increased adiposity, hypercholesterolemia, and hypertriglyceridemia associated with the metabolic syndrome. MitoQ also corrected hyperglycemia and hepatic steatosis, induced changes in multiple metabolically relevant lipid species, and decreased DNA oxidative damage (8-oxo-G) in multiple organs. Although MitoQ did not affect overall atherosclerotic plaque area in fat-fed ATM(+/+)/ApoE(-/-) and ATM(+/-)/ApoE(-/-) mice, MitoQ reduced the macrophage content and cell proliferation within plaques and 8-oxo-G. MitoQ also significantly reduced mtDNA oxidative damage in the liver. Our data suggest that MitoQ inhibits the development of multiple features of the metabolic syndrome in these mice by affecting redox signaling pathways that depend on mitochondrial ROS such as hydrogen peroxide. These findings strengthen the growing view that elevated mitochondrial ROS contributes to the etiology of the metabolic syndrome and suggest a potential therapeutic role for mitochondria-targeted antioxidants.
Brockmöller SF, Bucher E, Müller BM, et al., 2012, Integration of metabolomics and expression of glycerol-3-phosphate acyltransferase (GPAM) in breast cancer-link to patient survival, hormone receptor status, and metabolic profiling., J Proteome Res, Vol: 11, Pages: 850-860
Changes in lipid metabolism are an important but not well-characterized hallmark of cancer. On the basis of our recent findings of lipidomic changes in breast cancer, we investigated glycerol-3-phosphate acyltransferase (GPAM), a key enzyme in the lipid biosynthesis of triacylglycerols and phospholipids. GPAM protein expression was evaluated and linked to metabolomic and lipidomic profiles in a cohort of human breast carcinomas. In addition, GPAM mRNA expression was analyzed using the GeneSapiens in silico transcriptiomics database. High cytoplasmic GPAM expression was associated with hormone receptor negative status (p = 0.013). On the protein (p = 0.048) and mRNA (p = 0.001) levels, increased GPAM expression was associated with a better overall survival. Metabolomic analysis by GC-MS showed that sn-glycerol-3-phosphate, the substrate of GPAM, was elevated in breast cancer compared to normal breast tissue. LC-MS based lipidomic analysis identified significantly higher levels of phospholipids, especially phosphatidylcholines in GPAM protein positive tumors. In conclusion, our results suggest that GPAM is expressed in human breast cancer with associated changes in the cellular metabolism, in particular an increased synthesis of phospholipids, the major structural component of cellular membranes.
Jones OAH, Swain SC, Svendsen C, et al., 2012, Potential new method of mixture effects testing using metabolomics and Caenorhabditis elegans., J Proteome Res, Vol: 11, Pages: 1446-1453
The development of superior tools for molecular and computational biology in recent years has provided an opportunity for the creation of faster toxicological screens that are relevant for, but do not rely on, mammalian systems. In this study, NMR spectroscopy and GC-MS based metabolomics have been used in conjunction with multivariate statistics to examine the metabolic changes in the nematode Caenorhabditis elegans following exposure to different concentrations of the heavy metal nickel, the pesticide chlorpyrifos, and their mixture. Novel metabolic profiles were associated with both exposure and dose level. The biochemical responses were more closely matched when exposure was at the same effect level, even for different chemicals, than when exposure was for different levels of the same chemical (e.g., low versus high dose). Responses to the mixture reflected the contribution of the chemicals to the overall exposure. In common with the metabolic responses of several other species exposed to the same chemicals, we observed changes in branch chain amino acids and tricarboxylic acid cycle intermediates. These results form the basis for a rapid and economically viable toxicity test that defines the molecular effects of pollution/toxicant exposure in a manner that is relevant to higher vertebrates.
Sansone S-A, Rocca-Serra P, Field D, et al., 2012, Toward interoperable bioscience data., Nat Genet, Vol: 44, Pages: 121-126
To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.
Castro C, Sar F, Shaw WR, et al., 2012, A metabolomic strategy defines the regulation of lipid content and global metabolism by Δ9 desaturases in Caenorhabditis elegans, BMC Genomics, Vol: 13, ISSN: 1471-2164
BACKGROUND: Caenorhabditis elegans provides a genetically tractable model organism to investigate the network of genes involved in fat metabolism and how regulation is perturbed to produce the complex phenotype of obesity. C. elegans possess the full range of desaturases, including the Δ9 desaturases expressed by fat-5, fat-6 and fat-7. They regulate the biosynthesis of monounsaturated fatty acids, used for the synthesis of lipids including phospholipids, triglycerides and cholesteryl esters. RESULTS: Liquid chromatography mass spectrometry (LC-MS), gas chromatography mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy were used to define the metabolome of all the possible knock-outs for the Δ9 desaturases, including for the first time intact lipids. Despite the genes having similar enzymatic roles, excellent discrimination was achievable for all single and viable double mutants highlighting the distinctive roles of fat-6 and fat-7, both expressing steroyl-CoA desaturases. The metabolomic changes extend to aqueous metabolites demonstrating the influence Δ9 desaturases have on regulating global metabolism and highlighting how comprehensive metabolomics is more discriminatory than classically used dyes for fat staining. CONCLUSIONS: The propagation of metabolic changes across the network of metabolism demonstrates that modification of the Δ9 desaturases places C.elegans into a catabolic state compared with wildtype controls.
Atzori L, Griffin JL, Noto A, et al., 2012, Review metabolomics: a new approach to drug delivery in perinatology., Curr Med Chem, Vol: 19, Pages: 4654-4661
The purpose of this review is to describe the state of the art of the pharmacological applications in perinatal medicine and highlight how a new emerging discipline, metabolomics, may have a significant impact on understanding complex biological processes associated with the drugs actions. Currently, there is great demand for new information regarding the use of drugs, especially during the perinatal period in order to minimize the occurrence of adverse drug reactions and to maximize the desired therapeutic effect. Metabolomics is a functional genomic tool concerned with the high-throughput identification, quantification and characterization of small molecule metabolites. This new technique has been shown to have a great impact on classifying phenotypes, investigation of physiological status, diagnosing disease, measuring the response to treatment, discovering biomarkers, and identifying perturbed pathways due to disease or treatment. Metabolic profiles appear to be a key factor in predicting the outcome of a pathological condition and the individual's response to a pharmacological treatment. This new systems biology tool may have important potential implication for pharmacological science, in particular drug discovery, development, and prediction of the drug's effects on the body by explaining the mechanisms by which drug response causes adverse effects.
Dong JY, Deng LL, Cheng KK, et al., 2011, Investigation of <sup>1</sup>H NMR profile of vegetarian human urine using ANOVA-based multi-factor analysis, Gaodeng Xuexiao Huaxue Xuebao/Chemical Journal of Chinese Universities, Vol: 32, Pages: 2769-2776, ISSN: 0251-0790
In this study, a technique that combined both analysis of variance (ANOVA) and partial least squares-discriminant analysis (PLS-DA) was used to compare the urine 1H NMR spectra of healthy people from a vegetarian and omnivorous population. In ANOVA/PLS-DA, the variation in data was first decomposed into different variance components that each contains a single source of variation. Each of the resulting variance components was then analyzed using PLS-DA. The experimental results showed that ANOVA/PLS-DA is efficient in disentangling the effect of diet and gender on the metabolic profile, and the method could be used to extract biologically relevant information for result interpretation.
Dong J, Cheng KK, Xu J, et al., 2011, Group aggregating normalization method for the preprocessing of NMR-based metabolomic data, Chemometrics and Intelligent Laboratory Systems, Vol: 108, Pages: 123-132, ISSN: 0169-7439
Data normalization plays a crucial role in metabolomics to take into account the inevitable variation in sample concentration and the efficiency of sample preparation procedure. The conventional methods such as constant sum normalization (CSN) and probabilistic quotient normalization (PQN) are widely used, but both methods have their own shortcomings. In the current study, a new data normalization method called group aggregating normalization (GAN) is proposed, by which the samples were normalized so that they aggregate close to their group centers in a principal component analysis (PCA) subspace. This is in contrast with CSN and PQN which rely on a constant reference for all samples. The evaluation of GAN method using both simulated and experimental metabolomic data demonstrated that GAN produces more robust model in the subsequent multivariate data analysis, more superior than both CSN and PQN methods. The current study also demonstrated that some of the differential metabolites identified using the CSN or PQN method could be false positives due to improper data normalization. © 2011 Elsevier B.V.
Spann N, Aldridge DC, Griffin JL, et al., 2011, Size-dependent effects of low level cadmium and zinc exposure on the metabolome of the Asian clam, Corbicula fluminea., Aquat Toxicol, Vol: 105, Pages: 589-599
The toxic effects of low level metal contamination in sediments are currently poorly understood. We exposed different sized Asian clams, Corbicula fluminea, to sediment spiked with environmentally relevant concentrations of either zinc, cadmium or a zinc-cadmium mixture for one week. This freshwater bivalve is well suited for sediment toxicity tests as it lives partly buried in the sediment and utilises sediment particles as a food resource. After one week, the whole tissue composition of low molecular weight metabolites was analysed by nuclear magnetic resonance spectroscopy (NMR) and gas chromatography-mass spectrometry (GC-MS). The condition index (ratio of tissue dry weight to volume inside the shell valves) was also measured. Small and large clams were clearly differentiated by their metabolic composition and the two size classes showed opposite responses to the mixture spiked sediment. No effects of zinc alone on the metabolome were found and cadmium only influenced the smaller size class. The main perturbations were seen in amino acid and energy metabolism, with small clams using amino acids as an energy resource and larger clams primarily drawing on their larger storage reserves of carbohydrates. Our study demonstrates that metabolomics is a useful technique to test for low level toxicity which does not manifest in mortality or condition index changes. The differing effects between the two size classes stress that it is important to consider age/size when conducting metabolomic and ecotoxicology assessments, since testing for the effects on only one size class makes it more difficult to extrapolate laboratory results to the natural environment.
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