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Metabolites, Volume 6, Issue 1 (March 2016)

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Open AccessReview Evaluation of Cancer Metabolomics Using ex vivo High Resolution Magic Angle Spinning (HRMAS) Magnetic Resonance Spectroscopy (MRS)
Metabolites 2016, 6(1), 11; https://doi.org/10.3390/metabo6010011
Received: 25 January 2016 / Revised: 15 March 2016 / Accepted: 17 March 2016 / Published: 22 March 2016
Cited by 8 | Viewed by 1711 | PDF Full-text (3043 KB) | HTML Full-text | XML Full-text
Abstract
According to World Health Organization (WHO) estimates, cancer is responsible for more deaths than all coronary heart disease or stroke worldwide, serving as a major public health threat around the world. High resolution magic angle spinning (HRMAS) magnetic resonance spectroscopy (MRS) has demonstrated
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According to World Health Organization (WHO) estimates, cancer is responsible for more deaths than all coronary heart disease or stroke worldwide, serving as a major public health threat around the world. High resolution magic angle spinning (HRMAS) magnetic resonance spectroscopy (MRS) has demonstrated its usefulness in the identification of cancer metabolic markers with the potential to improve diagnosis and prognosis for the oncology clinic, due partially to its ability to preserve tissue architecture for subsequent histological and molecular pathology analysis. Capable of the quantification of individual metabolites, ratios of metabolites, and entire metabolomic profiles, HRMAS MRS is one of the major techniques now used in cancer metabolomic research. This article reviews and discusses literature reports of HRMAS MRS studies of cancer metabolomics published between 2010 and 2015 according to anatomical origins, including brain, breast, prostate, lung, gastrointestinal, and neuroendocrine cancers. These studies focused on improving diagnosis and understanding patient prognostication, monitoring treatment effects, as well as correlating with the use of in vivo MRS in cancer clinics. Full article
(This article belongs to the Special Issue Cancer Metabolomics 2016)
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Open AccessReview Cancer Metabolomics and the Human Metabolome Database
Metabolites 2016, 6(1), 10; https://doi.org/10.3390/metabo6010010
Received: 1 December 2015 / Revised: 23 February 2016 / Accepted: 25 February 2016 / Published: 2 March 2016
Cited by 23 | Viewed by 3958 | PDF Full-text (3181 KB) | HTML Full-text | XML Full-text
Abstract
The application of metabolomics towards cancer research has led to a renewed appreciation of metabolism in cancer development and progression. It has also led to the discovery of metabolite cancer biomarkers and the identification of a number of novel cancer causing metabolites. The
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The application of metabolomics towards cancer research has led to a renewed appreciation of metabolism in cancer development and progression. It has also led to the discovery of metabolite cancer biomarkers and the identification of a number of novel cancer causing metabolites. The rapid growth of metabolomics in cancer research is also leading to challenges. In particular, with so many cancer-associate metabolites being identified, it is often difficult to keep track of which compounds are associated with which cancers. It is also challenging to track down information on the specific pathways that particular metabolites, drugs or drug metabolites may be affecting. Even more frustrating are the difficulties associated with identifying metabolites from NMR or MS spectra. Fortunately, a number of metabolomics databases are emerging that are designed to address these challenges. One such database is the Human Metabolome Database (HMDB). The HMDB is currently the world’s largest and most comprehensive, organism-specific metabolomics database. It contains more than 40,000 metabolite entries, thousands of metabolite concentrations, >700 metabolic and disease-associated pathways, as well as information on dozens of cancer biomarkers. This review is intended to provide a brief summary of the HMDB and to offer some guidance on how it can be used in metabolomic studies of cancer. Full article
(This article belongs to the Special Issue Cancer Metabolomics 2016)
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Open AccessArticle Metabolomic Profiling of Submaximal Exercise at a Standardised Relative Intensity in Healthy Adults
Metabolites 2016, 6(1), 9; https://doi.org/10.3390/metabo6010009
Received: 22 December 2015 / Revised: 18 February 2016 / Accepted: 22 February 2016 / Published: 26 February 2016
Cited by 7 | Viewed by 2081 | PDF Full-text (2288 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Ten physically active subjects underwent two cycling exercise trials. In the first, aerobic capacity (VO2max) was determined and the second was a 45 min submaximal exercise test. Urine samples were collected separately the day before (day 1) , the day of
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Ten physically active subjects underwent two cycling exercise trials. In the first, aerobic capacity (VO2max) was determined and the second was a 45 min submaximal exercise test. Urine samples were collected separately the day before (day 1) , the day of (day 2), and the day after (day 3) the submaximal exercise test (12 samples per subject). Metabolomic profiling of the samples was carried out using hydrophilic interaction chromatography (HILIC) coupled to an Orbitrap Exactive mass spectrometer. Data were extracted, database searched and then subjected to principle components (PCA) and orthogonal partial least squares (OPLSDA) modelling. The best results were obtained from pre-treating the data by normalising the metabolites to their mean output on days 1 and 2 of the trial. This allowed PCA to separate the day 2 first void samples (D2S1) from the day 2 post-exercise samples (D2S3) PCA also separated the equivalent samples obtained on day 1 (D1S1 and D1S3). OPLSDA modelling separated both the D2S1 and D2S3 samples and D1S1 and D1S3 samples. The metabolites affected by the exercise samples included a range of purine metabolites and several acyl carnitines. Some metabolites were subject to diurnal variation these included bile acids and several amino acids, the variation of these metabolites was similar on day 1 and day 2 despite the exercise intervention on day 2. Using OPLS modelling it proved possible to identify a single abundant urinary metabolite provisionally identified as oxo-aminohexanoic acid (OHA) as being strongly correlated with VO2max when the levels in the D2S3 samples were considered. Full article
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Open AccessCommunication The Time Is Right to Focus on Model Organism Metabolomes
Metabolites 2016, 6(1), 8; https://doi.org/10.3390/metabo6010008
Received: 18 December 2015 / Revised: 30 January 2016 / Accepted: 2 February 2016 / Published: 15 February 2016
Cited by 14 | Viewed by 3346 | PDF Full-text (181 KB) | HTML Full-text | XML Full-text
Abstract
Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms
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Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research. Full article
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Open AccessArticle Visualization of Microfloral Metabolism for Marine Waste Recycling
Metabolites 2016, 6(1), 7; https://doi.org/10.3390/metabo6010007
Received: 30 September 2015 / Revised: 16 December 2015 / Accepted: 21 January 2016 / Published: 27 January 2016
Cited by 5 | Viewed by 2073 | PDF Full-text (1909 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Marine biomass including fishery products are precious protein resources for human foods and are an alternative to livestock animals in order to reduce the virtual water problem. However, a large amount of marine waste can be generated from fishery products and it is
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Marine biomass including fishery products are precious protein resources for human foods and are an alternative to livestock animals in order to reduce the virtual water problem. However, a large amount of marine waste can be generated from fishery products and it is not currently recycled. We evaluated the metabolism of digested marine waste using integrated analytical methods, under anaerobic conditions and the fertilization of abandoned agricultural soils. Dynamics of fish waste digestion revealed that samples of meat and bony parts had similar dynamics under anaerobic conditions in spite of large chemical variations in input marine wastes. Abandoned agricultural soils fertilized with fish waste accumulated some amino acids derived from fish waste, and accumulation of l-arginine and l-glutamine were higher in plant seedlings. Therefore, we have proposed an analytical method to visualize metabolic dynamics for recycling of fishery waste processes. Full article
(This article belongs to the Special Issue Marine Metabolomics)
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Open AccessEditorial Acknowledgement to Reviewers of Metabolites in 2015
Metabolites 2016, 6(1), 5; https://doi.org/10.3390/metabo6010005
Received: 22 January 2016 / Accepted: 22 January 2016 / Published: 22 January 2016
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Abstract
The editors of Metabolites would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...] Full article
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Open AccessReview Lysophosphatidylinositol Signalling and Metabolic Diseases
Metabolites 2016, 6(1), 6; https://doi.org/10.3390/metabo6010006
Received: 11 December 2015 / Revised: 7 January 2016 / Accepted: 11 January 2016 / Published: 15 January 2016
Cited by 5 | Viewed by 2084 | PDF Full-text (580 KB) | HTML Full-text | XML Full-text
Abstract
Metabolism is a chemical process used by cells to transform food-derived nutrients, such as proteins, carbohydrates and fats, into chemical and thermal energy. Whenever an alteration of this process occurs, the chemical balance within the cells is impaired and this can affect their
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Metabolism is a chemical process used by cells to transform food-derived nutrients, such as proteins, carbohydrates and fats, into chemical and thermal energy. Whenever an alteration of this process occurs, the chemical balance within the cells is impaired and this can affect their growth and response to the environment, leading to the development of a metabolic disease. Metabolic syndrome, a cluster of several metabolic risk factors such as abdominal obesity, insulin resistance, high cholesterol and high blood pressure, and atherogenic dyslipidaemia, is increasingly common in modern society. Metabolic syndrome, as well as other diseases, such as diabetes, obesity, hyperlipidaemia and hypertension, are associated with abnormal lipid metabolism. Cellular lipids are the major component of cell membranes; they represent also a valuable source of energy and therefore play a crucial role for both cellular and physiological energy homeostasis. In this review, we will focus on the physiological and pathophysiological roles of the lysophospholipid mediator lysophosphatidylinositol (LPI) and its receptor G-protein coupled receptor 55 (GPR55) in metabolic diseases. LPI is a bioactive lipid generated by phospholipase A (PLA) family of lipases which is believed to play an important role in several diseases. Indeed LPI can affect various functions such as cell growth, differentiation and motility in a number of cell-types. Recently published data suggest that LPI plays an important role in different physiological and pathological contexts, including a role in metabolism and glucose homeostasis. Full article
(This article belongs to the Special Issue Metabolomic Studies in Metabolic Diseases)
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Open AccessArticle Development of an Optimized Protocol for NMR Metabolomics Studies of Human Colon Cancer Cell Lines and First Insight from Testing of the Protocol Using DNA G-Quadruplex Ligands as Novel Anti-Cancer Drugs
Metabolites 2016, 6(1), 4; https://doi.org/10.3390/metabo6010004
Received: 25 November 2015 / Revised: 7 January 2016 / Accepted: 11 January 2016 / Published: 15 January 2016
Cited by 1 | Viewed by 3261 | PDF Full-text (1930 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The study of cell lines by nuclear magnetic resonance (NMR) spectroscopy metabolomics represents a powerful tool to understand how the local metabolism and biochemical pathways are influenced by external or internal stimuli. In particular, the use of adherent mammalian cells is emerging in
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The study of cell lines by nuclear magnetic resonance (NMR) spectroscopy metabolomics represents a powerful tool to understand how the local metabolism and biochemical pathways are influenced by external or internal stimuli. In particular, the use of adherent mammalian cells is emerging in the metabolomics field in order to understand the molecular mechanism of disease progression or, for example, the cellular response to drug treatments. Hereto metabolomics investigations for this kind of cells have generally been limited to mass spectrometry studies. This study proposes an optimized protocol for the analysis of the endo-metabolome of human colon cancer cells (HCT116) by NMR. The protocol includes experimental conditions such as washing, quenching and extraction. In order to test the proposed protocol, it was applied to an exploratory study of cancer cells with and without treatment by anti-cancer drugs, such as DNA G-quadruplex binders and Adriamycin (a traditional anti-cancer drug). The exploratory NMR metabolomics analysis resulted in NMR assignment of all endo-metabolites that could be detected and provided preliminary insights about the biological behavior of the drugs tested. Full article
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Open AccessCommunication Application of Pre-Column Labeling Liquid Chromatography for Canine Plasma-Free Amino Acid Analysis
Metabolites 2016, 6(1), 3; https://doi.org/10.3390/metabo6010003
Received: 2 December 2015 / Revised: 19 December 2015 / Accepted: 4 January 2016 / Published: 12 January 2016
Cited by 2 | Viewed by 1779 | PDF Full-text (1472 KB) | HTML Full-text | XML Full-text
Abstract
Plasma-free amino acid (PFAA) levels are a useful metric for diagnosing cancer and providing a prognosis. However, the use of analysis of PFAA levels has been limited in the veterinary medicine field. We addressed the application of liquid chromatography (LC) using a pre-column
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Plasma-free amino acid (PFAA) levels are a useful metric for diagnosing cancer and providing a prognosis. However, the use of analysis of PFAA levels has been limited in the veterinary medicine field. We addressed the application of liquid chromatography (LC) using a pre-column labeling technique for analysis of canine PFAA levels. This method significantly shortened the analysis time relative to conventional methods. No diurnal fluctuations were detected at 9:00 AM in most PFAA levels, and food intake increased the levels of some PFAAs, including valine, leucine, tyrosine, phenylalanine, and proline. These results indicate that LC with pre-column labeling is useful for measuring canine PFAA levels, for which time of day and interval after food intake must be taken into consideration. Full article
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Open AccessArticle Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting
Metabolites 2016, 6(1), 2; https://doi.org/10.3390/metabo6010002
Received: 23 September 2015 / Revised: 23 December 2015 / Accepted: 30 December 2015 / Published: 8 January 2016
Cited by 7 | Viewed by 3580 | PDF Full-text (2704 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from
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The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from both Scottish and Antarctic sediments to assess the influence of isolation location on secondary metabolite production. Due to the selective isolation method used, all 85 isolates belonged to the phyla Firmicutes and Actinobacteria, with the majority of isolates belonging to the genera Bacillus and Streptomyces. Based on morphology, thirty-eight isolates were chosen for chemical investigation. Molecular networking based on chemical profiles (HR-MS/MS) of fermentation extracts was used to compare complex metabolite extracts. The results revealed 40% and 42% of parent ions were produced by Antarctic and Scottish isolated bacteria, respectively, and only 8% of networked metabolites were shared between these locations, implying a high degree of biogeographic influence upon secondary metabolite production. The resulting molecular network contained over 3500 parent ions with a mass range of m/z 149–2558 illustrating the wealth of metabolites produced. Furthermore, seven fermentation extracts showed bioactivity against epithelial colon adenocarcinoma cells, demonstrating the potential for the discovery of novel bioactive compounds from these understudied locations. Full article
(This article belongs to the Special Issue Marine Metabolomics)
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Open AccessArticle Metabolic Flux Distribution during Defatting of Steatotic Human Hepatoma (HepG2) Cells
Metabolites 2016, 6(1), 1; https://doi.org/10.3390/metabo6010001
Received: 2 December 2015 / Revised: 23 December 2015 / Accepted: 29 December 2015 / Published: 4 January 2016
Cited by 9 | Viewed by 1887 | PDF Full-text (1139 KB) | HTML Full-text | XML Full-text
Abstract
Methods that rapidly decrease fat in steatotic hepatocytes may be helpful to recover severely fatty livers for transplantation. Defatting kinetics are highly dependent upon the extracellular medium composition; however, the pathways involved are poorly understood. Steatosis was induced in human hepatoma cells (HepG2)
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Methods that rapidly decrease fat in steatotic hepatocytes may be helpful to recover severely fatty livers for transplantation. Defatting kinetics are highly dependent upon the extracellular medium composition; however, the pathways involved are poorly understood. Steatosis was induced in human hepatoma cells (HepG2) by exposure to high levels of free fatty acids, followed by defatting using plain medium containing no fatty acids, or medium supplemented with a cocktail of defatting agents previously described before. We measured the levels of 28 extracellular metabolites and intracellular triglyceride, and fed the data into a steady-state mass balance model to estimate strictly intracellular fluxes. We found that during defatting, triglyceride content decreased, while beta-oxidation, the tricarboxylic acid cycle, and the urea cycle increased. These fluxes were augmented by defatting agents, and even more so by hyperoxic conditions. In all defatting conditions, the rate of extracellular glucose uptake/release was very small compared to the internal supply from glycogenolysis, and glycolysis remained highly active. Thus, in steatotic HepG2 cells, glycolysis and fatty acid oxidation may co-exist. Together, these pathways generate reducing equivalents that are supplied to mitochondrial oxidative phosphorylation. Full article
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