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Drury NE, van Doorn C, Woolley RL, Amos-Hirst RJ, Bi R, Spencer CM, Morris KP, Montgomerie J, Stickley J, Crucean A, Gill A, Hill M, Weber RJ, Najdekr L, Jankevics A, Southam AD, Lloyd GR, Jaber O, Kassai I, Pelella G, Khan NE, Botha P, Barron DJ, Madhani M, Dunn WB, Ives NJ, Kirchhof P, Jones TJ. Bilateral remote ischemic conditioning in children: A two-center, double-blind, randomized controlled trial in young children undergoing cardiac surgery. JTCVS Open 2024; 18:193-208. [PMID: 38690427 PMCID: PMC11056492 DOI: 10.1016/j.xjon.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/30/2024] [Accepted: 02/20/2024] [Indexed: 05/02/2024]
Abstract
Objective The study objective was to determine whether adequately delivered bilateral remote ischemic preconditioning is cardioprotective in young children undergoing surgery for 2 common congenital heart defects with or without cyanosis. Methods We performed a prospective, double-blind, randomized controlled trial at 2 centers in the United Kingdom. Children aged 3 to 36 months undergoing tetralogy of Fallot repair or ventricular septal defect closure were randomized 1:1 to receive bilateral preconditioning or sham intervention. Participants were followed up until hospital discharge or 30 days. The primary outcome was area under the curve for high-sensitivity troponin-T in the first 24 hours after surgery, analyzed by intention-to-treat. Right atrial biopsies were obtained in selected participants. Results Between October 2016 and December 2020, 120 eligible children were randomized to receive bilateral preconditioning (n = 60) or sham intervention (n = 60). The primary outcome, area under the curve for high-sensitivity troponin-T, was higher in the preconditioning group (mean: 70.0 ± 50.9 μg/L/h, n = 56) than in controls (mean: 55.6 ± 30.1 μg/L/h, n = 58) (mean difference, 13.2 μg/L/h; 95% CI, 0.5-25.8; P = .04). Subgroup analyses did not show a differential treatment effect by oxygen saturations (pinteraction = .25), but there was evidence of a differential effect by underlying defect (pinteraction = .04). Secondary outcomes and myocardial metabolism, quantified in atrial biopsies, were not different between randomized groups. Conclusions Bilateral remote ischemic preconditioning does not attenuate myocardial injury in children undergoing surgical repair for congenital heart defects, and there was evidence of potential harm in unstented tetralogy of Fallot. The routine use of remote ischemic preconditioning cannot be recommended for myocardial protection during pediatric cardiac surgery.
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Affiliation(s)
- Nigel E. Drury
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Paediatric Cardiac Surgery, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - Carin van Doorn
- Department of Congenital Cardiac Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Rebecca L. Woolley
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
- Institute of Applied Health Research, University of Birmingham, Birmingham, United Kingdom
| | - Rebecca J. Amos-Hirst
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
- Institute of Applied Health Research, University of Birmingham, Birmingham, United Kingdom
| | - Rehana Bi
- Department of Paediatric Cardiac Surgery, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - Collette M. Spencer
- Department of Congenital Cardiac Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Kevin P. Morris
- Department of Paediatric Intensive Care, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - James Montgomerie
- Department of Paediatric Cardiac Anesthesia, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - John Stickley
- Department of Paediatric Cardiac Surgery, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - Adrian Crucean
- Department of Paediatric Cardiac Surgery, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - Alicia Gill
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
- Institute of Applied Health Research, University of Birmingham, Birmingham, United Kingdom
| | - Matt Hill
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
- Institute of Applied Health Research, University of Birmingham, Birmingham, United Kingdom
| | - Ralf J.M. Weber
- Phenome Centre Birmingham, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Lukas Najdekr
- Phenome Centre Birmingham, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Andris Jankevics
- Phenome Centre Birmingham, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D. Southam
- Phenome Centre Birmingham, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Gavin R. Lloyd
- Phenome Centre Birmingham, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Osama Jaber
- Department of Congenital Cardiac Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Imre Kassai
- Department of Congenital Cardiac Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Giuseppe Pelella
- Department of Congenital Cardiac Surgery, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Natasha E. Khan
- Department of Paediatric Cardiac Surgery, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - Phil Botha
- Department of Paediatric Cardiac Surgery, Birmingham Children's Hospital, Birmingham, United Kingdom
| | - David J. Barron
- Division of Cardiovascular Surgery, Hospital for Sick Children, Toronto, Canada
- Department of Surgery, University of Toronto, Toronto, Canada
| | - Melanie Madhani
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Warwick B. Dunn
- Phenome Centre Birmingham, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Natalie J. Ives
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
- Institute of Applied Health Research, University of Birmingham, Birmingham, United Kingdom
| | - Paulus Kirchhof
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Cardiology, University Heart and Vascular Centre, UKE Hamburg, Hamburg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Timothy J. Jones
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Paediatric Cardiac Surgery, Birmingham Children's Hospital, Birmingham, United Kingdom
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2
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Viant MR, Amstalden E, Athersuch T, Bouhifd M, Camuzeaux S, Crizer DM, Driemert P, Ebbels T, Ekman D, Flick B, Giri V, Gómez-Romero M, Haake V, Herold M, Kende A, Lai F, Leonards PEG, Lim PP, Lloyd GR, Mosley J, Namini C, Rice JR, Romano S, Sands C, Smith MJ, Sobanski T, Southam AD, Swindale L, van Ravenzwaay B, Walk T, Weber RJM, Zickgraf FM, Kamp H. Demonstrating the reliability of in vivo metabolomics based chemical grouping: towards best practice. Arch Toxicol 2024; 98:1111-1123. [PMID: 38368582 PMCID: PMC10944399 DOI: 10.1007/s00204-024-03680-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/19/2024]
Abstract
While grouping/read-across is widely used to fill data gaps, chemical registration dossiers are often rejected due to weak category justifications based on structural similarity only. Metabolomics provides a route to robust chemical categories via evidence of shared molecular effects across source and target substances. To gain international acceptance, this approach must demonstrate high reliability, and best-practice guidance is required. The MetAbolomics ring Trial for CHemical groupING (MATCHING), comprising six industrial, government and academic ring-trial partners, evaluated inter-laboratory reproducibility and worked towards best-practice. An independent team selected eight substances (WY-14643, 4-chloro-3-nitroaniline, 17α-methyl-testosterone, trenbolone, aniline, dichlorprop-p, 2-chloroaniline, fenofibrate); ring-trial partners were blinded to their identities and modes-of-action. Plasma samples were derived from 28-day rat tests (two doses per substance), aliquoted, and distributed to partners. Each partner applied their preferred liquid chromatography-mass spectrometry (LC-MS) metabolomics workflows to acquire, process, quality assess, statistically analyze and report their grouping results to the European Chemicals Agency, to ensure the blinding conditions of the ring trial. Five of six partners, whose metabolomics datasets passed quality control, correctly identified the grouping of eight test substances into three categories, for both male and female rats. Strikingly, this was achieved even though a range of metabolomics approaches were used. Through assessing intrastudy quality-control samples, the sixth partner observed high technical variation and was unable to group the substances. By comparing workflows, we conclude that some heterogeneity in metabolomics methods is not detrimental to consistent grouping, and that assessing data quality prior to grouping is essential. We recommend development of international guidance for quality-control acceptance criteria. This study demonstrates the reliability of metabolomics for chemical grouping and works towards best-practice.
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Affiliation(s)
- Mark R Viant
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - E Amstalden
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - T Athersuch
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - M Bouhifd
- European Chemicals Agency, Telakkakatu 6, FI-00121, Helsinki, Finland
| | - S Camuzeaux
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - D M Crizer
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - P Driemert
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - T Ebbels
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - D Ekman
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - B Flick
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
- NUVISAN ICB GmbH, Toxicology, 13353, Berlin, Germany
| | - V Giri
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
| | - M Gómez-Romero
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - V Haake
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - M Herold
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - A Kende
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - F Lai
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - P E G Leonards
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - P P Lim
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - G R Lloyd
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - J Mosley
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - C Namini
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - J R Rice
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - S Romano
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - C Sands
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - M J Smith
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - T Sobanski
- European Chemicals Agency, Telakkakatu 6, FI-00121, Helsinki, Finland
| | - A D Southam
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - L Swindale
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - B van Ravenzwaay
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
- Environmental Sciences Consulting, 67122, Altrip, Germany
| | - T Walk
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - R J M Weber
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - F M Zickgraf
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
| | - H Kamp
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
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3
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Alimajstorovic Z, Mitchell JL, Yiangou A, Hancox T, Southam AD, Grech O, Ottridge R, Winder CL, Tahrani AA, Tan TM, Mollan SP, Dunn WB, Sinclair AJ. Determining the role of novel metabolic pathways in driving intracranial pressure reduction after weight loss. Brain Commun 2023; 5:fcad272. [PMID: 37901040 PMCID: PMC10608960 DOI: 10.1093/braincomms/fcad272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/07/2023] [Accepted: 10/17/2023] [Indexed: 10/31/2023] Open
Abstract
Idiopathic intracranial hypertension, a disease classically occurring in women with obesity, is characterized by raised intracranial pressure. Weight loss leads to the reduction in intracranial pressure. Additionally, pharmacological glucagon-like peptide-1 agonism reduces cerebrospinal fluid secretion and intracranial pressure. The potential mechanisms by which weight loss reduces intracranial pressure are unknown and were the focus of this study. Meal stimulation tests (fasted plasma sample, then samples at 15, 30, 60, 90 and 120 min following a standardized meal) were conducted pre- and post-bariatric surgery [early (2 weeks) and late (12 months)] in patients with active idiopathic intracranial hypertension. Dynamic changes in gut neuropeptides (glucagon-like peptide-1, gastric inhibitory polypeptide and ghrelin) and metabolites (untargeted ultra-high performance liquid chromatography-mass spectrometry) were evaluated. We determined the relationship between gut neuropeptides, metabolites and intracranial pressure. Eighteen idiopathic intracranial hypertension patients were included [Roux-en-Y gastric bypass (RYGB) n = 7, gastric banding n = 6 or sleeve gastrectomy n = 5]. At 2 weeks post-bariatric surgery, despite similar weight loss, RYGB had a 2-fold (50%) greater reduction in intracranial pressure compared to sleeve. Increased meal-stimulated glucagon-like peptide-1 secretion was observed after RYGB (+600%) compared to sleeve (+319%). There was no change in gastric inhibitory polypeptide and ghrelin. Dynamic changes in meal-stimulated metabolites after bariatric surgery consistently identified changes in lipid metabolites, predominantly ceramides, glycerophospholipids and lysoglycerophospholipids, which correlated with intracranial pressure. A greater number of differential lipid metabolites were observed in the RYGB cohort at 2 weeks, and these also correlated with intracranial pressure. In idiopathic intracranial hypertension, we identified novel changes in lipid metabolites and meal-stimulated glucagon-like peptide-1 levels following bariatric surgery which were associated with changes in intracranial pressure. RYGB was most effective at reducing intracranial pressure despite analogous weight loss to gastric sleeve at 2 weeks post-surgery and was associated with more pronounced changes in these metabolite pathways. We suggest that these novel perturbations in lipid metabolism and glucagon-like peptide-1 secretion are mechanistically important in driving a reduction in intracranial pressure following weight loss in patients with idiopathic intracranial hypertension. Therapeutic targeting of these pathways, for example with glucagon-like peptide-1 agonist infusion, could represent a therapeutic strategy.
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Affiliation(s)
- Zerin Alimajstorovic
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - James L Mitchell
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Birmingham B15 2GW, UK
| | - Andreas Yiangou
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Birmingham B15 2GW, UK
| | - Thomas Hancox
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew D Southam
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Olivia Grech
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ryan Ottridge
- Birmingham Clinical Trials Unit, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Catherine L Winder
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK
| | - Abd A Tahrani
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham B15 2TT, UK
| | - Tricia M Tan
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2BX, UK
| | - Susan P Mollan
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Birmingham Neuro-Ophthalmology, University Hospitals Birmingham, Queen Elizabeth Hospital, Birmingham B15 2GW, UK
| | - Warwick B Dunn
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L3 5TR, UK
| | - Alexandra J Sinclair
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham B15 2TT, UK
- Birmingham Neuro-Ophthalmology, University Hospitals Birmingham, Queen Elizabeth Hospital, Birmingham B15 2GW, UK
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4
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Bowen TJ, Southam AD, Hall AR, Weber RJM, Lloyd GR, Macdonald R, Wilson A, Pointon A, Viant MR. Simultaneously discovering the fate and biochemical effects of pharmaceuticals through untargeted metabolomics. Nat Commun 2023; 14:4653. [PMID: 37537184 PMCID: PMC10400635 DOI: 10.1038/s41467-023-40333-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Untargeted metabolomics is an established approach in toxicology for characterising endogenous metabolic responses to xenobiotic exposure. Detecting the xenobiotic and its biotransformation products as part of the metabolomics analysis provides an opportunity to simultaneously gain deep insights into its fate and metabolism, and to associate the internal relative dose directly with endogenous metabolic responses. This integration of untargeted exposure and response measurements into a single assay has yet to be fully demonstrated. Here we assemble a workflow to discover and analyse pharmaceutical-related measurements from routine untargeted UHPLC-MS metabolomics datasets, derived from in vivo (rat plasma and cardiac tissue, and human plasma) and in vitro (human cardiomyocytes) studies that were principally designed to investigate endogenous metabolic responses to drug exposure. Our findings clearly demonstrate how untargeted metabolomics can discover extensive biotransformation maps, temporally-changing relative systemic exposure, and direct associations of endogenous biochemical responses to the internal dose.
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Affiliation(s)
- Tara J Bowen
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andrew R Hall
- Safety Sciences, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Gavin R Lloyd
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ruth Macdonald
- Animal Sciences and Technology, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Amanda Wilson
- Integrated Bioanalysis, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Amy Pointon
- Safety Sciences, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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5
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Allaway D, Alexander JE, Carvell-Miller LJ, Reynolds RM, Winder CL, Weber RJM, Lloyd GR, Southam AD, Dunn WB. Suitability of Dried Blood Spots for Accelerating Veterinary Biobank Collections and Identifying Metabolomics Biomarkers With Minimal Resources. Front Vet Sci 2022; 9:887163. [PMID: 35812865 PMCID: PMC9258959 DOI: 10.3389/fvets.2022.887163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Biomarker discovery using biobank samples collected from veterinary clinics would deliver insights into the diverse population of pets and accelerate diagnostic development. The acquisition, preparation, processing, and storage of biofluid samples in sufficient volumes and at a quality suitable for later analysis with most suitable discovery methods remain challenging. Metabolomics analysis is a valuable approach to detect health/disease phenotypes. Pre-processing changes during preparation of plasma/serum samples may induce variability that may be overcome using dried blood spots (DBSs). We report a proof of principle study by metabolite fingerprinting applying UHPLC-MS of plasma and DBSs acquired from healthy adult dogs and cats (age range 1–9 years), representing each of 4 dog breeds (Labrador retriever, Beagle, Petit Basset Griffon Vendeen, and Norfolk terrier) and the British domestic shorthair cat (n = 10 per group). Blood samples (20 and 40 μL) for DBSs were loaded onto filter paper, air-dried at room temperature (3 h), and sealed and stored (4°C for ~72 h) prior to storage at −80°C. Plasma from the same blood draw (250 μL) was prepared and stored at −80°C within 1 h of sampling. Metabolite fingerprinting of the DBSs and plasma produced similar numbers of metabolite features that had similar abilities to discriminate between biological classes and correctly assign blinded samples. These provide evidence that DBSs, sampled in a manner amenable to application in in-clinic/in-field processing, are a suitable sample for biomarker discovery using UHPLC-MS metabolomics. Further, given appropriate owner consent, the volumes tested (20–40 μL) make the acquisition of remnant blood from blood samples drawn for other reasons available for biobanking and other research activities. Together, this makes possible large-scale biobanking of veterinary samples, gaining sufficient material sooner and enabling quicker identification of biomarkers of interest.
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Affiliation(s)
- David Allaway
- WALTHAM Petcare Science Institute, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, United Kingdom
- *Correspondence: David Allaway
| | - Janet E. Alexander
- WALTHAM Petcare Science Institute, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, United Kingdom
| | - Laura J. Carvell-Miller
- WALTHAM Petcare Science Institute, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, United Kingdom
| | - Rhiannon M. Reynolds
- WALTHAM Petcare Science Institute, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, United Kingdom
| | - Catherine L. Winder
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ralf J. M. Weber
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
| | - Gavin R. Lloyd
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D. Southam
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
| | - Warwick B. Dunn
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, United Kingdom
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
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6
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Wilcock DJ, Badrock AP, Wong CW, Owen R, Guerin M, Southam AD, Johnston H, Telfer BA, Fullwood P, Watson J, Ferguson H, Ferguson J, Lloyd GR, Jankevics A, Dunn WB, Wellbrock C, Lorigan P, Ceol C, Francavilla C, Smith MP, Hurlstone AFL. Oxidative stress from DGAT1 oncoprotein inhibition in melanoma suppresses tumor growth when ROS defenses are also breached. Cell Rep 2022; 39:110995. [PMID: 35732120 PMCID: PMC9638004 DOI: 10.1016/j.celrep.2022.110995] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 03/30/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022] Open
Abstract
Dysregulated cellular metabolism is a cancer hallmark for which few druggable oncoprotein targets have been identified. Increased fatty acid (FA) acquisition allows cancer cells to meet their heightened membrane biogenesis, bioenergy, and signaling needs. Excess FAs are toxic to non-transformed cells but surprisingly not to cancer cells. Molecules underlying this cancer adaptation may provide alternative drug targets. Here, we demonstrate that diacylglycerol O-acyltransferase 1 (DGAT1), an enzyme integral to triacylglyceride synthesis and lipid droplet formation, is frequently up-regulated in melanoma, allowing melanoma cells to tolerate excess FA. DGAT1 over-expression alone transforms p53-mutant zebrafish melanocytes and co-operates with oncogenic BRAF or NRAS for more rapid melanoma formation. Antagonism of DGAT1 induces oxidative stress in melanoma cells, which adapt by up-regulating cellular reactive oxygen species defenses. We show that inhibiting both DGAT1 and superoxide dismutase 1 profoundly suppress tumor growth through eliciting intolerable oxidative stress.
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Affiliation(s)
- Daniel J Wilcock
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Andrew P Badrock
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Chun W Wong
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Rhys Owen
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Melissa Guerin
- Program in Molecular Medicine, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andrew D Southam
- School of Biosciences, Edgbaston, University of Birmingham, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Hannah Johnston
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Brian A Telfer
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Paul Fullwood
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Joanne Watson
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Harriet Ferguson
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Jennifer Ferguson
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Gavin R Lloyd
- School of Biosciences, Edgbaston, University of Birmingham, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andris Jankevics
- School of Biosciences, Edgbaston, University of Birmingham, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Warwick B Dunn
- School of Biosciences, Edgbaston, University of Birmingham, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Claudia Wellbrock
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Paul Lorigan
- Division of Cancer Studies, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK; Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Withington, Manchester M20 4BX, UK
| | - Craig Ceol
- Program in Molecular Medicine, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Michael P Smith
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK.
| | - Adam F L Hurlstone
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Dover Street, Manchester M13 9PT, UK; Lydia Becker Institute of Immunology, The University of Manchester, Dover Street, Manchester M13 9PT, UK.
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7
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Jiang Y, Southam AD, Trova S, Beke F, Alhazmi B, Francis T, Radotra A, di Maio A, Drayson MT, Bunce CM, Khanim FL. Valproic acid disables the Nrf2 anti-oxidant response in acute myeloid leukaemia cells enhancing reactive oxygen species-mediated killing. Br J Cancer 2022; 126:275-286. [PMID: 34686779 PMCID: PMC8770569 DOI: 10.1038/s41416-021-01570-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/27/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND We previously demonstrated the in vitro killing of AML cells by the combination of the lipid-lowering agent bezafibrate (BEZ) and the contraceptive hormone medroxyprogesterone acetate (MPA). A phase II trial demonstrated in vivo safety and efficacy of BEZ and MPA (BaP) in elderly, relapsed/refractory AML and high-risk myelodysplastic syndrome (MDS) patients. However, we observed dose-limiting toxicities in a second trial that attempted to improve outcomes via escalation of BaP doses. Thus we sought to identify a third repurposed drug that potentiates activity of low dose BaP (BaP 0.1 mM). METHODS AND RESULTS We demonstrate that addition of a commonly used anti-epileptic, valproic acid (VAL) to low dose BaP (BaP 0.1 mM)(VBaP) enhanced killing of AML cell lines/primary AML cells to levels similar to high dose BaP (BaP 0.5 mM). Similarly, addition of VAL to BaP 0.1 mM enhanced reactive oxygen species (ROS), lipid peroxidation and inhibition of de novo fatty acid synthesis. Overexpression of Nrf2 in K562 and KG1a completely inhibited ROS production and rescued cells from VAL/BaP 0.1 mM/VBaP killing. CONCLUSIONS Given the good safety data of low-dose BaP in elderly/relapsed/refractory AML patients, and that VAL alone is well-tolerated, we propose VBaP as a novel therapeutic combination for AML.
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Affiliation(s)
- Yao Jiang
- grid.6572.60000 0004 1936 7486School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Andrew D. Southam
- grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Birmingham, UK
| | - Sandro Trova
- grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Birmingham, UK
| | - Flavio Beke
- grid.5335.00000000121885934CRUK Cancer Institute, University of Cambridge, Cambridge, UK
| | - Bader Alhazmi
- grid.6572.60000 0004 1936 7486School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Thomas Francis
- grid.13097.3c0000 0001 2322 6764Centre for Human & Applied Physiological Sciences, School of Basic & Medical Biosciences, King’s College London, London, UK
| | - Anshul Radotra
- grid.412570.50000 0004 0400 5079University Hospitals Coventry and Warwickshire, Clifford Bridge Rd, Coventry, UK
| | - Alessandro di Maio
- grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Birmingham, UK
| | - Mark T. Drayson
- grid.6572.60000 0004 1936 7486Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Chris M. Bunce
- grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Birmingham, UK
| | - Farhat L. Khanim
- grid.6572.60000 0004 1936 7486School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
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8
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Corbin LJ, Hughes DA, Chetwynd AJ, Taylor AE, Southam AD, Jankevics A, Weber RJM, Groom A, Dunn WB, Timpson NJ. Correction to: Metabolic characterisation of disturbances in the APOC3/triglyceride‑rich lipoprotein pathway through sample‑based recall by genotype. Metabolomics 2021; 17:15. [PMID: 33484338 PMCID: PMC7919761 DOI: 10.1007/s11306-020-01765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Laura J Corbin
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Andrew J Chetwynd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Amy E Taylor
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, BS8 2BN, UK
| | - Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andris Jankevics
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alix Groom
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.
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9
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Thorne LS, Rochford G, Williams TD, Southam AD, Rodriguez-Blanco G, Dunn WB, Hodges NJ. Cytoglobin protects cancer cells from apoptosis by regulation of mitochondrial cardiolipin. Sci Rep 2021; 11:985. [PMID: 33441751 PMCID: PMC7806642 DOI: 10.1038/s41598-020-79830-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
Cytoglobin is important in the progression of oral squamous cell carcinoma but the molecular and cellular basis remain to be elucidated. In the current study, we develop a new cell model to study the function of cytoglobin in oral squamous carcinoma and response to cisplatin. Transcriptomic profiling showed cytoglobin mediated changes in expression of genes related to stress response, redox metabolism, mitochondrial function, cell adhesion, and fatty acid metabolism. Cellular and biochemical studies show that cytoglobin expression results in changes to phenotype associated with cancer progression including: increased cellular proliferation, motility and cell cycle progression. Cytoglobin also protects cells from cisplatin-induced apoptosis and oxidative stress with levels of the antioxidant glutathione increased and total and mitochondrial reactive oxygen species levels reduced. The mechanism of cisplatin resistance involved inhibition of caspase 9 activation and cytoglobin protected mitochondria from oxidative stress-induced fission. To understand the mechanism behind these phenotypic changes we employed lipidomic analysis and demonstrate that levels of the redox sensitive and apoptosis regulating cardiolipin are significantly up-regulated in cells expressing cytoglobin. In conclusion, our data shows that cytoglobin expression results in important phenotypic changes that could be exploited by cancer cells in vivo to facilitate disease progression.
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Affiliation(s)
- Lorna S Thorne
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Garret Rochford
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Timothy D Williams
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Giovanny Rodriguez-Blanco
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Nikolas J Hodges
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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10
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Southam AD, Pursell H, Frigerio G, Jankevics A, Weber RJM, Dunn WB. Characterization of Monophasic Solvent-Based Tissue Extractions for the Detection of Polar Metabolites and Lipids Applying Ultrahigh-Performance Liquid Chromatography-Mass Spectrometry Clinical Metabolic Phenotyping Assays. J Proteome Res 2020; 20:831-840. [PMID: 33236910 DOI: 10.1021/acs.jproteome.0c00660] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolic phenotyping of tissues uses metabolomics and lipidomics to measure the relative polar and nonpolar (lipid) metabolite levels in biological samples. This approach aims to understand disease biochemistry and identify biochemical markers of disease. Sample preparation methods must be reproducible, sensitive (high metabolite and lipid yield), and ideally rapid. We evaluated three biphasic methods for polar and nonpolar compound extraction (chloroform/methanol/water, dichloromethane/methanol/water, and methyl tert-butyl ether [MTBE]/methanol/water), a monophasic method for polar compound extraction (acetonitrile/methanol/water), and a monophasic method for nonpolar compound extraction (isopropanol/water). All methods were applied to mammalian heart, kidney, and liver tissues. Polar extracts were analyzed by hydrophilic interaction chromatography (HILIC) ultrahigh-performance liquid chromatography-mass spectrometry (UHPLC-MS) and nonpolar extracts by C18 reversed-phase UHPLC-MS. Method reproducibility and yield were assessed using multiple annotated endogenous compounds (putatively and MS/MS annotated). Monophasic methods had the highest yield and high reproducibility for both polar (positive ion: median relative standard deviation (RSD) < 18%; negative ion: median RSD < 28%) and nonpolar (positive and negative ion: median RSD < 15%) extractions for heart, kidneys, and liver. The polar monophasic method extracted higher levels of lipid than biphasic polar extractions, and these lipids caused minimal detection suppression for other compounds during HILIC UHPLC-MS. The nonpolar monophasic method had similar or greater detection responses of all detected lipid classes compared to biphasic methods (including increased phosphatidylinositol, phosphatidylserine, and cardiolipin responses). Monophasic methods are quicker and simpler than biphasic methods and are therefore most suited for future automation.
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Affiliation(s)
- Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Harriet Pursell
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Gianfranco Frigerio
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan 20122, Italy
| | - Andris Jankevics
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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11
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Corbin LJ, Hughes DA, Chetwynd AJ, Taylor AE, Southam AD, Jankevics A, Weber RJM, Groom A, Dunn WB, Timpson NJ. Metabolic characterisation of disturbances in the APOC3/triglyceride-rich lipoprotein pathway through sample-based recall by genotype. Metabolomics 2020; 16:69. [PMID: 32494907 PMCID: PMC7270992 DOI: 10.1007/s11306-020-01689-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 05/15/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION High plasma triacylglyceride levels are known to be associated with increased risk of atherosclerotic cardiovascular disease. Apolipoprotein C-III (apoC-III) is a key regulator of plasma triacylglyceride levels and is associated with hypertriglyceridemia via a number of pathways. There is consistent evidence for an association of cardiovascular events with blood apoC-III level, with support from human genetic studies of APOC3 variants. As such, apoC-III has been recognised as a potential therapeutic target for patients with severe hypertriglyceridaemia with one of the most promising apoC-III-targeting drugs, volanesorsen, having recently progressed through Phase III trials. OBJECTIVES To exploit a rare loss of function variant in APOC3 (rs138326449) to characterise the potential long-term treatment effects of apoC-III targeting interventions on the metabolome. METHODS In a recall-by-genotype study, 115 plasma samples were analysed by UHPLC-MS to acquire non-targeted metabolomics data. The study included samples from 57 adolescents and 33 adults. Overall, 12 985 metabolic features were tested for an association with APOC3 genotype. RESULTS 161 uniquely annotated metabolites were found to be associated with rs138326449(APOC3). The highest proportion of associated metabolites belonged to the acyl-acyl glycerophospholipid and triacylglyceride metabolite classes. In addition to the anticipated (on-target) reduction of metabolites in the triacylglyceride and related classes, carriers of the rare variant exhibited previously unreported increases in levels of a number of metabolites from the acyl-alkyl glycerophospholipid class. CONCLUSION Overall, our results suggest that therapies targeting apoC-III may potentially achieve a broad shift in lipid profile that favours better metabolic health.
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Affiliation(s)
- Laura J Corbin
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Andrew J Chetwynd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Amy E Taylor
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- NIHR Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, BS8 2BN, UK
| | - Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andris Jankevics
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alix Groom
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.
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12
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Southam AD, Haglington LD, Najdekr L, Jankevics A, Weber RJM, Dunn WB. Assessment of human plasma and urine sample preparation for reproducible and high-throughput UHPLC-MS clinical metabolic phenotyping. Analyst 2020; 145:6511-6523. [DOI: 10.1039/d0an01319f] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this study we assess multiple sample preparation methods for UHPLC-MS metabolic phenotyping analysis of human urine and plasma. All methods are discussed in terms of metabolite and lipid coverage and reproducibility.
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Affiliation(s)
- Andrew D. Southam
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
| | | | - Lukáš Najdekr
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
| | - Andris Jankevics
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
| | - Ralf J. M. Weber
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
| | - Warwick B. Dunn
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
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13
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Thompson JW, Adams KJ, Adamski J, Asad Y, Borts D, Bowden JA, Byram G, Dang V, Dunn WB, Fernandez F, Fiehn O, Gaul DA, Hühmer AFR, Kalli A, Koal T, Koeniger S, Mandal R, Meier F, Naser FJ, O’Neil D, Pal A, Patti GJ, Pham-Tuan H, Prehn C, Raynaud FI, Shen T, Southam AD, St. John-Williams L, Sulek K, Vasilopoulou CG, Viant M, Winder CL, Wishart D, Zhang L, Zheng J, Moseley MA. International Ring Trial of a High Resolution Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis. Anal Chem 2019; 91:14407-14416. [PMID: 31638379 PMCID: PMC7310668 DOI: 10.1021/acs.analchem.9b02908] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A challenge facing metabolomics in the analysis of large human cohorts is the cross-laboratory comparability of quantitative metabolomics measurements. In this study, 14 laboratories analyzed various blood specimens using a common experimental protocol provided with the Biocrates AbsoluteIDQ p400HR kit, to quantify up to 408 metabolites. The specimens included human plasma and serum from male and female donors, mouse and rat plasma, as well as NIST SRM 1950 reference plasma. The metabolite classes covered range from polar (e.g., amino acids and biogenic amines) to nonpolar (e.g., diacyl- and triacyl-glycerols), and they span 11 common metabolite classes. The manuscript describes a strict system suitability testing (SST) criteria used to evaluate each laboratory's readiness to perform the assay, and provides the SST Skyline documents for public dissemination. The study found approximately 250 metabolites were routinely quantified in the sample types tested, using Orbitrap instruments. Interlaboratory variance for the NIST SRM-1950 has a median of 10% for amino acids, 24% for biogenic amines, 38% for acylcarnitines, 25% for glycerolipids, 23% for glycerophospholipids, 16% for cholesteryl esters, 15% for sphingolipids, and 9% for hexoses. Comparing to consensus values for NIST SRM-1950, nearly 80% of comparable analytes demonstrated bias of <50% from the reference value. The findings of this study result in recommendations of best practices for system suitability, quality control, and calibration. We demonstrate that with appropriate controls, high-resolution metabolomics can provide accurate results with good precision across laboratories, and the p400HR therefore is a reliable approach for generating consistent and comparable metabolomics data.
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Affiliation(s)
- J. Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Duke School of Medicine, 701 W Main Street, Durham, NC 27701
- Department of Pharmacology and Cancer Biology, Duke School of Medicine, Durham, NC
| | - Kendra J. Adams
- Duke Proteomics and Metabolomics Shared Resource, Duke School of Medicine, 701 W Main Street, Durham, NC 27701
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, 85350 Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yasmin Asad
- Drug Metabolism Pharmacokinetics and Metabolomics group, Cancer Research UK Cancer Therapeutics Unit, The Institute for Cancer Research, 15 Cotswold Road, Sutton Surrey, SM2 5NG, UK
| | - David Borts
- College of Veterinary Medicine, Iowa State University, Ames, IA 50011
- Thermo Fisher Scientific, San Jose, CA
| | - John A. Bowden
- National Institute of Standards and Technology, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC 29412, United States
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, 1333 Center Road, University of Florida, Gainesville, Florida 32610, United States
| | - Gregory Byram
- UC Davis Genome Center – Metabolomics, Davis, CA 95618
| | - Viet Dang
- College of Veterinary Medicine, Iowa State University, Ames, IA 50011
| | | | - Facundo Fernandez
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400
| | - Oliver Fiehn
- UC Davis Genome Center – Metabolomics, Davis, CA 95618
| | - David A. Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400
| | | | | | | | | | - Rupasri Mandal
- Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8
| | - Florian Meier
- Max Planck Institute of Biochemistry, Munich, Germany
| | - Fuad J. Naser
- Washington University, Departments of Chemistry, Genetics, and Medicine. Saint Louis, Missouri 63110 USA
| | - Donna O’Neil
- University of Birmingham and Phenome Centre Birmingham, UK
| | - Akos Pal
- Drug Metabolism Pharmacokinetics and Metabolomics group, Cancer Research UK Cancer Therapeutics Unit, The Institute for Cancer Research, 15 Cotswold Road, Sutton Surrey, SM2 5NG, UK
| | - Gary J. Patti
- Washington University, Departments of Chemistry, Genetics, and Medicine. Saint Louis, Missouri 63110 USA
| | | | - Cornelia Prehn
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Florence I. Raynaud
- Drug Metabolism Pharmacokinetics and Metabolomics group, Cancer Research UK Cancer Therapeutics Unit, The Institute for Cancer Research, 15 Cotswold Road, Sutton Surrey, SM2 5NG, UK
| | - Tong Shen
- UC Davis Genome Center – Metabolomics, Davis, CA 95618
| | | | - Lisa St. John-Williams
- Duke Proteomics and Metabolomics Shared Resource, Duke School of Medicine, 701 W Main Street, Durham, NC 27701
| | - Karolina Sulek
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | | | - Mark Viant
- University of Birmingham and Phenome Centre Birmingham, UK
| | | | - David Wishart
- Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8
| | - Lun Zhang
- Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8
| | - Jiamin Zheng
- Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8
| | - M. Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Duke School of Medicine, 701 W Main Street, Durham, NC 27701
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14
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Bryant J, Batis N, Franke AC, Clancey G, Hartley M, Ryan G, Brooks J, Southam AD, Barnes N, Parish J, Roberts S, Khanim F, Spruce R, Mehanna H. Repurposed quinacrine synergizes with cisplatin, reducing the effective dose required for treatment of head and neck squamous cell carcinoma. Oncotarget 2019; 10:5229-5244. [PMID: 31497252 PMCID: PMC6718257 DOI: 10.18632/oncotarget.27156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/17/2019] [Indexed: 12/03/2022] Open
Abstract
Despite highly toxic treatments, head and neck squamous cell carcinoma (HNSCC) have poor outcomes. There is an unmet need for more effective, less toxic therapies. Repurposing of clinically-approved drugs, with known safety profiles, may provide a time- and cost-effective approach to address this need. We have developed the AcceleraTED platform to repurpose drugs for HNSCC treatment; using in vitro assays (cell viability, clonogenic survival, apoptosis) and in vivo models (xenograft tumors in NOD/SCID/gamma mice). Screening a library of clinically-approved drugs identified the anti-malarial agent quinacrine as a candidate, which significantly reduced viability in a concentration dependent manner in five HNSCC cell lines (IC50 0.63–1.85 μM) and in six primary HNSCC samples (IC50 ~2 μM). Decreased clonogenic survival, increased apoptosis and accumulation of LC3-II (indicating altered autophagy) were also observed. Effects were additional to those resulting from standard treatments (cisplatin +/– irradiation) alone. In vivo, daily treatment with 100 mg/kg oral quinacrine plus cisplatin significantly inhibited tumor outgrowth, extending median time to reach maximum tumor volume from 20 to 32 days (p
< 0.0001) versus control, and from 28 to 32 days versus 2 mg/kg cisplatin alone. Importantly, combination therapy enabled the dose of cisplatin to be halved to 1 mg/kg, whilst maintaining the same impairment of tumor growth. Treatment was well tolerated; murine plasma levels reached a steady concentration of 0.5 μg/mL, comparable to levels achievable and tolerated in humans. Consequently, due to its favorable toxicity profile and proven safety, quinacrine may be particularly useful in reducing cisplatin dose, especially in frail and older patients; warranting a clinical trial.
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Affiliation(s)
- Jennifer Bryant
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK.,Joint first authors
| | - Nikolaos Batis
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK.,Joint first authors
| | - Anna Clara Franke
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK
| | - Gabriella Clancey
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK
| | - Margaret Hartley
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK
| | - Gordon Ryan
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK
| | - Jill Brooks
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK
| | - Andrew D Southam
- School of Biosciences, University of Birmingham, Birmingham, UK.,Phenome Centre Birmingham, University of Birmingham, Birmingham, UK
| | - Nicholas Barnes
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.,School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joanna Parish
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sally Roberts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Farhat Khanim
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Rachel Spruce
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK.,Joint senior authors
| | - Hisham Mehanna
- Institute of Head and Neck Studies and Education (InHANSE), University of Birmingham, Birmingham, UK.,University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.,Joint senior authors
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15
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D'Elia RV, Goodchild SA, Winder CL, Southam AD, Weber RJM, Stahl FM, Docx C, Patel V, Green AC, Viant MR, Lukaszewski RA, Dunn WB. Multiple metabolic pathways are predictive of ricin intoxication in a rat model. Metabolomics 2019; 15:102. [PMID: 31270703 PMCID: PMC6610267 DOI: 10.1007/s11306-019-1547-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/28/2019] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Exposure to ricin can be lethal and treatments that are under development have short windows of opportunity for administration after exposure. It is therefore essential to achieve early detection of ricin exposure to provide the best prognosis for exposed individuals. Ricin toxin can be detected in clinical samples via several antibody-based techniques, but the efficacy of these can be limited due to the rapid processing and cellular uptake of toxin in the body and subsequent low blood ricin concentrations. Other diagnostic tools that perform, in an orthogonal manner, are therefore desirable. OBJECTIVES To determine time-dependent metabolic changes in Sprague-Dawley rats following intravenous exposure to ricin. METHODS Sprague-Dawley rats were intravenously exposed to ricin and multiple blood samples were collected from each animal for up to 48 h following exposure in two independent studies. Plasma samples were analysed applying HILIC and C18 reversed phase UHPLC-MS assays followed by univariate and multivariate analysis. RESULTS In Sprague-Dawley rats we have demonstrated that metabolic changes measured in blood can distinguish between rats exposed intravenously to ricin and controls prior to the onset of behavioral signs of intoxication after 24 h. A total of 37 metabolites were significantly altered following exposure to ricin when compared to controls. The arginine/proline, bile acid and triacylglyceride metabolic pathways were highlighted as being important with two triacylglycerides at 8 h post exposure giving an AUROC score of 0.94. At 16 h and 24 h the AUROC score increased to 0.98 and 1.0 with the number of metabolites in the panel increasing to 5 and 7, respectively. CONCLUSIONS These data demonstrate that metabolites may be a useful tool to diagnose and detect ricin exposure, thus increasing the effectiveness of supportive therapy and future ricin-specific medical treatments.
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Affiliation(s)
| | | | - Catherine L Winder
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andrew D Southam
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ralf J M Weber
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Cerys Docx
- Dstl Porton Down, Salisbury, SP4 0JQ, UK
| | | | | | - Mark R Viant
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Warwick B Dunn
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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16
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Denbigh JL, Perez-Guaita D, Vernooij RR, Tobin MJ, Bambery KR, Xu Y, Southam AD, Khanim FL, Drayson MT, Lockyer NP, Goodacre R, Wood BR. Probing the action of a novel anti-leukaemic drug therapy at the single cell level using modern vibrational spectroscopy techniques. Sci Rep 2017; 7:2649. [PMID: 28572622 PMCID: PMC5453947 DOI: 10.1038/s41598-017-02069-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/07/2017] [Indexed: 01/07/2023] Open
Abstract
Acute myeloid leukaemia (AML) is a life threatening cancer for which there is an urgent clinical need for novel therapeutic approaches. A redeployed drug combination of bezafibrate and medroxyprogesterone acetate (BaP) has shown anti-leukaemic activity in vitro and in vivo. Elucidation of the BaP mechanism of action is required in order to understand how to maximise the clinical benefit. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, Synchrotron radiation FTIR (S-FTIR) and Raman microspectroscopy are powerful complementary techniques which were employed to probe the biochemical composition of two AML cell lines in the presence and absence of BaP. Analysis was performed on single living cells along with dehydrated and fixed cells to provide a large and detailed data set. A consideration of the main spectral differences in conjunction with multivariate statistical analysis reveals a significant change to the cellular lipid composition with drug treatment; furthermore, this response is not caused by cell apoptosis. No change to the DNA of either cell line was observed suggesting this combination therapy primarily targets lipid biosynthesis or effects bioactive lipids that activate specific signalling pathways.
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Affiliation(s)
- Joanna L Denbigh
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M1 7DN, United Kingdom.,Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, United Kingdom
| | - David Perez-Guaita
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria, 3800, Australia
| | - Robbin R Vernooij
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria, 3800, Australia
| | - Mark J Tobin
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria, 3168, Australia
| | - Keith R Bambery
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria, 3168, Australia
| | - Yun Xu
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Andrew D Southam
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Farhat L Khanim
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Mark T Drayson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Nicholas P Lockyer
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Royston Goodacre
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Bayden R Wood
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria, 3800, Australia.
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17
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Abstract
INTRODUCTION Cellular metabolism is altered during cancer initiation and progression, which allows cancer cells to increase anabolic synthesis, avoid apoptosis and adapt to low nutrient and oxygen availability. The metabolic nature of cancer enables patient cancer status to be monitored by metabolomics and lipidomics. Additionally, monitoring metabolic status of patients or biological models can be used to greater understand the action of anticancer therapeutics. OBJECTIVES Discuss how metabolomics and lipidomics can be used to (i) identify metabolic biomarkers of cancer and (ii) understand the mechanism-of-action of anticancer therapies. Discuss considerations that can maximize the clinical value of metabolic cancer biomarkers including case-control, prognostic and longitudinal study designs. METHODS A literature search of the current relevant primary research was performed. RESULTS Metabolomics and lipidomics can identify metabolic signatures that associate with cancer diagnosis, prognosis and disease progression. Discriminatory metabolites were most commonly linked to lipid or energy metabolism. Case-control studies outnumbered prognostic and longitudinal approaches. Prognostic studies were able to correlate metabolic features with future cancer risk, whereas longitudinal studies were most effective for studying cancer progression. Metabolomics and lipidomics can help to understand the mechanism-of-action of anticancer therapeutics and mechanisms of drug resistance. CONCLUSION Metabolomics and lipidomics can be used to identify biomarkers associated with cancer and to better understand anticancer therapies.
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Affiliation(s)
- Emily G. Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, 28668 Madrid, Spain
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA UK
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH UK
| | - Andrew D. Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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18
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Madu UL, Ogundeji AO, Mochochoko BM, Pohl CH, Albertyn J, Swart CW, Allwood JW, Southam AD, Dunn WB, May RC, Sebolai OM. Cryptococcal 3-Hydroxy Fatty Acids Protect Cells Against Amoebal Phagocytosis. Front Microbiol 2015; 6:1351. [PMID: 26696972 PMCID: PMC4673343 DOI: 10.3389/fmicb.2015.01351] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/16/2015] [Indexed: 11/21/2022] Open
Abstract
We previously reported on a 3-hydroxy fatty acid that is secreted via cryptococcal capsular protuberances - possibly to promote pathogenesis and survival. Thus, we investigated the role of this molecule in mediating the fate of Cryptococcus (C.) neoformans and the related species C. gattii when predated upon by amoebae. We show that this molecule protects cells against the phagocytic effects of amoebae. C. neoformans UOFS Y-1378 (which produces 3-hydroxy fatty acids) was less sensitive toward amoebae compared to C. neoformans LMPE 046 and C. gattii R265 (both do not produce 3-hydroxy fatty acids) and addition of 3-hydroxy fatty acids to C. neoformans LMPE 046 and C. gattii R265 culture media, causes these strains to become more resistant to amoebal predation. Conversely, addition of aspirin (a 3-hydroxy fatty acid inhibitor) to C. neoformans UOFS Y-1378 culture media made cells more susceptible to amoebae. Our data suggest that this molecule is secreted at a high enough concentration to effect intracellular signaling within amoeba, which in turn, promotes fungal survival.
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Affiliation(s)
- Uju L Madu
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa
| | - Adepemi O Ogundeji
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa
| | - Bonang M Mochochoko
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa
| | - Carolina H Pohl
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa
| | - Jacobus Albertyn
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa
| | - Chantel W Swart
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa
| | | | | | - Warwick B Dunn
- School of Biosciences, University of Birmingham Birmingham, UK
| | - Robin C May
- School of Biosciences, University of Birmingham Birmingham, UK ; Institute of Microbiology and Infection and the School of Biosciences, University of Birmingham Birmingham, UK
| | - Olihile M Sebolai
- Pathogenic Yeast Research Group, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State Bloemfontein, South Africa ; Institute of Microbiology and Infection and the School of Biosciences, University of Birmingham Birmingham, UK
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19
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Southam AD, Khanim FL, Hayden RE, Constantinou JK, Koczula KM, Michell RH, Viant MR, Drayson MT, Bunce CM. Drug Redeployment to Kill Leukemia and Lymphoma Cells by Disrupting SCD1-Mediated Synthesis of Monounsaturated Fatty Acids. Cancer Res 2015; 75:2530-40. [PMID: 25943877 DOI: 10.1158/0008-5472.can-15-0202] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/07/2015] [Indexed: 11/16/2022]
Abstract
The redeployed drug combination of bezafibrate and medroxyprogesterone acetate (designated BaP) has potent in vivo anticancer activity in acute myelogenous leukemia (AML) and endemic Burkitt lymphoma (eBL) patients; however, its mechanism-of-action is unclear. Given that elevated fatty acid biosynthesis is a hallmark of many cancers and that these drugs can affect lipid metabolism, we hypothesized that BaP exerts anticancer effects by disrupting lipogenesis. We applied mass spectrometry-based lipidomics and gene and protein expression measurements of key lipogenic enzymes [acetyl CoA carboxylase 1 (ACC1), fatty acid synthase (FASN), and stearoyl CoA desaturase 1 (SCD1)] to AML and eBL cell lines treated with BaP. BaP treatment decreased fatty acid and phospholipid biosynthesis from (13)C D-glucose. The proportion of phospholipid species with saturated and monounsaturated acyl chains was also decreased after treatment, whereas those with polyunsaturated chains increased. BaP decreased SCD1 protein levels in each cell line (0.46- to 0.62-fold; P < 0.023) and decreased FASN protein levels across all cell lines (0.87-fold decrease; P = 1.7 × 10(-4)). Changes to ACC1 protein levels were mostly insignificant. Supplementation with the SCD1 enzymatic product, oleate, rescued AML and e-BL cells from BaP cell killing and decreased levels of BaP-induced reactive oxygen species, whereas supplementation with the SCD1 substrate (and FASN product), palmitate, did not rescue cells. In conclusion, these data suggest that the critical anticancer actions of BaP are decreases in SCD1 levels and monounsaturated fatty acid synthesis. To our knowledge, this is the first time that clinically available antileukemic and antilymphoma drugs targeting SCD1 have been reported.
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Affiliation(s)
- Andrew D Southam
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
| | - Farhat L Khanim
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rachel E Hayden
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Katarzyna M Koczula
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Robert H Michell
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Mark T Drayson
- School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Chris M Bunce
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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20
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Southam AD, Lange A, Al-Salhi R, Hill EM, Tyler CR, Viant MR. Distinguishing between the metabolome and xenobiotic exposome in environmental field samples analysed by direct-infusion mass spectrometry based metabolomics and lipidomics. Metabolomics 2014; 10:1050-1058. [PMID: 25374485 PMCID: PMC4213387 DOI: 10.1007/s11306-014-0693-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/25/2014] [Indexed: 12/23/2022]
Abstract
Environmental metabolomics is increasingly used to investigate organismal responses to complex chemical mixtures, including waste water effluent (WWE). In parallel, increasingly sensitive analytical methods are being used in metabolomics studies, particularly mass spectrometry. This introduces a considerable, yet overlooked, challenge that high analytical sensitivity will not only improve the detection of endogenous metabolites in biological specimens but also exogenous chemicals. If these often unknown xenobiotic features are not removed from the "biological" dataset, they will bias the interpretation and could lead to incorrect conclusions about the biotic response. Here we illustrate and validate a novel workflow classifying the origin of peaks detected in biological samples as: endogenous, xenobiotics, or metabolised xenobiotics. The workflow is demonstrated using direct infusion mass spectrometry-based metabolomic analysis of testes from roach exposed to different concentrations of a complex WWE. We show that xenobiotics and their metabolic products can be detected in roach testes (including triclosan, chloroxylenol and chlorophene), and that these compounds have a disproportionately high level of statistical significance within the total (bio)chemical changes induced by the WWE. Overall we have demonstrated that this workflow extracts more information from an environmental metabolomics study of complex mixture exposures than was possible previously.
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Affiliation(s)
- Andrew D. Southam
- 0000 0004 1936 7486grid.6572.6School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Anke Lange
- 0000 0004 1936 8024grid.8391.3Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD UK
| | - Raghad Al-Salhi
- 0000 0004 1936 7590grid.12082.39School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG UK
| | - Elizabeth M. Hill
- 0000 0004 1936 7590grid.12082.39School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG UK
| | - Charles R. Tyler
- 0000 0004 1936 8024grid.8391.3Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD UK
| | - Mark R. Viant
- 0000 0004 1936 7486grid.6572.6School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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21
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Mirbahai L, Williams TD, Yin G, Southam AD, Sommer U, Li N, Bignell JP, Lyons BP, Viant MR, Chipman JK. Disruption of DNA methylation via S-adenosylhomocysteine is a key process in high incidence liver carcinogenesis. Clin Epigenetics 2013. [PMCID: PMC3751557 DOI: 10.1186/1868-7083-5-s1-s9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Mirbahai L, Southam AD, Sommer U, Williams TD, Bignell JP, Lyons BP, Viant MR, Chipman JK. Disruption of DNA Methylation via S-Adenosylhomocysteine Is a Key Process in High Incidence Liver Carcinogenesis in Fish. J Proteome Res 2013; 12:2895-904. [DOI: 10.1021/pr400195u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Leda Mirbahai
- School of
Biosciences, University of Birmingham,
Edgbaston, Birmingham, United
Kingdom
| | - Andrew D. Southam
- School of
Biosciences, University of Birmingham,
Edgbaston, Birmingham, United
Kingdom
| | - Ulf Sommer
- NERC Biomolecular
Analysis Facility
− Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United
Kingdom
| | - Tim D. Williams
- School of
Biosciences, University of Birmingham,
Edgbaston, Birmingham, United
Kingdom
| | - John P. Bignell
- Cefas, Weymouth Laboratory, Weymouth, Dorset, United Kingdom
| | - Brett P. Lyons
- Cefas, Weymouth Laboratory, Weymouth, Dorset, United Kingdom
| | - Mark R. Viant
- School of
Biosciences, University of Birmingham,
Edgbaston, Birmingham, United
Kingdom
- NERC Biomolecular
Analysis Facility
− Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United
Kingdom
| | - James K. Chipman
- School of
Biosciences, University of Birmingham,
Edgbaston, Birmingham, United
Kingdom
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23
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Weber RJM, Southam AD, Sommer U, Viant MR. Characterization of isotopic abundance measurements in high resolution FT-ICR and Orbitrap mass spectra for improved confidence of metabolite identification. Anal Chem 2011; 83:3737-43. [PMID: 21466230 DOI: 10.1021/ac2001803] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Currently there is limited information available on the accuracy and precision of relative isotopic abundance (RIA) measurements using high-resolution direct-infusion mass spectrometry (HR DIMS), and it is unclear if this information can benefit automated peak annotation in metabolomics. Here we characterize the accuracy of RIA measurements on the Thermo LTQ FT Ultra (resolution of 100,000-750,000) and LTQ Orbitrap (R = 100,000) mass spectrometers. This first involved reoptimizing the SIM-stitching method (Southam, A. D. Anal. Chem. 2007, 79, 4595-4602) for the LTQ FT Ultra, which achieved a ca. 3-fold sensitivity increase compared to the original method while maintaining a root-mean-squared mass error of 0.16 ppm. Using this method, we show the quality of RIA measurements is highly dependent on signal-to-noise ratio (SNR), with RIA accuracy increasing with higher SNR. Furthermore, a negative offset between the theoretical and empirically calculated numbers of carbon atoms was observed for both mass spectrometers. Increasing the resolution of the LTQ FT Ultra lowered both the sensitivity and the quality of RIA measurements. Overall, although the errors in the empirically calculated number of carbons can be large (e.g., 10 carbons), we demonstrate that RIA measurements do improve automated peak annotation, increasing the number of single empirical formula assignments by >3-fold compared to using accurate mass alone.
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Affiliation(s)
- Ralf J M Weber
- Centre for Systems Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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24
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Southam AD, Lange A, Hines A, Hill EM, Katsu Y, Iguchi T, Tyler CR, Viant MR. Metabolomics reveals target and off-target toxicities of a model organophosphate pesticide to roach (Rutilus rutilus): implications for biomonitoring. Environ Sci Technol 2011; 45:3759-67. [PMID: 21410251 PMCID: PMC3076994 DOI: 10.1021/es103814d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The ability of targeted and nontargeted metabolomics to discover chronic ecotoxicological effects is largely unexplored. Fenitrothion, an organophosphate pesticide, is categorized as a "red list" pollutant, being particularly hazardous to aquatic life. It acts primarily as a cholinesterase inhibitor, but evidence suggests it can also act as an androgen receptor antagonist. Whole-organism fenitrothion-induced toxicity is well-established, but information regarding target and off-target molecular toxicities is limited. Here we study the molecular responses of male roach ( Rutilus rutilus ) exposed to fenitrothion, including environmentally realistic concentrations, for 28 days. Acetylcholine was assessed in brain; steroid metabolism was measured in testes and plasma; and NMR and mass spectrometry-based metabolomics were conducted on testes and liver to discover off-target toxicity. O-demethylation was confirmed as a major route of pesticide degradation. Fenitrothion significantly depleted acetylcholine, confirming its primary mode of action, and 11-ketotestosterone in plasma and cortisone in testes, showing disruption of steroid metabolism. Metabolomics revealed significant perturbations to the hepatic phosphagen system and previously undocumented effects on phenylalanine metabolism in liver and testes. On the basis of several unexpected molecular responses that were opposite to the anticipated acute toxicity, we propose that chronic pesticide exposure induces an adapting phenotype in roach, which may have considerable implications for interpreting molecular biomarker responses in field-sampled fish.
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Affiliation(s)
- Andrew D. Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Anke Lange
- School of Biosciences, University of Exeter, Exeter EX4 4PS, United Kingdom
| | - Adam Hines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Elizabeth M. Hill
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
| | - Yoshinao Katsu
- Okazaki Institute for Integrative Bioscience, Okazaki 444-8787, Japan
| | - Taisen Iguchi
- Okazaki Institute for Integrative Bioscience, Okazaki 444-8787, Japan
| | - Charles R. Tyler
- School of Biosciences, University of Exeter, Exeter EX4 4PS, United Kingdom
| | - Mark R. Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- Phone: +44(0)121 414-2219; fax: +44(0)121 414-5925; e-mail:
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Small HJ, Williams TD, Sturve J, Chipman JK, Southam AD, Bean TP, Lyons BP, Stentiford GD. Gene expression analyses of hepatocellular adenoma and hepatocellular carcinoma from the marine flatfish Limanda limanda. Dis Aquat Organ 2010; 88:127-141. [PMID: 20225674 DOI: 10.3354/dao02148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
At selected sites around the UK, the offshore sentinel flatfish species dab Limanda limanda are found to contain elevated levels of macroscopic liver tumors. Previous proteomic and metabolomic studies have demonstrated that differences exist between tumor and non-tumor tissues; however, these differing features were not identified, and little is known about the changes at the gene expression level, or whether prognostic markers are present and can be identified. A flounder Platichthys flesus custom cDNA microarray and RT-PCR were used to investigate hepatic mRNA expression in the histologically confirmed tumors, hepatocellular adenoma (HA) and hepatocellular carcinoma (HC) from dab, and in adjacent normal tissue from the same fish. Differences in gene expression were observed between tumor and normal tissues, and between tumor types. A class-prediction approach using 50 transcripts revealed sufficient group-specific expression profiles to allow segregation of samples dependent on their tumor type or the sex of the host. Vitellogenins were found to display the greatest induction (up to 500-fold induction) in some HC tumors from female fish and in both HA and HC tumors from males. To the best of our knowledge, this is the first report of the association of vitellogenin expression with tumors of wild fish.
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Affiliation(s)
- Hamish J Small
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, UK
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Payne TG, Southam AD, Arvanitis TN, Viant MR. A signal filtering method for improved quantification and noise discrimination in fourier transform ion cyclotron resonance mass spectrometry-based metabolomics data. J Am Soc Mass Spectrom 2009; 20:1087-95. [PMID: 19269189 DOI: 10.1016/j.jasms.2009.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Revised: 01/30/2009] [Accepted: 02/03/2009] [Indexed: 05/08/2023]
Abstract
Direct-infusion electrospray-ionization Fourier transform ion cyclotron resonance mass spectrometry (DI ESI FT-ICR MS) is increasingly being utilized in metabolomics, including the high sensitivity selected ion monitoring (SIM)-stitching approach. Accurate signal quantification and the discrimination of real signals from noise remain major challenges for this approach, with both adversely affected by factors including ion suppression during electrospray, ion-ion interactions in the detector cell, and thermally-induced white noise. This is particularly problematic for complex mixture analysis where hundreds of metabolites are present near the noise level. Here we address relative signal quantification and noise discrimination issues in SIM-stitched DI ESI FT-ICR MS-based metabolomics. Using liver tissue, we first optimized the number of scans (n) acquired per SIM window to address the balance between quantification accuracy versus acquisition time (and thus sample throughput); a minimum of n = 5 is recommended. Secondly, we characterized and computationally-corrected an effect whereby an ion's intensity is dependent upon its location within a SIM window, exhibiting a 3-fold higher intensity at the high m/z end. This resulted in significantly improved quantification accuracy. Finally, we thoroughly characterized a three-stage filter to discriminate noise from real signals, which comprised a signal-to-noise-ratio (SNR) hard threshold, then a "replicate" filter (retaining only peaks in r-out-of-3 replicate analyses), and then a "sample" filter (retaining only peaks in >s% of biological samples). We document the benefits of three-stage filtering versus one- and two-stage filters, and show the importance of selecting filter parameters that balance the confidence that a signal is real versus the total number of peaks detected.
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Affiliation(s)
- Tristan G Payne
- School of Electronic, Electrical and Computer Engineering, University of Birmingham, Birmingham, United Kingdom
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Southam AD, Easton JM, Stentiford GD, Ludwig C, Arvanitis TN, Viant MR. Metabolic changes in flatfish hepatic tumours revealed by NMR-based metabolomics and metabolic correlation networks. J Proteome Res 2009; 7:5277-85. [PMID: 19367724 DOI: 10.1021/pr800353t] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Histopathologically well-characterized fish liver was analyzed by 800 MHz 1H NMR metabolomics to identify metabolic changes between healthy and tumor tissue. Data were analyzed by multivariate statistics and metabolic correlation networks, and results revealed elevated anaerobic metabolism and reduced choline metabolism in tumor tissue. Significant negative correlations were observed between alanine-acetate (p = 3.0 x 10(-5)) and between proline-acetate (p = 0.003) in tumors only, suggesting alanine and proline are utilized as alternative energy sources in flatfish liver tumors.
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Affiliation(s)
- Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Southam AD, Payne TG, Cooper HJ, Arvanitis TN, Viant MR. Dynamic range and mass accuracy of wide-scan direct infusion nanoelectrospray fourier transform ion cyclotron resonance mass spectrometry-based metabolomics increased by the spectral stitching method. Anal Chem 2007; 79:4595-602. [PMID: 17511421 DOI: 10.1021/ac062446p] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Direct infusion nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry (DI nESI FT-ICR MS) offers high mass accuracy and resolution for analyzing complex metabolite mixtures. High dynamic range across a wide mass range, however, can only be achieved at the expense of mass accuracy, since the large numbers of ions entering the ICR detector induce adverse space-charge effects. Here we report an optimized strategy for wide-scan DI nESI FT-ICR MS that increases dynamic range but maintains high mass accuracy. It comprises the collection of multiple adjacent selected ion monitoring (SIM) windows that are stitched together using novel algorithms. The final SIM-stitching method, derived from several optimization experiments, comprises 21 adjoining SIM windows each of width m/z 30 (from m/z 70 to 500; adjacent windows overlap by m/z 10) with an automated gain control (AGC) target of 1 x 10(5) charges. SIM-stitching and wide-scan range (WSR; Thermo Electron) were compared using a defined standard to assess mass accuracy and a liver extract to assess peak count and dynamic range. SIM-stitching decreased the maximum mass error by 1.3- and 4.3-fold, and increased the peak count by 5.3- and 1.8-fold, versus WSR (AGC targets of 1 x 10(5) and 5 x 10(5), respectively). SIM-stitching achieved an rms mass error of 0.18 ppm and detected over 3000 peaks in liver extract. This novel approach increases metabolome coverage, has very high mass accuracy, and at 5.5 min/sample is conducive for high-throughput metabolomics.
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Affiliation(s)
- Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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