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Frontiñan-Rubio J, Llanos-González E, González VJ, Vázquez E, Durán-Prado M. Subchronic Graphene Exposure Reshapes Skin Cell Metabolism. J Proteome Res 2022; 21:1675-1685. [PMID: 35611947 PMCID: PMC9251767 DOI: 10.1021/acs.jproteome.2c00064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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In recent years,
the toxicity of graphene-related materials (GRMs)
has been evaluated in diverse models to guarantee their safety. In
most applications, sublethal doses of GRMs contact human barriers
such as skin in a subchronic way. Herein, the subchronic effect (30
day exposure) of three GRMs (GO 1, GO 2, and FLG) with different oxidation
degrees and sizes was studied. The effects of these materials on human
skin cells, HaCaTs, were assayed through high-throughput metabolic-based
readout and other cell-based assays. A differential effect was found
between the different GRMs. GO 2 induced a metabolic remodeling in
epithelial cells, increasing the level of tricarboxylic acid components,
mirrored by increased cell proliferation and changes in cell phenotype.
The oxidation degree, size, and method of manufacture of GRMs dictated
harmful effects on cell metabolism and behavior generated by nontoxic
exposures. Therefore, a “safe by design” procedure is
necessary when working with these nanomaterials.
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Affiliation(s)
| | | | - Viviana Jehová González
- Instituto Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain.,Faculty of Chemical Science and Technology, Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Ester Vázquez
- Instituto Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain.,Faculty of Chemical Science and Technology, Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Mario Durán-Prado
- Faculty of Medicine, Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
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2
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Jeon Y, Lim Y, Yeom J, Kim EK. Comparative metabolic profiling of posterior parietal cortex, amygdala, and hippocampus in conditioned fear memory. Mol Brain 2021; 14:153. [PMID: 34615530 PMCID: PMC8493686 DOI: 10.1186/s13041-021-00863-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/23/2021] [Indexed: 02/04/2023] Open
Abstract
Fear conditioning and retrieval are suitable models to investigate the biological basis of various mental disorders. Hippocampus and amygdala neurons consolidate conditioned stimulus (CS)-dependent fear memory. Posterior parietal cortex is considered important for the CS-dependent conditioning and retrieval of fear memory. Metabolomic screening among functionally related brain areas provides molecular signatures and biomarkers to improve the treatment of psychopathologies. Herein, we analyzed and compared changes of metabolites in the hippocampus, amygdala, and posterior parietal cortex under the fear retrieval condition. Metabolite profiles of posterior parietal cortex and amygdala were similarly changed after fear memory retrieval. While the retrieval of fear memory perturbed various metabolic pathways, most metabolic pathways that overlapped among the three brain regions had high ranks in the enrichment analysis of posterior parietal cortex. In posterior parietal cortex, the most perturbed pathways were pantothenate and CoA biosynthesis, purine metabolism, glutathione metabolism, and NAD+ dependent signaling. Metabolites of posterior parietal cortex including 4'-phosphopantetheine, xanthine, glutathione, ADP-ribose, ADP-ribose 2'-phosphate, and cyclic ADP-ribose were significantly regulated in these metabolic pathways. These results point to the importance of metabolites of posterior parietal cortex in conditioned fear memory retrieval and may provide potential biomarker candidates for traumatic memory-related mental disorders.
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Affiliation(s)
- Yoonjeong Jeon
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
- Neurometabolomics Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
| | - Yun Lim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
| | - Jiwoo Yeom
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
- Neurometabolomics Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
| | - Eun-Kyoung Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea.
- Neurometabolomics Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea.
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3
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Muthubharathi BC, Gowripriya T, Balamurugan K. Metabolomics: small molecules that matter more. Mol Omics 2021; 17:210-229. [PMID: 33598670 DOI: 10.1039/d0mo00176g] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics, an analytical study with high-throughput profiling, helps to understand interactions within a biological system. Small molecules, called metabolites or metabolomes with the size of <1500 Da, depict the status of a biological system in a different manner. Currently, we are in need to globally analyze the metabolome and the pathways involved in healthy, as well as diseased conditions, for possible therapeutic applications. Metabolome analysis has revealed high-abundance molecules during different conditions such as diet, environmental stress, microbiota, and disease and treatment states. As a result, it is hard to understand the complete and stable network of metabolites of a biological system. This review helps readers know the available techniques to study metabolomics in addition to other major omics such as genomics, transcriptomics, and proteomics. This review also discusses the metabolomics in various pathological conditions and the importance of metabolomics in therapeutic applications.
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Ortega MA, Saez MA, Sainz F, Fraile-Martínez O, García-Gallego S, Pekarek L, Bravo C, Coca S, Mon MÁ, Buján J, García-Honduvilla N, Asúnsolo Á. Lipidomic profiling of chorionic villi in the placentas of women with chronic venous disease. Int J Med Sci 2020; 17:2790-2798. [PMID: 33162806 PMCID: PMC7645335 DOI: 10.7150/ijms.49236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/09/2020] [Indexed: 12/26/2022] Open
Abstract
Background: Chronic venous disease (CVD) is a prevalent lower limb venous pathology that especially affects women, who also show an increased risk of this disease during pregnancy. Studies have shown significant structural changes in the placentas of women with CVD and several markers of tissue damage have been also described. Patients and Methods: To try to understand the different placental pathologies, research efforts have focused on examining metabolomic profiles as indicators of the repercussions of these vascular disorders. This study examines changes produced in the metabolomic profiles of chorionic villi in the placentas of women with CVD. In a study population of 12 pregnant women, 6 with and 6 without CVD, we compared through mass spectroscopy coupled to ultra-high performance liquid chromatography (UHPLC-MS), 240 metabolites in chorionic villus samples. Results: This study is the first to detect in the placental villi of pregnant women with CVD, modifications in lysophosphatidylcholines and amino acids along with diminished levels of other lipids such as triglycerides, sphingomyelins, and non-esterified omega 9 fatty acids, suggesting a role of these abnormalities in the pathogenesis of CVD. Conclusions: Our findings are a starting point for future studies designed to examine the impacts of CVD on maternal and fetal well-being.
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Affiliation(s)
- Miguel A Ortega
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- Ramón y Cajal Institute of Healthcare Research (IRYCIS), Madrid, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Miguel A Saez
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
- Pathological Anatomy Service, Central University Hospital of Defence-UAH Madrid, Spain
| | - Felipe Sainz
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- Angiology and Vascular Surgery Service, Central University Hospital of Defence-UAH Madrid, Spain
| | - Oscar Fraile-Martínez
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Sandra García-Gallego
- Ramón y Cajal Institute of Healthcare Research (IRYCIS), Madrid, Spain
- Department of Organic and Inorganic Chemistry, and Research Institute in Chemistry “Andrés M. del Río” (IQAR), University of Alcalá, 28805 Madrid, Spain
| | - Leonel Pekarek
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Coral Bravo
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- Service of Gynecology and Obstetrics, Section of Fetal Maternal Medicine, Central University Hospital of Defence-UAH Madrid, Spain
| | - Santiago Coca
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- Ramón y Cajal Institute of Healthcare Research (IRYCIS), Madrid, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Melchor Álvarez- Mon
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- Ramón y Cajal Institute of Healthcare Research (IRYCIS), Madrid, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
- Internal Medicine and Oncology Service Service, University Hospital Príncipe de Asturias, CIBEREHD, Alcalá de Henares, Madrid, Spain
| | - Julia Buján
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- Ramón y Cajal Institute of Healthcare Research (IRYCIS), Madrid, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Natalio García-Honduvilla
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- Ramón y Cajal Institute of Healthcare Research (IRYCIS), Madrid, Spain
- University Center for the Defense of Madrid (CUD-ACD), 28047 Madrid, Spain
| | - Ángel Asúnsolo
- Ramón y Cajal Institute of Healthcare Research (IRYCIS), Madrid, Spain
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Madrid, Spain
- Department of Epidemiology & Biostatistics, Graduate School of Public Health and Health Policy, University of New York, New York, NY, United States
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5
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Abstract
Metabolomics, a comprehensive analysis of metabolites in biological specimens (e.g., cells, body fluids, tissues, exhaled air, plants), offers promising tools in health, nutrition, biotechnology, and food sciences. Here we describe methods of LC-MS/MS-based analyses for cell metabolomics. Using methods employed in this section, over 1000 endogenous and exogenous metabolites can be detected, annotated, and quantified relatively by nontargeted analysis approach, whereas targeted metabolomics analysis enables us to quantify 188 endogenous metabolites.
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Affiliation(s)
- Anna Artati
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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6
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Lo Re O, Douet J, Buschbeck M, Fusilli C, Pazienza V, Panebianco C, Castracani CC, Mazza T, Li Volti G, Vinciguerra M. Histone variant macroH2A1 rewires carbohydrate and lipid metabolism of hepatocellular carcinoma cells towards cancer stem cells. Epigenetics 2018; 13:829-845. [PMID: 30165787 DOI: 10.1080/15592294.2018.1514239] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinomas (HCCs) contain a sub-population of cancer stem cells (CSCs) that are responsible for tumor relapse, metastasis, and chemoresistance. We recently showed that loss of macroH2A1, a variant of the histone H2A and an epigenetic regulator of stem-cell function, in HCC leads to CSC-like features such as resistance to chemotherapeutic agents and growth of large and relatively undifferentiated tumors in xenograft models. These HCC cells silenced for macroH2A1 also exhibited stem-like metabolic changes consistent with enhanced glycolysis. However, there is no consensus as to the metabolic characteristics of CSCs that render them adaptable to microenvironmental changes by conveniently shifting energy production source or by acquiring intermediate metabolic phenotypes. Here, we assessed long-term proliferation, energy metabolism, and central carbon metabolism in human hepatoma HepG2 cells depleted in macroH2A1. MacroH2A1-depleted HepG2 cells were insensitive to serum exhaustion and showed two distinct, but interdependent changes in glucose and lipid metabolism in CSCs: (1) massive upregulation of acetyl-coA that is transformed into enhanced lipid content and (2) increased activation of the pentose phosphate pathway, diverting glycolytic intermediates to provide precursors for nucleotide synthesis. Integration of metabolomic analyses with RNA-Seq data revealed a critical role for the Liver X Receptor pathway, whose inhibition resulted in attenuated CSCs-like features. These findings shed light on the metabolic phenotype of epigenetically modified CSC-like hepatic cells, and highlight a potential approach for selective therapeutic targeting.
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Affiliation(s)
- Oriana Lo Re
- a Center for Translational Medicine, International Clinical Research Center , St'Anne University Hospital , Brno , Czech Republic.,b Department of Biology, Faculty of Medicine , Masaryk University , Brno , Czech Republic
| | - Julien Douet
- d Josep Carreras Leukemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol , Universitat Autònoma de Barcelona , Badalona , Spain.,e Programme of Predictive and Personalized Medicine of Cancer , Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona , Spain
| | - Marcus Buschbeck
- d Josep Carreras Leukemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol , Universitat Autònoma de Barcelona , Badalona , Spain.,e Programme of Predictive and Personalized Medicine of Cancer , Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Badalona , Spain
| | - Caterina Fusilli
- c IRCCS Casa Sollievo della Sofferenza , UO of Bioinformatics , San Giovanni Rotondo , Italy
| | - Valerio Pazienza
- f Gastroenterology unit , IRCCS Casa Sollievo della Sofferenza , San Giovanni Rotondo , Italy
| | - Concetta Panebianco
- f Gastroenterology unit , IRCCS Casa Sollievo della Sofferenza , San Giovanni Rotondo , Italy
| | | | - Tommaso Mazza
- c IRCCS Casa Sollievo della Sofferenza , UO of Bioinformatics , San Giovanni Rotondo , Italy
| | - Giovanni Li Volti
- g Department of Biomedical and Biotechnological Sciences , University of Catania , Catania , Italy
| | - Manlio Vinciguerra
- a Center for Translational Medicine, International Clinical Research Center , St'Anne University Hospital , Brno , Czech Republic.,h Institute for Liver and Digestive Health, Division of Medicine , University College London (UCL) , London , UK
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7
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Dulka BN, Bourdon AK, Clinard CT, Muvvala MBK, Campagna SR, Cooper MA. Metabolomics reveals distinct neurochemical profiles associated with stress resilience. Neurobiol Stress 2017; 7:103-112. [PMID: 28828396 PMCID: PMC5552108 DOI: 10.1016/j.ynstr.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/11/2017] [Accepted: 08/05/2017] [Indexed: 11/27/2022] Open
Abstract
Acute social defeat represents a naturalistic form of conditioned fear and is an excellent model in which to investigate the biological basis of stress resilience. While there is growing interest in identifying biomarkers of stress resilience, until recently, it has not been feasible to associate levels of large numbers of neurochemicals and metabolites to stress-related phenotypes. The objective of the present study was to use an untargeted metabolomics approach to identify known and unknown neurochemicals in select brain regions that distinguish susceptible and resistant individuals in two rodent models of acute social defeat. In the first experiment, male mice were first phenotyped as resistant or susceptible. Then, mice were subjected to acute social defeat, and tissues were immediately collected from the ventromedial prefrontal cortex (vmPFC), basolateral/central amygdala (BLA/CeA), nucleus accumbens (NAc), and dorsal hippocampus (dHPC). Ultra-high performance liquid chromatography coupled with high resolution mass spectrometry (UPLC-HRMS) was used for the detection of water-soluble neurochemicals. In the second experiment, male Syrian hamsters were paired in daily agonistic encounters for 2 weeks, during which they formed stable dominant-subordinate relationships. Then, 24 h after the last dominance encounter, animals were exposed to acute social defeat stress. Immediately after social defeat, tissue was collected from the vmPFC, BLA/CeA, NAc, and dHPC for analysis using UPLC-HRMS. Although no single biomarker characterized stress-related phenotypes in both species, commonalities were found. For instance, in both model systems, animals resistant to social defeat stress also show increased concentration of molecules to protect against oxidative stress in the NAc and vmPFC. Additionally, in both mice and hamsters, unidentified spectral features were preliminarily annotated as potential targets for future experiments. Overall, these findings suggest that a metabolomics approach can identify functional groups of neurochemicals that may serve as novel targets for the diagnosis, treatment, or prevention of stress-related mental illness.
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Affiliation(s)
- Brooke N Dulka
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States
| | - Catherine T Clinard
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Mohan B K Muvvala
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States.,Biological Small Molecule Mass Spectrometry Core, University of Tennessee, Knoxville, TN 37996, United States
| | - Matthew A Cooper
- Department of Psychology, University of Tennessee, Knoxville, TN 37996, United States
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8
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Ternon E, Perino E, Manconi R, Pronzato R, Thomas OP. How Environmental Factors Affect the Production of Guanidine Alkaloids by the Mediterranean Sponge Crambe crambe. Mar Drugs 2017. [PMID: 28621725 PMCID: PMC5484131 DOI: 10.3390/md15060181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Most marine sponges are known to produce a large array of low molecular-weight metabolites which have applications in the pharmaceutical industry. The production of so-called specialized metabolites may be closely related to environmental factors. In this context, assessing the contribution of factors like temperature, nutrients or light to the metabolomes of sponges provides relevant insights into their chemical ecology as well as the supply issue of natural sponge products. The sponge Crambe crambe was chosen as a model due to its high content of specialized metabolites belonging to polycyclic guanidine alkaloids (PGA). First results were obtained with field data of both wild and farmed specimens collected in two seasons and geographic areas of the North-Western Mediterranean. Then, further insights into factors responsible for changes in the metabolism were gained with sponges cultivated under controlled conditions in an aquarium. Comparative metabolomics showed a clear influence of the seasons and to a lesser extent of the geography while no effect of depth or farming was observed. Interestingly, sponge farming did not limit the production of PGA, while ex situ experiments did not show significant effects of several abiotic factors on the specialized metabolome at a one-month time scale. Some hypotheses were finally proposed to explain the very limited variations of PGA in C. crambe placed under different environmental conditions.
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Affiliation(s)
- Eva Ternon
- Université Côte d'Azur, CNRS, OCA, IRD, Géoazur, 250 rue Albert Einstein, 06560 Valbonne, France.
| | - Erica Perino
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Corso Europa 26, 16132 Genoa, Italy.
| | - Renata Manconi
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Via Muroni 25, 07100 Sassari, Italy.
| | - Roberto Pronzato
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Corso Europa 26, 16132 Genoa, Italy.
| | - Olivier P Thomas
- Université Côte d'Azur, CNRS, OCA, IRD, Géoazur, 250 rue Albert Einstein, 06560 Valbonne, France.
- Marine Biodiscovery, School of Chemistry, National University of Ireland Galway, University Road, H91 TK33 Galway, Ireland.
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9
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Jeanneret F, Tonoli D, Rossier MF, Saugy M, Boccard J, Rudaz S. Evaluation of steroidomics by liquid chromatography hyphenated to mass spectrometry as a powerful analytical strategy for measuring human steroid perturbations. J Chromatogr A 2015. [PMID: 26195035 DOI: 10.1016/j.chroma.2015.07.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review presents the evolution of steroid analytical techniques, including gas chromatography coupled to mass spectrometry (GC-MS), immunoassay (IA) and targeted liquid chromatography coupled to mass spectrometry (LC-MS), and it evaluates the potential of extended steroid profiles by a metabolomics-based approach, namely steroidomics. Steroids regulate essential biological functions including growth and reproduction, and perturbations of the steroid homeostasis can generate serious physiological issues; therefore, specific and sensitive methods have been developed to measure steroid concentrations. GC-MS measuring several steroids simultaneously was considered the first historical standard method for analysis. Steroids were then quantified by immunoassay, allowing a higher throughput; however, major drawbacks included the measurement of a single compound instead of a panel and cross-reactivity reactions. Targeted LC-MS methods with selected reaction monitoring (SRM) were then introduced for quantifying a small steroid subset without the problems of cross-reactivity. The next step was the integration of metabolomic approaches in the context of steroid analyses. As metabolomics tends to identify and quantify all the metabolites (i.e., the metabolome) in a specific system, appropriate strategies were proposed for discovering new biomarkers. Steroidomics, defined as the untargeted analysis of the steroid content in a sample, was implemented in several fields, including doping analysis, clinical studies, in vivo or in vitro toxicology assays, and more. This review discusses the current analytical methods for assessing steroid changes and compares them to steroidomics. Steroids, their pathways, their implications in diseases and the biological matrices in which they are analysed will first be described. Then, the different analytical strategies will be presented with a focus on their ability to obtain relevant information on the steroid pattern. The future technical requirements for improving steroid analysis will also be presented.
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Affiliation(s)
- Fabienne Jeanneret
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1211 Geneva 4, Switzerland; Human Protein Sciences Department, University of Geneva, 1211 Geneva 4, Switzerland; Swiss Centre for Applied Human Toxicology, Geneva, Switzerland
| | - David Tonoli
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1211 Geneva 4, Switzerland; Human Protein Sciences Department, University of Geneva, 1211 Geneva 4, Switzerland; Swiss Centre for Applied Human Toxicology, Geneva, Switzerland
| | - Michel F Rossier
- Swiss Centre for Applied Human Toxicology, Geneva, Switzerland; Institut Central (ICHV), Hôpital du Valais, Sion, Switzerland
| | - Martial Saugy
- Swiss Laboratory for Doping Analyses, University Center of Legal Medicine, Epalinges, Switzerland
| | - Julien Boccard
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1211 Geneva 4, Switzerland
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1211 Geneva 4, Switzerland; Swiss Centre for Applied Human Toxicology, Geneva, Switzerland.
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10
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Misra BB, Assmann SM, Chen S. Plant single-cell and single-cell-type metabolomics. TRENDS IN PLANT SCIENCE 2014; 19:637-46. [PMID: 24946988 DOI: 10.1016/j.tplants.2014.05.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 05/19/2023]
Abstract
In conjunction with genomics, transcriptomics, and proteomics, plant metabolomics is providing large data sets that are paving the way towards a comprehensive and holistic understanding of plant growth, development, defense, and productivity. However, dilution effects from organ- and tissue-based sampling of metabolomes have limited our understanding of the intricate regulation of metabolic pathways and networks at the cellular level. Recent advances in metabolomics methodologies, along with the post-genomic expansion of bioinformatics knowledge and functional genomics tools, have allowed the gathering of enriched information on individual cells and single cell types. Here we review progress, current status, opportunities, and challenges presented by single cell-based metabolomics research in plants.
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Affiliation(s)
- Biswapriya B Misra
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Sarah M Assmann
- Department of Biology, Penn State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| | - Sixue Chen
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
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11
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Dazard JEJ, Sandlers Y, Doerner SK, Berger NA, Brunengraber H. Metabolomics of ApcMin/+ mice genetically susceptible to intestinal cancer. BMC SYSTEMS BIOLOGY 2014; 8:72. [PMID: 24954394 PMCID: PMC4099115 DOI: 10.1186/1752-0509-8-72] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/10/2014] [Indexed: 12/20/2022]
Abstract
Background To determine how diets high in saturated fat could increase polyp formation in the mouse model of intestinal neoplasia, ApcMin/+, we conducted large-scale metabolome analysis and association study of colon and small intestine polyp formation from plasma and liver samples of ApcMin/+ vs. wild-type littermates, kept on low vs. high-fat diet. Label-free mass spectrometry was used to quantify untargeted plasma and acyl-CoA liver compounds, respectively. Differences in contrasts of interest were analyzed statistically by unsupervised and supervised modeling approaches, namely Principal Component Analysis and Linear Model of analysis of variance. Correlation between plasma metabolite concentrations and polyp numbers was analyzed with a zero-inflated Generalized Linear Model. Results Plasma metabolome in parallel to promotion of tumor development comprises a clearly distinct profile in ApcMin/+ mice vs. wild type littermates, which is further altered by high-fat diet. Further, functional metabolomics pathway and network analyses in ApcMin/+ mice on high-fat diet revealed associations between polyp formation and plasma metabolic compounds including those involved in amino-acids metabolism as well as nicotinamide and hippuric acid metabolic pathways. Finally, we also show changes in liver acyl-CoA profiles, which may result from a combination of ApcMin/+-mediated tumor progression and high fat diet. The biological significance of these findings is discussed in the context of intestinal cancer progression. Conclusions These studies show that high-throughput metabolomics combined with appropriate statistical modeling and large scale functional approaches can be used to monitor and infer changes and interactions in the metabolome and genome of the host under controlled experimental conditions. Further these studies demonstrate the impact of diet on metabolic pathways and its relation to intestinal cancer progression. Based on our results, metabolic signatures and metabolic pathways of polyposis and intestinal carcinoma have been identified, which may serve as useful targets for the development of therapeutic interventions.
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Affiliation(s)
- Jean-Eudes J Dazard
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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12
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Vanyushkina AA, Kamashev DE, Altukhov IA, Govorun VM. Identification of intracellular Spiroplasma melliferum metabolites by the HPLC-MS method. BIOCHEMISTRY (MOSCOW) 2013; 77:864-77. [PMID: 22860908 DOI: 10.1134/s000629791208007x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In contrast to the abundance of systems-oriented approaches describing changes on the transcriptome or proteome level, relatively few studies have employed the metabolome. The goal of the presented research was to identify as many intracellular metabolites as possible in a Spiroplasma melliferum extract by flow injection time-of-flight mass spectrometry. The Mollicutes class bacterium S. melliferum is a member of a unique category of bacteria that have in common the absence of a cell wall, a reduced genome, and simplified metabolic pathways. Metabolite identification was confirmed by fragmentation of previously detected ions by target mass spectrometry. The selected liquid chromatography approach, hydrophilic interaction chromatography with amino and silica columns, effectively separates highly polar cellular metabolites prior to their detection on a high accuracy mass spectrometer in positive and negative acquisition mode for each column. Here we present reliable measurement of 76 metabolites, including components of sugar, amino acid, and nucleotide metabolism. We have identified about a third of the possible intracellular S. melliferum metabolites predicted by genome annotation.
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Affiliation(s)
- A A Vanyushkina
- Russian Research Center Kurchatov Institute, pl. Akademika Kurchatova 1, 123182 Moscow, Russia.
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13
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Harrison SJ, Herrgård MJ. The Uses and Future Prospects of Metabolomics and Targeted Metabolite Profiling in Cell Factory Development. Ind Biotechnol (New Rochelle N Y) 2013. [DOI: 10.1089/ind.2013.0008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Scott J. Harrison
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Markus J. Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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14
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Kotłowska A. Application of Steroid Hormone Metabolomics in Search of Biomarkers in Clinical Research. Drug Dev Res 2012. [DOI: 10.1002/ddr.21028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alicja Kotłowska
- Department of Food Sciences; Faculty of Pharmacy, Medical University of Gdańsk; Al. Gen. J. Hallera 107; 80-416; Gdańsk; Poland
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15
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Zhang X, Choi FFK, Zhou Y, Leung FP, Tan S, Lin S, Xu H, Jia W, Sung JJY, Cai Z, Bian Z. Metabolite profiling of plasma and urine from rats with TNBS-induced acute colitis using UPLC-ESI-QTOF-MS-based metabonomics--a pilot study. FEBS J 2012; 279:2322-38. [PMID: 22520047 DOI: 10.1111/j.1742-4658.2012.08612.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The incidence of inflammatory bowel disease, a relapsing intestinal condition whose precise etiology is still unclear, has continually increased over recent years. Metabolic profiling is an effective method with high sample throughput that can detect and identify potential biomarkers, and thus may be useful in investigating the pathogenesis of inflammatory bowel disease. In this study, using a metabonomics approach, a pilot study based on ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOF-MS) was performed to characterize the metabolic profile of plasma and urine samples of rats with experimental colitis induced by 2,4,6-trinitrobenzene sulfonic acid. Acquired metabolic profile data were processed by multivariate data analysis for differentiation and screening of potential biomarkers. Five metabolites were identified in urine: two tryptophan metabolites [4-(2-aminophenyl)-2,4-dioxobutanoic acid and 4,6-cihydroxyquinoline], two gut microbial metabolites (phenyl-acetylglycine and p-cresol glucuronide), and the bile acid 12α-hydroxy-3-oxocholadienic acid. Seven metabolites were identified in plasma: three members of the bile acid/alcohol group (cholic acid, 12α-hydroxy-3-oxocholadienic acid and cholestane-3,7,12,24,25-pentol) and four lysophosphatidylcholines [LysoPC(20:4), LysoPC(16:0), LysoPC(18:1) and LysoPC(18:0)]. These metabolites are associated with damage of the intestinal barrier function, microbiota homeostasis, immune modulation and the inflammatory response, and play important roles in the pathogenesis of inflammatory bowel disease. Our results positively support application of the metabonomic approach in study of the pathophysiological mechanism of inflammatory bowel disease.
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Affiliation(s)
- Xiaojun Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, China
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16
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Halama A, Möller G, Adamski J. Metabolic signatures in apoptotic human cancer cell lines. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:325-35. [PMID: 21332381 DOI: 10.1089/omi.2010.0121] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cancer cells have several specific metabolic features, which have been explored for targeted therapies. Agents that promote apoptosis in tumors are currently considered as a powerful tool for cancer therapeutics. The present study aimed to design a fast, reliable and robust system for metabolite measurements in cells lines to observe impact of apoptosis on the metabolome. For that purpose the NBS (newborn screen) mass spectrometry-based metabolomics assay was adapted for cell culture approach. In HEK 293 and in cancer cell lines HepG2, PC3, and MCF7 we searched for metabolic biomarkers of apoptosis differing from that of necrosis. Already nontreated cell lines revealed distinct concentrations of metabolites. Several metabolites indicative for apoptotic processes in cell culture including aspartate, glutamate, methionine, alanine, glycine, propionyl carnitine (C3-carnitine), and malonyl carnitine (C3DC-carnitine) were observed. In some cell lines metabolite changes were visible as early as 4 h after apoptosis induction and preceeding the detection by caspase 3/7 assay. We demonstrated for the first time that the metabolomic signatures might be used in the tests of efficacy of agents causing apoptosis in cell culture. These signatures could be obtained in fast high-throughput screening.
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Affiliation(s)
- Anna Halama
- Helmholtz Zentrum München, Institute of Experimental Genetics, Genome Analysis Center, Neuherberg, Germany
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17
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Barr J, Vázquez-Chantada M, Alonso C, Pérez-Cormenzana M, Mayo R, Galán A, Caballería J, Martín-Duce A, Tran A, Wagner C, Luka Z, Lu SC, Castro A, Le Marchand-Brustel Y, Martínez-Chantar ML, Veyrie N, Clément K, Tordjman J, Gual P, Mato JM. Liquid chromatography-mass spectrometry-based parallel metabolic profiling of human and mouse model serum reveals putative biomarkers associated with the progression of nonalcoholic fatty liver disease. J Proteome Res 2011; 9:4501-12. [PMID: 20684516 DOI: 10.1021/pr1002593] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common form of chronic liver disease in most western countries. Current NAFLD diagnosis methods (e.g., liver biopsy analysis or imaging techniques) are poorly suited as tests for such a prevalent condition, from both a clinical and financial point of view. The present work aims to demonstrate the potential utility of serum metabolic profiling in defining phenotypic biomarkers that could be useful in NAFLD management. A parallel animal model/human NAFLD exploratory metabolomics approach was employed, using ultra performance liquid chromatography-mass spectrometry (UPLC-MS) to analyze 42 serum samples collected from nondiabetic, morbidly obese, biopsy-proven NAFLD patients, and 17 animals belonging to the glycine N-methyltransferase knockout (GNMT-KO) NAFLD mouse model. Multivariate statistical analysis of the data revealed a series of common biomarkers that were significantly altered in the NAFLD (GNMT-KO) subjects in comparison to their normal liver counterparts (WT). Many of the compounds observed could be associated with biochemical perturbations associated with liver dysfunction (e.g., reduced Creatine) and inflammation (e.g., eicosanoid signaling). This differential metabolic phenotyping approach may have a future role as a supplement for clinical decision making in NAFLD and in the adaption to more individualized treatment protocols.
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Affiliation(s)
- Jonathan Barr
- OWL Genomics, Bizkaia Technology Park, 48160-Derio, Bizkaia, Spain
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18
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Griffiths W, Koal T, Wang Y, Kohl M, Enot D, Deigner HP. Targeted Metabolomics for Biomarker Discovery. Angew Chem Int Ed Engl 2010; 49:5426-45. [DOI: 10.1002/anie.200905579] [Citation(s) in RCA: 259] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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19
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Griffiths W, Koal T, Wang Y, Kohl M, Enot D, Deigner HP. “Targeted Metabolomics” in der Biomarkerforschung. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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20
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Liu Y, Wen J, Wang Y, Li Y, Xu W. Postulating Modes of Action of Compounds with Antimicrobial Activities through Metabolomics Analysis. Chromatographia 2009. [DOI: 10.1365/s10337-009-1447-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Abstract
The metabolism of steroids at position 17 is catalysed by a growing number of 17beta-hydroxysteroid dehydrogenases (17beta-HSDs). Several human diseases like breast or prostate cancer, endometriosis,metabolic syndrome and mental diseases were associated with dysfunctions of 17beta-HSDs, which consequently became drug targets. This review will focus on identities of 17beta-HSDs and recent advances in analyses of their physiological roles in steroid and lipid metabolism. It will also address the potential of metabolomics in drug development.
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Affiliation(s)
- Cornelia Prehn
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Neuherberg, Germany
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22
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Muller PA, Klomp LW. Novel perspectives in mammalian copper metabolism through the use of genome-wide approaches. Am J Clin Nutr 2008; 88:821S-5S. [PMID: 18779301 DOI: 10.1093/ajcn/88.3.821s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The transition metal copper plays an essential role in many biological processes but is highly toxic in excess. Recent studies have characterized a highly conserved set of proteins that mediate cellular copper import, distribution, sequestration, utilization, and export. Nevertheless, the pathogenesis of copper overload and copper deficiency disorders is not well understood, and we are only beginning to comprehend the results of mild copper overload or deficiency in relation to nutritional uptake and common diseases at the population level. Technological advances open the possibility to dissect the complete genome for genetic variants predisposing to copper overload or depletion and for variations in gene expression generated by either reduced or excessive copper intake. We discuss the potential of integrated genome-wide applications to advance our knowledge of copper homeostasis and to develop molecular biomarker profiles as indicators of copper status.
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Affiliation(s)
- Patricia Aj Muller
- Laboratory for Metabolic and Endocrine Diseases, UMC Utrecht, Utrecht, Netherlands
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23
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Griffiths WJ, Hornshaw M, Woffendin G, Baker SF, Lockhart A, Heidelberger S, Gustafsson M, Sjövall J, Wang Y. Discovering oxysterols in plasma: a window on the metabolome. J Proteome Res 2008; 7:3602-12. [PMID: 18605750 DOI: 10.1021/pr8001639] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While the proteome defines the expressed gene products, the metabolome results from reactions controlled by such gene products. Plasma represents an accessible "window" to the metabolome both in regard of availability and content. The wide range of the plasma metabolome, in terms of molecular diversity and abundance, makes its comprehensive analysis challenging. Here we demonstrate an analytical method designed to target one region of the metabolome, that is, oxysterols. Since the discovery of their biological activity as ligands to nuclear receptors there has been a reawakening of interest in oxysterols and their analysis. In addition, the oxysterols, 24S- and 27-hydroxycholesterol, are currently under investigation as potential biomarkers associated with neurodegenerative disorders such as Alzheimer's disease and multiple sclerosis; widespread analysis of these lipids in clinical studies will require the development of robust, sensitive and rapid analytical techniques. In this communication we present results of an investigation of the oxysterols content of human plasma using a newly developed high-performance liquid chromatography-mass spectrometry (HPLC-MS) method incorporating charge-tagging and high-resolution MS. The method has allowed the identification in plasma of monohydroxylated cholesterol molecules, 7alpha-, 24S-, and 27-hydroxycholesterol; the cholestenetriol 7alpha,27-dihydroxycholesterol; and 3beta-hydroxycholest-5-en-27-oic acid and its metabolite 3beta,7alpha-dihydroxycholest-5-en-27-oic acid. The methodology described is also applicable for the analysis of other sterols in plasma, that is, cholesterol, 7-dehydrocholesterol, and desmosterol, as well as cholesterol 5,6- seco-sterols and steroid hormones. Although involving derivatization, sample preparation is straightforward and chromatographic analysis rapid (17 min), while the MS method offers high sensitivity (ng/mL of sterol in plasma, or pg on-column) and specificity. The methodology is suitable for targeted metabolomic analysis of sterols, oxysterols, and steroid hormones opening a "window" to view this region of the metabolome.
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Affiliation(s)
- William J Griffiths
- Institute of Mass Spectrometry, School of Medicine, Grove Building, Swansea University, Singleton Park, Swansea, UK.
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24
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Analytical strategies for LC-MS-based targeted metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:236-42. [PMID: 18502704 DOI: 10.1016/j.jchromb.2008.04.031] [Citation(s) in RCA: 319] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 04/14/2008] [Accepted: 04/22/2008] [Indexed: 11/20/2022]
Abstract
Recent advances in mass spectrometry are enabling improved analysis of endogenous metabolites. Here we discuss several issues relevant to developing liquid chromatography-electrospray ionization-mass spectrometry methods for targeted metabolomics (i.e., quantitative analysis of dozens to hundreds of specific metabolites). Sample preparation and liquid chromatography approaches are discussed, with an eye towards the challenge of dealing with a diversity of metabolite classes in parallel. Evidence is presented that heated electrospray ionization (ESI) generally gives improved signal compared to the more traditional unheated ESI. Applicability to targeted metabolomics of triple quadrupole mass spectrometry operating in multiple reaction monitoring (MRM) mode and high mass resolution full scan mass spectrometry (e.g., time-of-flight, Orbitrap) are described. We suggest that both are viable solutions, with MRM preferred when targeting a more limited number of analytes, and full scan preferred for its potential ability to bridge targeted and untargeted metabolomics.
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25
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Shyur LF, Yang NS. Metabolomics for phytomedicine research and drug development. Curr Opin Chem Biol 2008; 12:66-71. [DOI: 10.1016/j.cbpa.2008.01.032] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Accepted: 01/21/2008] [Indexed: 12/14/2022]
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