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Alpizar-Sosa E, Zimbres FM, Mantilla BS, Dickie EA, Wei W, Burle-Caldas GA, Filipe LNS, Van Bocxlaer K, Price HP, Ibarra-Meneses AV, Beaudry F, Fernandez-Prada C, Whitfield PD, Barrett MP, Denny PW. Evaluation of the Leishmania Inositol Phosphorylceramide Synthase as a Drug Target Using a Chemical and Genetic Approach. ACS Infect Dis 2024; 10:2913-2928. [PMID: 39023360 PMCID: PMC11320567 DOI: 10.1021/acsinfecdis.4c00284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
The lack of effective vaccines and the development of resistance to the current treatments highlight the urgent need for new anti-leishmanials. Sphingolipid metabolism has been proposed as a promising source of Leishmania-specific targets as these lipids are key structural components of the eukaryotic plasma membrane and are involved in distinct cellular events. Inositol phosphorylceramide (IPC) is the primary sphingolipid in the Leishmania species and is the product of a reaction mediated by IPC synthase (IPCS). The antihistamine clemastine fumarate has been identified as an inhibitor of IPCS in L. major and a potent anti-leishmanial in vivo. Here we sought to further examine the target of this compound in the more tractable species L. mexicana, using an approach combining genomic, proteomic, metabolomic and lipidomic technologies, with molecular and biochemical studies. While the data demonstrated that the response to clemastine fumarate was largely conserved, unexpected disturbances beyond sphingolipid metabolism were identified. Furthermore, while deletion of the gene encoding LmxIPCS had little impact in vitro, it did influence clemastine fumarate efficacy and, importantly, in vivo pathogenicity. Together, these data demonstrate that clemastine does inhibit LmxIPCS and cause associated metabolic disturbances, but its primary target may lie elsewhere.
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Affiliation(s)
| | - Flavia M. Zimbres
- Department
of Biosciences, University of Durham, South Road, Durham, DH1 3LE, U.K.
| | - Brian S. Mantilla
- Department
of Biosciences, University of Durham, South Road, Durham, DH1 3LE, U.K.
| | - Emily A. Dickie
- School
of Infection and Immunity, College of Medical, Veterinary and Life
Sciences, University of Glasgow, Glasgow G12 8TA, U.K.
| | - Wenbin Wei
- Department
of Biosciences, University of Durham, South Road, Durham, DH1 3LE, U.K.
| | - Gabriela A. Burle-Caldas
- Department
of Biosciences, University of Durham, South Road, Durham, DH1 3LE, U.K.
- Departamento
de Bioquímica e Imunologia, Universidade
Federal de Minas Gerais, Caixa Postal 486 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Laura N. S. Filipe
- Department
of Biosciences, University of Durham, South Road, Durham, DH1 3LE, U.K.
| | - Katrien Van Bocxlaer
- York
Biomedical Research Institute, Hull York Medical School, University of York, York YO10 5NG, U.K.
| | - Helen P. Price
- School
of Life Sciences, Keele University, Staffordshire, ST5 5BG, U.K.
| | - Ana V. Ibarra-Meneses
- Département
de Pathologie et Microbiologie, Faculté de Médecine
Vétérinaire, Université
de Montréal, Saint-Hyacinthe, Quebec J2S 2M2, Canada
| | - Francis Beaudry
- Département
de Biomédecine, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec J2S 2M2, Canada
| | - Christopher Fernandez-Prada
- Département
de Pathologie et Microbiologie, Faculté de Médecine
Vétérinaire, Université
de Montréal, Saint-Hyacinthe, Quebec J2S 2M2, Canada
| | - Philip D. Whitfield
- School
of Infection and Immunity, College of Medical, Veterinary and Life
Sciences, University of Glasgow, Glasgow G12 8TA, U.K.
| | - Michael P. Barrett
- School
of Infection and Immunity, College of Medical, Veterinary and Life
Sciences, University of Glasgow, Glasgow G12 8TA, U.K.
| | - Paul W. Denny
- Department
of Biosciences, University of Durham, South Road, Durham, DH1 3LE, U.K.
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2
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Rimbi PT, O'Boyle N, Douce GR, Pizza M, Rosini R, Roe AJ. Enhancing a multi-purpose artificial urine for culture and gene expression studies of uropathogenic Escherichia coli strains. J Appl Microbiol 2024; 135:lxae067. [PMID: 38486355 DOI: 10.1093/jambio/lxae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/09/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
AIMS The main objective of this study was to modify a recently reported multi-purpose artificial urine (MP-AU) for culture and gene expression studies of uropathogenic Escherichia coli (UPEC) strains. METHODS AND RESULTS We used liquid chromatography mass spectrometry (LC-MS) to identify and adjust the metabolic profile of MP-AU closer to that of pooled human urine (PHU). Modification in this way facilitated growth of UPEC strains with growth rates similar to those obtained in PHU. Transcriptomic analysis of UPEC strains cultured in enhanced artificial urine (enhanced AU) and PHU showed that the gene expression profiles are similar, with <7% of genes differentially expressed between the two conditions. CONCLUSIONS Enhancing an MP-AU with metabolites identified in PHU allows the enhanced AU to be used as a substitute for the culture and in vitro gene expression studies of UPEC strains.
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Affiliation(s)
- Patricia T Rimbi
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Nicky O'Boyle
- School of Microbiology, University College Cork, National University of Ireland, Cork T12 K8AF, Ireland
- Department of Pathology, School of Medicine, University College Cork, Cork T12 K8AF, Ireland
| | - Gillian R Douce
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Mariagrazia Pizza
- Department of Life Sciences, Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Andrew J Roe
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, United Kingdom
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3
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Simwela NV, Guiguemde WA, Straimer J, Regnault C, Stokes BH, Tavernelli LE, Yokokawa F, Taft B, Diagana TT, Barrett MP, Waters AP. A conserved metabolic signature associated with response to fast-acting anti-malarial agents. Microbiol Spectr 2023; 11:e0397622. [PMID: 37800971 PMCID: PMC10714989 DOI: 10.1128/spectrum.03976-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 01/27/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE In malaria drug discovery, understanding the mode of action of lead compounds is important as it helps in predicting the potential emergence of drug resistance in the field when these drugs are eventually deployed. In this study, we have employed metabolomics technologies to characterize the potential targets of anti-malarial drug candidates in the developmental pipeline at NITD. We show that NITD fast-acting leads belonging to spiroindolone and imidazothiadiazole class induce a common biochemical theme in drug-exposed malaria parasites which is similar to another fast-acting, clinically available drug, DHA. These biochemical features which are absent in a slower acting NITD lead (GNF17) point to hemoglobin digestion and inhibition of the pyrimidine pathway as potential action points for these drugs. These biochemical themes can be used to identify and inform on the mode of action of fast drug candidates of similar profiles in future drug discovery programs.
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Affiliation(s)
- Nelson V. Simwela
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | | | - Judith Straimer
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | - Clement Regnault
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Barbara H. Stokes
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Luis E. Tavernelli
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Fumiaki Yokokawa
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | - Benjamin Taft
- Novartis Institute for Tropical Diseases, Emeryville, California, USA
| | | | - Michael P. Barrett
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | - Andrew P. Waters
- Institute of Infection, Immunity and Inflammation, Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
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4
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Rubić I, Weidt S, Burchmore R, Kovačević A, Kuleš J, Eckersall PD, Torti M, Jović I, Kovačić M, Gotić J, Barić Rafaj R, Novak P, Samardžija M, Mrljak V. Metabolome Profiling in the Plasma of Dogs with Idiopathic Dilated Cardiomyopathy: A Multiplatform Mass-Spectrometry-Based Approach. Int J Mol Sci 2023; 24:15182. [PMID: 37894863 PMCID: PMC10607069 DOI: 10.3390/ijms242015182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Dilated cardiomyopathy is one of the important diseases in dogs and humans. The second most common cause of heart failure in dogs is idiopathic dilated cardiomyopathy (iDCM), which results in heart failure or sudden cardiac death due to arrhythmia. This study aimed to determine changes in the plasma metabolome of dogs with iDCM compared to healthy dogs. For that purpose, a multiplatform mass-spectrometry-based approach was used. In this study, we included two groups of dogs: 12 dogs with iDCM and 8 healthy dogs. A total of 272 metabolites were detected in the plasma samples of dogs by combining three approaches but four MS-based platforms (GC-MS, LC-MS (untargeted), LC-MS (targeted), and FIA-MS (targeted) methods). Our findings demonstrated changes in the canine plasma metabolome involved in the development of iDCM, including the different concentrations of amino acids, biogenic amines, acylcarnitines, triglycerides and diglycerides, sphingomyelins, and organic acids. The results of this study will enable the detection and monitoring of pathophysiological mechanisms involved in the development of iDCM in the future.
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Affiliation(s)
- Ivana Rubić
- Laboratory of Proteomics, Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Stefan Weidt
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow G61 1QH, UK; (S.W.); (R.B.)
| | - Richard Burchmore
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow G61 1QH, UK; (S.W.); (R.B.)
| | - Alan Kovačević
- Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Josipa Kuleš
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (J.K.); (R.B.R.)
| | - Peter David Eckersall
- Institute of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK;
- Interdisciplinary Laboratory of Clinical Analysis of the University of Murcia (Interlab-UMU), Department of Animal Medicine and Surgery, Veterinary School, University of Murcia, 30100 Murcia, Spain
| | - Marin Torti
- Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (M.T.); (I.J.); (J.G.)
| | - Ines Jović
- Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (M.T.); (I.J.); (J.G.)
| | - Mislav Kovačić
- Department of Biology, University of Osijek, 31000 Osijek, Croatia;
| | - Jelena Gotić
- Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (M.T.); (I.J.); (J.G.)
| | - Renata Barić Rafaj
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (J.K.); (R.B.R.)
| | - Predrag Novak
- Department of Chemistry, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia;
| | - Marko Samardžija
- Reproduction and Obstetrics, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Vladimir Mrljak
- Laboratory of Proteomics, Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Clinic for Internal Diseases, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; (M.T.); (I.J.); (J.G.)
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5
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Cortada-Garcia J, Daly R, Arnold SA, Burgess K. Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis. Sci Rep 2023; 13:12990. [PMID: 37563133 PMCID: PMC10415327 DOI: 10.1038/s41598-023-39661-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Metabolomics is a powerful tool for the identification of genetic targets for bioprocess optimisation. However, in most cases, only the biosynthetic pathway directed to product formation is analysed, limiting the identification of these targets. Some studies have used untargeted metabolomics, allowing a more unbiased approach, but data interpretation using multivariate analysis is usually not straightforward and requires time and effort. Here we show, for the first time, the application of metabolic pathway enrichment analysis using untargeted and targeted metabolomics data to identify genetic targets for bioprocess improvement in a more streamlined way. The analysis of an Escherichia coli succinate production bioprocess with this methodology revealed three significantly modulated pathways during the product formation phase: the pentose phosphate pathway, pantothenate and CoA biosynthesis and ascorbate and aldarate metabolism. From these, the two former pathways are consistent with previous efforts to improve succinate production in Escherichia coli. Furthermore, to the best of our knowledge, ascorbate and aldarate metabolism is a newly identified target that has so far never been explored for improving succinate production in this microorganism. This methodology therefore represents a powerful tool for the streamlined identification of strain engineering targets that can accelerate bioprocess optimisation.
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Affiliation(s)
- Joan Cortada-Garcia
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, G61 1QH, UK
| | - S Alison Arnold
- Ingenza Ltd., Roslin Innovation Centre, Roslin, EH25 9RG, UK
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK.
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6
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Gilthead Seabream Liver Integrative Proteomics and Metabolomics Analysis Reveals Regulation by Different Prosurvival Pathways in the Metabolic Adaptation to Stress. Int J Mol Sci 2022; 23:ijms232315395. [PMID: 36499720 PMCID: PMC9741202 DOI: 10.3390/ijms232315395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
The study of the molecular mechanisms of stress appraisal on farmed fish is paramount to ensuring a sustainable aquaculture. Stress exposure can either culminate in the organism's adaptation or aggravate into a metabolic shutdown, characterized by irreversible cellular damage and deleterious effects on fish performance, welfare, and survival. Multiomics can improve our understanding of the complex stressed phenotype in fish and the molecular mediators that regulate the underlying processes of the molecular stress response. We profiled the stress proteome and metabolome of Sparus aurata responding to different challenges common to aquaculture production, characterizing the disturbed pathways in the fish liver, i.e., the central organ in mounting the stress response. Label-free shotgun proteomics and untargeted metabolomics analyses identified 1738 proteins and 120 metabolites, separately. Mass spectrometry data have been made fully accessible via ProteomeXchange, with the identifier PXD036392, and via MetaboLights, with the identifier MTBLS5940. Integrative multivariate statistical analysis, performed with data integration analysis for biomarker discovery using latent components (DIABLO), depicted the 10 most-relevant features. Functional analysis of these selected features revealed an intricate network of regulatory components, modulating different signaling pathways related to cellular stress, e.g., the mTORC1 pathway, the unfolded protein response, endocytosis, and autophagy to different extents according to the stress nature. These results shed light on the dynamics and extent of this species' metabolic reprogramming under chronic stress, supporting future studies on stress markers' discovery and fish welfare research.
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7
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King AJ, Daly L, Rowe J, Joy KH, Greenwood RC, Devillepoix HA, Suttle MD, Chan QH, Russell SS, Bates HC, Bryson JF, Clay PL, Vida D, Lee MR, O’Brien Á, Hallis LJ, Stephen NR, Tartèse R, Sansom EK, Towner MC, Cupak M, Shober PM, Bland PA, Findlay R, Franchi IA, Verchovsky AB, Abernethy FA, Grady MM, Floyd CJ, Van Ginneken M, Bridges J, Hicks LJ, Jones RH, Mitchell JT, Genge MJ, Jenkins L, Martin PE, Sephton MA, Watson JS, Salge T, Shirley KA, Curtis RJ, Warren TJ, Bowles NE, Stuart FM, Di Nicola L, Györe D, Boyce AJ, Shaw KM, Elliott T, Steele RC, Povinec P, Laubenstein M, Sanderson D, Cresswell A, Jull AJ, Sýkora I, Sridhar S, Harrison RJ, Willcocks FM, Harrison CS, Hallatt D, Wozniakiewicz PJ, Burchell MJ, Alesbrook LS, Dignam A, Almeida NV, Smith CL, Clark B, Humphreys-Williams ER, Schofield PF, Cornwell LT, Spathis V, Morgan GH, Perkins MJ, Kacerek R, Campbell-Burns P, Colas F, Zanda B, Vernazza P, Bouley S, Jeanne S, Hankey M, Collins GS, Young JS, Shaw C, Horak J, Jones D, James N, Bosley S, Shuttleworth A, Dickinson P, McMullan I, Robson D, Smedley AR, Stanley B, Bassom R, McIntyre M, Suttle AA, Fleet R, Bastiaens L, Ihász MB, McMullan S, Boazman SJ, Dickeson ZI, Grindrod PM, Pickersgill AE, Weir CJ, Suttle FM, Farrelly S, Spencer I, Naqvi S, Mayne B, Skilton D, Kirk D, Mounsey A, Mounsey SE, Mounsey S, Godfrey P, Bond L, Bond V, Wilcock C, Wilcock H, Wilcock R. The Winchcombe meteorite, a unique and pristine witness from the outer solar system. SCIENCE ADVANCES 2022; 8:eabq3925. [PMID: 36383648 PMCID: PMC9668287 DOI: 10.1126/sciadv.abq3925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Direct links between carbonaceous chondrites and their parent bodies in the solar system are rare. The Winchcombe meteorite is the most accurately recorded carbonaceous chondrite fall. Its pre-atmospheric orbit and cosmic-ray exposure age confirm that it arrived on Earth shortly after ejection from a primitive asteroid. Recovered only hours after falling, the composition of the Winchcombe meteorite is largely unmodified by the terrestrial environment. It contains abundant hydrated silicates formed during fluid-rock reactions, and carbon- and nitrogen-bearing organic matter including soluble protein amino acids. The near-pristine hydrogen isotopic composition of the Winchcombe meteorite is comparable to the terrestrial hydrosphere, providing further evidence that volatile-rich carbonaceous asteroids played an important role in the origin of Earth's water.
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Affiliation(s)
- Ashley J. King
- Natural History Museum, London SW7 5BD, UK
- System for Capture of Asteroid and Meteorite Paths (SCAMP), UK
- UK Fireball Alliance (UKFAll), UK
| | - Luke Daly
- UK Fireball Alliance (UKFAll), UK
- University of Glasgow, Glasgow G12 8QQ, UK
- University of Oxford, Oxford OX1 3AN, UK
- University of Sydney, Sydney 2006, NSW, Australia
- UK Fireball Network (UKFN), UK
| | - James Rowe
- System for Capture of Asteroid and Meteorite Paths (SCAMP), UK
- UK Fireball Alliance (UKFAll), UK
| | - Katherine H. Joy
- UK Fireball Alliance (UKFAll), UK
- The University of Manchester, Manchester M13 9PL, UK
| | | | | | - Martin D. Suttle
- Natural History Museum, London SW7 5BD, UK
- UK Fireball Network (UKFN), UK
- The Open University, Milton Keynes MK7 6AA, UK
| | - Queenie H. S. Chan
- The Open University, Milton Keynes MK7 6AA, UK
- Royal Holloway, University of London, Egham TW20 0EX, UK
| | | | | | | | | | - Denis Vida
- Western University, London N6A 3K7, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Finlay M. Stuart
- Scottish Universities Environmental Research Centre (SUERC), East Kilbride G75 0QF, UK
| | - Luigia Di Nicola
- Scottish Universities Environmental Research Centre (SUERC), East Kilbride G75 0QF, UK
| | - Domokos Györe
- Scottish Universities Environmental Research Centre (SUERC), East Kilbride G75 0QF, UK
- Isomass Scientific Inc., Calgary T2H 3A9, Canada
| | - Adrian J. Boyce
- Scottish Universities Environmental Research Centre (SUERC), East Kilbride G75 0QF, UK
| | | | | | | | | | | | - David Sanderson
- Scottish Universities Environmental Research Centre (SUERC), East Kilbride G75 0QF, UK
| | - Alan Cresswell
- Scottish Universities Environmental Research Centre (SUERC), East Kilbride G75 0QF, UK
| | - Anthony J. T. Jull
- University of Arizona, Tucson, AZ 85721, USA
- Institute for Nuclear Research, Debrecen, Hungary
| | - Ivan Sýkora
- Comenius University, Bratislava 842 48, Slovakia
| | | | | | | | - Catherine S. Harrison
- Natural History Museum, London SW7 5BD, UK
- The University of Manchester, Manchester M13 9PL, UK
| | - Daniel Hallatt
- University of Kent, Canterbury CT2 7NH, UK
- Université de Lille, Lille 59000, France
| | | | | | | | | | | | - Caroline L. Smith
- Natural History Museum, London SW7 5BD, UK
- University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | | | | | | | | | | | - Richard Kacerek
- UK Fireball Alliance (UKFAll), UK
- UK Meteor Observation Network (UKMON), UK
| | | | - Francois Colas
- Observatoire de Paris, Paris 75014, France
- Fireball Recovery and InterPlanetary Recovery (FRIPON), France
| | - Brigitte Zanda
- Fireball Recovery and InterPlanetary Recovery (FRIPON), France
- Muséum National d’Histoire Naturelle, Paris 75005, France
| | - Pierre Vernazza
- Fireball Recovery and InterPlanetary Recovery (FRIPON), France
- Aix-Marseille Université, Marseille 13007, France
| | - Sylvain Bouley
- Fireball Recovery and InterPlanetary Recovery (FRIPON), France
- Université Paris-Saclay, Orsay 91405, France
| | - Simon Jeanne
- Observatoire de Paris, Paris 75014, France
- Fireball Recovery and InterPlanetary Recovery (FRIPON), France
| | | | - Gareth S. Collins
- UK Fireball Alliance (UKFAll), UK
- Imperial College London, London SW7 2BP, UK
| | - John S. Young
- UK Fireball Network (UKFN), UK
- University of Cambridge, Cambridge CB2 3EQ, UK
| | - Clive Shaw
- UK Fireball Network (UKFN), UK
- University of Cambridge, Cambridge CB2 3EQ, UK
| | - Jana Horak
- System for Capture of Asteroid and Meteorite Paths (SCAMP), UK
- UK Fireball Alliance (UKFAll), UK
- Amgueddfa Cymru—National Museum Wales, Cardiff CF10 3NP, UK
| | - Dave Jones
- UK Meteor Observation Network (UKMON), UK
| | | | | | | | | | | | - Derek Robson
- UK Meteor Observation Network (UKMON), UK
- NEMETODE Network, UK
| | - Andrew R. D. Smedley
- System for Capture of Asteroid and Meteorite Paths (SCAMP), UK
- UK Fireball Alliance (UKFAll), UK
- The University of Manchester, Manchester M13 9PL, UK
| | | | - Richard Bassom
- UK Meteor Observation Network (UKMON), UK
- Global Meteor Network (GMN)
| | - Mark McIntyre
- UK Fireball Alliance (UKFAll), UK
- UK Meteor Observation Network (UKMON), UK
- Global Meteor Network (GMN)
| | | | | | | | | | - Sarah McMullan
- UK Fireball Alliance (UKFAll), UK
- UK Fireball Network (UKFN), UK
- Imperial College London, London SW7 2BP, UK
| | - Sarah J. Boazman
- European Space Research and Technology Centre (ESTEC), Keplerlaan 1, 2201 AZ Noordwijk, Netherlands
| | | | | | - Annemarie E. Pickersgill
- University of Glasgow, Glasgow G12 8QQ, UK
- Scottish Universities Environmental Research Centre (SUERC), East Kilbride G75 0QF, UK
| | | | | | | | | | | | - Ben Mayne
- Toucan Energy Ltd., London SE1 4PG, UK
| | | | - Dan Kirk
- Toucan Energy Ltd., London SE1 4PG, UK
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8
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O'Brien ÁC, Hallis LJ, Regnault C, Morrison D, Blackburn G, Steele A, Daly L, Tait A, Tremblay MM, Telenko DE, Gunn J, McKay E, Mari N, Salik MA, Ascough P, Toney J, Griffin S, Whitfield P, Lee M. Using Organic Contaminants to Constrain the Terrestrial Journey of the Martian Meteorite Lafayette. ASTROBIOLOGY 2022; 22:1351-1362. [PMID: 36264546 PMCID: PMC9618387 DOI: 10.1089/ast.2021.0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
A key part of the search for extraterrestrial life is the detection of organic molecules since these molecules form the basis of all living things on Earth. Instrument suites such as SHERLOC (Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals) onboard the NASA Perseverance rover and the Mars Organic Molecule Analyzer onboard the future ExoMars Rosalind Franklin rover are designed to detect organic molecules at the martian surface. However, size, mass, and power limitations mean that these instrument suites cannot yet match the instrumental capabilities available in Earth-based laboratories. Until Mars Sample Return, the only martian samples available for study on Earth are martian meteorites. This is a collection of largely basaltic igneous rocks that have been exposed to varying degrees of terrestrial contamination. The low organic molecule abundance within igneous rocks and the expectation of terrestrial contamination make the identification of martian organics within these meteorites highly challenging. The Lafayette martian meteorite exhibits little evidence of terrestrial weathering, potentially making it a good candidate for the detection of martian organics despite uncertainties surrounding its fall history. In this study, we used ultrapure solvents to extract organic matter from triplicate samples of Lafayette and analyzed these extracts via hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS). Two hundred twenty-four metabolites (organic molecules) were detected in Lafayette at concentrations more than twice those present in the procedural blanks. In addition, a large number of plant-derived metabolites were putatively identified, the presence of which supports the unconfirmed report that Lafayette fell in a semirural location in Indiana. Remarkably, the putative identification of the mycotoxin deoxynivalenol (or vomitoxin), alongside the report that the collector was possibly a student at Purdue University, can be used to identify the most likely fall year as 1919.
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Affiliation(s)
- Áine Clare O'Brien
- School of Geographical and Earth Sciences, University of Glasgow, Lilybank Gardens, Glasgow, UK
- SUERC, University of Glasgow, East Kilbride, UK
| | - Lydia Jane Hallis
- School of Geographical and Earth Sciences, University of Glasgow, Lilybank Gardens, Glasgow, UK
| | - Clement Regnault
- Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Switchback Rd, Bearsden, Glasgow, UK
| | | | - Gavin Blackburn
- Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Switchback Rd, Bearsden, Glasgow, UK
| | - Andrew Steele
- Carnegie Planets, Carnegie Science, Washington DC, USA
| | - Luke Daly
- School of Geographical and Earth Sciences, University of Glasgow, Lilybank Gardens, Glasgow, UK
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, Australia
- Department of Materials, University of Oxford, Oxford, UK
| | - Alastair Tait
- School of Earth, Atmosphere & Environment Monash University, Rainforest Walk Clayton, Victoria, Australia
| | - Marissa Marie Tremblay
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Darcy E.P. Telenko
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Jacqueline Gunn
- School of Professional Services, Glasgow Caledonian University, Cowcaddens Road, Glasgow, UK
| | | | - Nicola Mari
- Dipartimento di Scienze della Terra e dell'Ambiente, University of Pavia, Pavia, Italy
| | - Mohammad Ali Salik
- School of Geographical and Earth Sciences, University of Glasgow, Lilybank Gardens, Glasgow, UK
| | | | - Jaime Toney
- School of Geographical and Earth Sciences, University of Glasgow, Lilybank Gardens, Glasgow, UK
| | - Sammy Griffin
- School of Geographical and Earth Sciences, University of Glasgow, Lilybank Gardens, Glasgow, UK
| | - Phil Whitfield
- Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Switchback Rd, Bearsden, Glasgow, UK
| | - Martin Lee
- School of Geographical and Earth Sciences, University of Glasgow, Lilybank Gardens, Glasgow, UK
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9
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Alpizar-Sosa EA, Ithnin NRB, Wei W, Pountain AW, Weidt SK, Donachie AM, Ritchie R, Dickie EA, Burchmore RJS, Denny PW, Barrett MP. Amphotericin B resistance in Leishmania mexicana: Alterations to sterol metabolism and oxidative stress response. PLoS Negl Trop Dis 2022; 16:e0010779. [PMID: 36170238 PMCID: PMC9581426 DOI: 10.1371/journal.pntd.0010779] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/19/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Amphotericin B is increasingly used in treatment of leishmaniasis. Here, fourteen independent lines of Leishmania mexicana and one L. infantum line were selected for resistance to either amphotericin B or the related polyene antimicrobial, nystatin. Sterol profiling revealed that, in each resistant line, the predominant wild-type sterol, ergosta-5,7,24-trienol, was replaced by other sterol intermediates. Broadly, two different profiles emerged among the resistant lines. Whole genome sequencing then showed that these distinct profiles were due either to mutations in the sterol methyl transferase (C24SMT) gene locus or the sterol C5 desaturase (C5DS) gene. In three lines an additional deletion of the miltefosine transporter gene was found. Differences in sensitivity to amphotericin B were apparent, depending on whether cells were grown in HOMEM, supplemented with foetal bovine serum, or a serum free defined medium (DM). Metabolomic analysis after exposure to AmB showed that a large increase in glucose flux via the pentose phosphate pathway preceded cell death in cells sustained in HOMEM but not DM, indicating the oxidative stress was more significantly induced under HOMEM conditions. Several of the lines were tested for their ability to infect macrophages and replicate as amastigote forms, alongside their ability to establish infections in mice. While several AmB resistant lines showed reduced virulence, at least two lines displayed heightened virulence in mice whilst retaining their resistance phenotype, emphasising the risks of resistance emerging to this critical drug.
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Affiliation(s)
- Edubiel A. Alpizar-Sosa
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Nur Raihana Binti Ithnin
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Medical Microbiology, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Wenbin Wei
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Andrew W. Pountain
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Institute for Computational Medicine, New York University Grossman School of Medicine, New York City, New York, United States of America
| | - Stefan K. Weidt
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Anne M. Donachie
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ryan Ritchie
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Emily A. Dickie
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Richard J. S. Burchmore
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Paul W. Denny
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Michael P. Barrett
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, College of Medical, Veterinary & Life Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
- * E-mail:
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10
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Metabolomic Profiling of End-Stage Heart Failure Secondary to Chronic Chagas Cardiomyopathy. Int J Mol Sci 2022; 23:ijms231810456. [PMID: 36142367 PMCID: PMC9499603 DOI: 10.3390/ijms231810456] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Chronic Chagas cardiomyopathy (CCC) is the most frequent and severe clinical form of chronic Chagas disease, representing one of the leading causes of morbidity and mortality in Latin America, and a growing global public health problem. There is currently no approved treatment for CCC; however, omics technologies have enabled significant progress to be made in the search for new therapeutic targets. The metabolic alterations associated with pathogenic mechanisms of CCC and their relationship to cellular and immunopathogenic processes in cardiac tissue remain largely unknown. This exploratory study aimed to evaluate the potential underlying pathogenic mechanisms in the failing myocardium of patients with end-stage heart failure (ESHF) secondary to CCC by applying an untargeted metabolomic profiling approach. Cardiac tissue samples from the left ventricle of patients with ESHF of CCC etiology (n = 7) and healthy donors (n = 7) were analyzed using liquid chromatography-mass spectrometry. Metabolite profiles showed altered branched-chain amino acid and acylcarnitine levels, decreased fatty acid uptake and oxidation, increased activity of the pentose phosphate pathway, dysregulation of the TCA cycle, and alterations in critical cellular antioxidant systems. These findings suggest processes of energy deficit, alterations in substrate availability, and enhanced production of reactive oxygen species in the affected myocardium. This profile potentially contributes to the development and maintenance of a chronic inflammatory state that leads to progression and severity of CCC. Further studies involving larger sample sizes and comparisons with heart failure patients without CCC are needed to validate these results, opening an avenue to investigate new therapeutic approaches for the treatment and prevention of progression of this unique and severe cardiomyopathy.
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11
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Apostolopoulou NG, Smeti E, Lamorgese M, Varkitzi I, Whitfield P, Regnault C, Spatharis S. Microalgae show a range of responses to exometabolites of foreign species. ALGAL RES 2022; 62:None. [PMID: 35311224 PMCID: PMC8924005 DOI: 10.1016/j.algal.2021.102627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/14/2021] [Accepted: 12/23/2021] [Indexed: 12/01/2022]
Abstract
Studies on microalgae interspecific interactions have so far focused either on nutrient competition or allelopathic effects due to excreted substances from Harmful Algal Bloom (HAB) species. Evidence from plants, bacteria and specific microalgae groups, point to a range of responses mediated by sensing or direct chemical impact of exometabolites from foreign species. Such processes remain under-investigated, especially in non-HAB microalgae, despite the importance of such knowledge in ecology and industrial applications. Here, we study the directional effect of exometabolites of 4 "foreign" species Heterosigma akashiwo, Phaeocystis sp., Tetraselmis sp. and Thalassiosira sp. to each of three "target" species across a total of 12 treatments. We disentangle these effects from nutrient competition by adding cell free medium of each "foreign" species into our treatment cultures. We measured the biomass response, to the foreign exometabolites, as cell number and photosynthetic biomass (Chla), whereas nutrient use was measured as residual phosphorus (PO4) and intracellular phosphorus (P). Exometabolites from filtrate of foreign species were putatively annotated by untargeted metabolomics analysis and were discussed in association to observed responses of target species. Among others, these metabolites included L-histidinal, Tiliacorine and dimethylsulfoniopropionate (DMSP). Our findings show that species show a range of responses with the most common being biomass suppression, and less frequent biomass enhancement and intracellular P storage. Filtrate from the green microalgae Tetraselmis caused the most pronounced negative effects suggesting that non-HAB species can also cause negative chemical interference. A candidate metabolite inducing this response is L-histidinal which was measured in high abundance uniquely in Tetraselmis and its L-histidine form derived from bacteria was previously confirmed as a microalgal algicidal. H. akashiwo also induced biomass suppression on other microalgae and a candidate metabolite for this response is Tiliacorine, a plant-derived alkaloid with confirmed cytotoxic activity.
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Affiliation(s)
- Natalia G. Apostolopoulou
- Department of Ecology and Systematics, National and Kapodistrian University of Athens, 10679, Greece
- School of Life Sciences, University of Glasgow, G12 8QQ, UK
| | - Evangelia Smeti
- Institute of Marine Biological Resources and Inland Waters, HCMR Hellenic Centre for Marine Research, PO Box 713, Anavyssos 19013, Greece
| | | | - Ioanna Varkitzi
- Institute of Oceanography, HCMR Hellenic Centre for Marine Research, PO Box 713, Anavyssos 19013, Greece
| | | | | | - Sofie Spatharis
- School of Life Sciences, University of Glasgow, G12 8QQ, UK
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, G12 8QQ, UK
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12
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Multi Platforms Strategies and Metabolomics Approaches for the Investigation of Comprehensive Metabolite Profile in Dogs with Babesia canis Infection. Int J Mol Sci 2022; 23:ijms23031575. [PMID: 35163517 PMCID: PMC8835742 DOI: 10.3390/ijms23031575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
Canine babesiosis is an important tick-borne disease worldwide, caused by parasites of the Babesia genus. Although the disease process primarily affects erythrocytes, it may also have multisystemic consequences. The goal of this study was to explore and characterize the serum metabolome, by identifying potential metabolites and metabolic pathways in dogs naturally infected with Babesia canis using liquid and gas chromatography coupled to mass spectrometry. The study included 12 dogs naturally infected with B. canis and 12 healthy dogs. By combining three different analytical platforms using untargeted and targeted approaches, 295 metabolites were detected. The untargeted ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) metabolomics approach identified 64 metabolites, the targeted UHPLC-MS/MS metabolomics approach identified 205 metabolites, and the GC-MS metabolomics approach identified 26 metabolites. Biological functions of differentially abundant metabolites indicate the involvement of various pathways in canine babesiosis including the following: glutathione metabolism; alanine, aspartate, and glutamate metabolism; glyoxylate and dicarboxylate metabolism; cysteine and methionine metabolism; and phenylalanine, tyrosine, and tryptophan biosynthesis. This study confirmed that host–pathogen interactions could be studied by metabolomics to assess chemical changes in the host, such that the differences in serum metabolome between dogs with B. canis infection and healthy dogs can be detected with liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) methods. Our study provides novel insight into pathophysiological mechanisms of B. canis infection.
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Integrated Metabolomics and Proteomics Dynamics of Serum Samples Reveals Dietary Zeolite Clinoptilolite Supplementation Restores Energy Balance in High Yielding Dairy Cows. Metabolites 2021; 11:metabo11120842. [PMID: 34940600 PMCID: PMC8705350 DOI: 10.3390/metabo11120842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
Dairy cows can suffer from a negative energy balance (NEB) during their transition from the dry period to early lactation, which can increase the risk of postpartum diseases such as clinical ketosis, mastitis, and fatty liver. Zeolite clinoptilolite (CPL), due to its ion-exchange property, has often been used to treat NEB in animals. However, limited information is available on the dynamics of global metabolomics and proteomic profiles in serum that could provide a better understanding of the associated altered biological pathways in response to CPL. Thus, in the present study, a total 64 serum samples were collected from 8 control and 8 CPL-treated cows at different time points in the prepartum and postpartum stages. Labelled proteomics and untargeted metabolomics resulted in identification of 64 and 21 differentially expressed proteins and metabolites, respectively, which appear to play key roles in restoring energy balance (EB) after CPL supplementation. Joint pathway and interaction analysis revealed cross-talks among valproic acid, leucic acid, glycerol, fibronectin, and kinninogen-1, which could be responsible for restoring NEB. By using a global proteomics and metabolomics strategy, the present study concluded that CPL supplementation could lower NEB in just a few weeks, and explained the possible underlying pathways employed by CPL.
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14
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McCreath G, Whitfield PD, Roe AJ, Watson MJ, Sim MAB. A Metabolomics approach for the diagnosis Of SecondAry InfeCtions in COVID-19 (MOSAIC): a study protocol. BMC Infect Dis 2021; 21:1204. [PMID: 34856937 PMCID: PMC8637512 DOI: 10.1186/s12879-021-06832-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/29/2021] [Indexed: 01/08/2023] Open
Abstract
Background Critically ill patients with COVID-19 are at an increased risk of developing secondary bacterial infections. These are both difficult to diagnose and are associated with an increased mortality. Metabolomics may aid clinicians in diagnosing secondary bacterial infections in COVID-19 through identification and quantification of disease specific biomarkers, with the aim of identifying underlying causative microorganisms and directing antimicrobial therapy. Methods This is a multi-centre prospective diagnostic observational study. Patients with COVID-19 will be recruited from critical care units in three Scottish hospitals. Three serial blood samples will be taken from patients, and an additional sample taken if a patient shows clinical or microbiological evidence of secondary infection. Samples will be analysed using LC–MS and subjected to bioinformatic processing and statistical analysis to explore the metabolite changes associated with bacterial infections in COVID-19 patients. Comparisons of the data sets will be made with standard microbiological and biochemical methods of diagnosing infection. Discussion Metabolomics analyses may provide additional strategies for identifying secondary infections, which might permit faster initiation of specific tailored antimicrobial therapy to critically ill patients with COVID-19.
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Affiliation(s)
- Gordan McCreath
- Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, University Place, Glasgow, Scotland.
| | - Phillip D Whitfield
- Glasgow Polyomics, University of Glasgow, Garscube Campus, Glasgow, Scotland
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, University Place, Glasgow, Scotland
| | - Malcolm J Watson
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasglow, G12 8QQ, Scotland
| | - Malcolm A B Sim
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasglow, G12 8QQ, Scotland
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15
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Multi-Omics Approach to Elucidate Cerebrospinal Fluid Changes in Dogs with Intervertebral Disc Herniation. Int J Mol Sci 2021; 22:ijms222111678. [PMID: 34769107 PMCID: PMC8583948 DOI: 10.3390/ijms222111678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
Herniation of the intervertebral disc (IVDH) is the most common cause of neurological and intervertebral disc degeneration-related diseases. Since the disc starts to degenerate before it can be observed by currently available diagnostic methods, there is an urgent need for novel diagnostic approaches. To identify molecular networks and pathways which may play important roles in intervertebral disc herniation, as well as to reveal the potential features which could be useful for monitoring disease progression and prognosis, multi-omics profiling, including high-resolution liquid chromatography-mass spectrometry (LC-MS)-based metabolomics and tandem mass tag (TMT)-based proteomics was performed. Cerebrospinal fluid of nine dogs with IVDH and six healthy controls were used for the analyses, and an additional five IVDH samples were used for proteomic data validation. Furthermore, multi-omics data were integrated to decipher a complex interaction between individual omics layers, leading to an improved prediction model. Together with metabolic pathways related to amino acids and lipid metabolism and coagulation cascades, our integromics prediction model identified the key features in IVDH, namely the proteins follistatin Like 1 (FSTL1), secretogranin V (SCG5), nucleobindin 1 (NUCB1), calcitonin re-ceptor-stimulating peptide 2 precursor (CRSP2) and the metabolites N-acetyl-D-glucosamine and adenine, involved in neuropathic pain, myelination, and neurotransmission and inflammatory response, respectively. Their clinical application is to be further investigated. The utilization of a novel integrative interdisciplinary approach may provide new opportunities to apply innovative diagnostic and monitoring methods as well as improve treatment strategies and personalized care for patients with degenerative spinal disorders.
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Kuleš J, Rubić I, Beer Ljubić B, Bilić P, Barić Rafaj R, Brkljačić M, Burchmore R, Eckersall D, Mrljak V. Combined Untargeted and Targeted Metabolomics Approaches Reveal Urinary Changes of Amino Acids and Energy Metabolism in Canine Babesiosis With Different Levels of Kidney Function. Front Microbiol 2021; 12:715701. [PMID: 34603243 PMCID: PMC8484968 DOI: 10.3389/fmicb.2021.715701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Canine babesiosis is a tick-borne disease with a worldwide distribution, caused by the haemoprotozoan parasites of the genus Babesia. One of the most prevalent complication is acute kidney injury, and an early diagnosis of altered kidney function remains a challenge for veterinary practice. The aim of this study was to assess the urine metabolic profile from dogs with babesiosis and different degree of kidney function using untargeted and targeted MS-based metabolomics approaches. In this study, 22 dogs naturally infected with Babesia canis and 12 healthy dogs were included. Untargeted metabolomics approach identified 601 features with a differential abundance between the healthy group and groups of dogs with babesiosis and different level of kidney function, with 27 of them identified as a match to known standards; while targeted approach identified 17 metabolites with significantly different concentrations between the groups. A pattern of significantly altered metabolites referring to the inflammatory host response, oxidative stress, and energy metabolism modulation in babesiosis was presented. Our findings have demonstrated that kidney dysfunction accompanying canine babesiosis was associated with changes in amino acid metabolism, energy metabolism, fatty acid metabolism, and biochemical pathways such as urea cycle and ammonia detoxication. These findings will enable the inclusion of urinary markers for the detection and monitoring of renal damage in babesiosis, as well as in other similar diseases.
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Affiliation(s)
- Josipa Kuleš
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Ivana Rubić
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Blanka Beer Ljubić
- Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Petra Bilić
- Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Renata Barić Rafaj
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Mirna Brkljačić
- Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Richard Burchmore
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - David Eckersall
- College of Medical, Veterinary, and Life Sciences, Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Vladimir Mrljak
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
- Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
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17
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Feng X, Zhang W, Kuipers F, Kema I, Barcaru A, Horvatovich P. Dynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms. Anal Chim Acta 2021; 1173:338674. [PMID: 34172146 DOI: 10.1016/j.aca.2021.338674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022]
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics generates large datasets that need to be interpreted using high-performance data pre-processing tools such as XCMS, mzMine, and Progenesis. These pre-processing tools rely heavily on accurate peak detection, which depends on proper setting of the peak detection mass tolerance (PDMT). The PDMT is usually set with a fixed value in either ppm or Da units. However, this fixed value may result in duplicates or missed peak detection and inaccurate peak quantification. To improve the accuracy of peak detection, we developed the dynamic binning method, which considers peak broadening described by the physics of ion separation and sets the PDMT dynamically in function of m/z. In our method, the PDMT is proportional to (mz)2 for Fourier-transform ion cyclotron resonance (FTICR), to (mz)1.5 for Orbitrap and to m/z for Quadrupole time-of-flight (Q-TOF), and is a constant for Quadrupole mass analyzer. The dynamic binning method was implemented in XCMS [1,2], and the adopted source code is available in GitHub at https://github.com/xiaodfeng/DynamicXCMS. We have compared the performance of the XCMS implemented dynamic binning with different popular lipidomics pre-processing tools to find differential compounds. We generated set samples with 43 lipid internal standards that were differentially spiked to aliquots of one human plasma lipid sample using Orbitrap LC-MS/MS. The performance of various pipelines using matched parameter sets was quantified by a quality score system that reflects the ability of a pre-processing pipeline to detect differential peaks spiked at various concentrations. The quality score indicated that our dynamic binning method improves the quantification performance of XCMS (maximum p-value 9.8·10-3 of two-sample Wilcoxon test) over its original implementation. We also showed that the XCMS with dynamic binning found differential spiked-in lipids better or with similar performance as mzMine and Progenesis do.
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Affiliation(s)
- Xiaodong Feng
- Department of Laboratory Medicine, University Medical Center Groningen, Hanzeplein 1, 9713, GZ Groningen, the Netherlands
| | - Wenxuan Zhang
- Department of Pediatrics, University Medical Center Groningen, Hanzeplein 1, 9713, GZ Groningen, the Netherlands; Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV Groningen, the Netherlands
| | - Folkert Kuipers
- Department of Laboratory Medicine, University Medical Center Groningen, Hanzeplein 1, 9713, GZ Groningen, the Netherlands; Department of Pediatrics, University Medical Center Groningen, Hanzeplein 1, 9713, GZ Groningen, the Netherlands
| | - Ido Kema
- Department of Laboratory Medicine, University Medical Center Groningen, Hanzeplein 1, 9713, GZ Groningen, the Netherlands
| | - Andrei Barcaru
- Department of Laboratory Medicine, University Medical Center Groningen, Hanzeplein 1, 9713, GZ Groningen, the Netherlands
| | - Péter Horvatovich
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV Groningen, the Netherlands.
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Nile DL, Rae C, Walker DJ, Waddington JC, Vincent I, Burgess K, Gaze MN, Mairs RJ, Chalmers AJ. Inhibition of glycolysis and mitochondrial respiration promotes radiosensitisation of neuroblastoma and glioma cells. Cancer Metab 2021; 9:24. [PMID: 34011385 PMCID: PMC8136224 DOI: 10.1186/s40170-021-00258-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neuroblastoma accounts for 7% of paediatric malignancies but is responsible for 15% of all childhood cancer deaths. Despite rigorous treatment involving chemotherapy, surgery, radiotherapy and immunotherapy, the 5-year overall survival rate of high-risk disease remains < 40%, highlighting the need for improved therapy. Since neuroblastoma cells exhibit aberrant metabolism, we determined whether their sensitivity to radiotherapy could be enhanced by drugs affecting cancer cell metabolism. METHODS Using a panel of neuroblastoma and glioma cells, we determined the radiosensitising effects of inhibitors of glycolysis (2-DG) and mitochondrial function (metformin). Mechanisms underlying radiosensitisation were determined by metabolomic and bioenergetic profiling, flow cytometry and live cell imaging and by evaluating different treatment schedules. RESULTS The radiosensitising effects of 2-DG were greatly enhanced by combination with the antidiabetic biguanide, metformin. Metabolomic analysis and cellular bioenergetic profiling revealed this combination to elicit severe disruption of key glycolytic and mitochondrial metabolites, causing significant reductions in ATP generation and enhancing radiosensitivity. Combination treatment induced G2/M arrest that persisted for at least 24 h post-irradiation, promoting apoptotic cell death in a large proportion of cells. CONCLUSION Our findings demonstrate that the radiosensitising effect of 2-DG was significantly enhanced by its combination with metformin. This clearly demonstrates that dual metabolic targeting has potential to improve clinical outcomes in children with high-risk neuroblastoma by overcoming radioresistance.
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Affiliation(s)
- Donna L Nile
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
- Present Address: Integrated Covid Hub North East (ICHNE) Innovation Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE4 5BX, UK.
| | - Colin Rae
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - David J Walker
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Present Address: School of Medicine, University of Dundee, Dundee, DD1 4HN, UK
| | | | - Isabel Vincent
- Glasgow Polyomics Facility, University of Glasgow, Glasgow, G61 1QH, UK
- Present Address: Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Karl Burgess
- Glasgow Polyomics Facility, University of Glasgow, Glasgow, G61 1QH, UK
- Present Address: School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Mark N Gaze
- Department of Oncology, University College London Hospitals NHS Foundation Trust, London, NW1 2BU, UK
| | - Robert J Mairs
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Anthony J Chalmers
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
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19
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Rossitto G, Maiolino G, Lerco S, Ceolotto G, Blackburn G, Mary S, Antonelli G, Berton C, Bisogni V, Cesari M, Seccia TM, Lenzini L, Pinato A, Montezano A, Touyz RM, Petrie MC, Daly R, Welsh P, Plebani M, Rossi GP, Delles C. High sodium intake, glomerular hyperfiltration, and protein catabolism in patients with essential hypertension. Cardiovasc Res 2021; 117:1372-1381. [PMID: 33053160 PMCID: PMC8064429 DOI: 10.1093/cvr/cvaa205] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/28/2020] [Accepted: 07/10/2020] [Indexed: 01/01/2023] Open
Abstract
AIMS A blood pressure (BP)-independent metabolic shift towards a catabolic state upon high sodium (Na+) diet, ultimately favouring body fluid preservation, has recently been described in pre-clinical controlled settings. We sought to investigate the real-life impact of high Na+ intake on measures of renal Na+/water handling and metabolic signatures, as surrogates for cardiovascular risk, in hypertensive patients. METHODS AND RESULTS We analysed clinical and biochemical data from 766 consecutive patients with essential hypertension, collected at the time of screening for secondary causes. The systematic screening protocol included 24 h urine (24 h-u-) collection on usual diet and avoidance of renin-angiotensin-aldosterone system-confounding medications. Urinary 24 h-Na+ excretion, used to define classes of Na+ intake (low ≤2.3 g/day; medium 2.3-5 g/day; high >5 g/day), was an independent predictor of glomerular filtration rate after correction for age, sex, BP, BMI, aldosterone, and potassium excretion [P = 0.001; low: 94.1 (69.9-118.8) vs. high: 127.5 (108.3-147.8) mL/min/1.73 m2]. Renal Na+ and water handling diverged, with higher fractional excretion of Na+ and lower fractional excretion of water in those with evidence of high Na+ intake [FENa: low 0.39% (0.30-0.47) vs. high 0.81% (0.73-0.98), P < 0.001; FEwater: low 1.13% (0.73-1.72) vs. high 0.89% (0.69-1.12), P = 0.015]. Despite higher FENa, these patients showed higher absolute 24 h Na+ reabsorption and higher associated tubular energy expenditure, estimated by tubular Na+/ATP stoichiometry, accordingly [Δhigh-low = 18 (12-24) kcal/day, P < 0.001]. At non-targeted liquid chromatography/mass spectrometry plasma metabolomics in an unselected subcohort (n = 67), metabolites which were more abundant in high versus low Na+ intake (P < 0.05) mostly entailed intermediates or end products of protein catabolism/urea cycle. CONCLUSION When exposed to high Na+ intake, kidneys dissociate Na+ and water handling. In hypertensive patients, this comes at the cost of higher glomerular filtration rate, increased tubular energy expenditure, and protein catabolism from endogenous (muscle) or excess exogenous (dietary) sources. Glomerular hyperfiltration and the metabolic shift may have broad implications on global cardiovascular risk independent of BP.
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Affiliation(s)
- Giacomo Rossitto
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre 126 University Place, University of Glasgow, Glasgow G12 8TA, UK
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Giuseppe Maiolino
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Silvia Lerco
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Giulio Ceolotto
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Gavin Blackburn
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Campus, Bearsden, Glasgow G61 1BD, UK
| | - Sheon Mary
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre 126 University Place, University of Glasgow, Glasgow G12 8TA, UK
| | - Giorgia Antonelli
- Laboratory Medicine, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Chiara Berton
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Valeria Bisogni
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Maurizio Cesari
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Teresa Maria Seccia
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Livia Lenzini
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Alessio Pinato
- Laboratory Medicine, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Augusto Montezano
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre 126 University Place, University of Glasgow, Glasgow G12 8TA, UK
| | - Rhian M Touyz
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre 126 University Place, University of Glasgow, Glasgow G12 8TA, UK
| | - Mark C Petrie
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre 126 University Place, University of Glasgow, Glasgow G12 8TA, UK
| | - Ronan Daly
- Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Research Centre, Garscube Campus, Bearsden, Glasgow G61 1BD, UK
| | - Paul Welsh
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre 126 University Place, University of Glasgow, Glasgow G12 8TA, UK
| | - Mario Plebani
- Laboratory Medicine, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Gian Paolo Rossi
- Clinica dell’Ipertensione, DIMED, University of Padua, University Hospital, via Giustiniani 2, Padua 35126, Italy
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre 126 University Place, University of Glasgow, Glasgow G12 8TA, UK
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20
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Ranking Metabolite Sets by Their Activity Levels. Metabolites 2021; 11:metabo11020103. [PMID: 33670102 PMCID: PMC7916825 DOI: 10.3390/metabo11020103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/03/2021] [Accepted: 02/07/2021] [Indexed: 11/17/2022] Open
Abstract
Related metabolites can be grouped into sets in many ways, e.g., by their participation in series of chemical reactions (forming metabolic pathways), or based on fragmentation spectral similarities or shared chemical substructures. Understanding how such metabolite sets change in relation to experimental factors can be incredibly useful in the interpretation and understanding of complex metabolomics data sets. However, many of the available tools that are used to perform this analysis are not entirely suitable for the analysis of untargeted metabolomics measurements. Here, we present PALS (Pathway Activity Level Scoring), a Python library, command line tool, and Web application that performs the ranking of significantly changing metabolite sets over different experimental conditions. The main algorithm in PALS is based on the pathway level analysis of gene expression (PLAGE) factorisation method and is denoted as mPLAGE (PLAGE for metabolomics). As an example of an application, PALS is used to analyse metabolites grouped as metabolic pathways and by shared tandem mass spectrometry fragmentation patterns. A comparison of mPLAGE with two other commonly used methods (overrepresentation analysis (ORA) and gene set enrichment analysis (GSEA)) is also given and reveals that mPLAGE is more robust to missing features and noisy data than the alternatives. As further examples, PALS is also applied to human African trypanosomiasis, Rhamnaceae, and American Gut Project data. In addition, normalisation can have a significant impact on pathway analysis results, and PALS offers a framework to further investigate this. PALS is freely available from our project Web site.
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21
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Mina JGM, Charlton RL, Alpizar-Sosa E, Escrivani DO, Brown C, Alqaisi A, Borsodi MPG, Figueiredo CP, de Lima EV, Dickie EA, Wei W, Coutinho-Silva R, Merritt A, Smith TK, Barrett MP, Rossi-Bergmann B, Denny PW, Steel PG. Antileishmanial Chemotherapy through Clemastine Fumarate Mediated Inhibition of the Leishmania Inositol Phosphorylceramide Synthase. ACS Infect Dis 2021; 7:47-63. [PMID: 33291887 PMCID: PMC7802075 DOI: 10.1021/acsinfecdis.0c00546] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Current chemotherapeutics for leishmaniasis have multiple deficiencies, and there is a need for new safe, efficacious, and affordable medicines. This study describes a successful drug repurposing approach that identifies the over-the-counter antihistamine, clemastine fumarate, as a potential antileishmanial drug candidate. The screening for inhibitors of the sphingolipid synthase (inositol phosphorylceramide synthase, IPCS) afforded, following secondary screening against Leishmania major (Lmj) promastigotes, 16 active compounds. Further refinement through the dose response against LmjIPCS and intramacrophage L. major amastigotes identified clemastine fumarate with good activity and selectivity with respect to the host macrophage. On target engagement was supported by diminished sensitivity in a sphingolipid-deficient L. major mutant (ΔLmjLCB2) and altered phospholipid and sphingolipid profiles upon treatment with clemastine fumarate. The drug also induced an enhanced host cell response to infection indicative of polypharmacology. The activity was sustained across a panel of Old and New World Leishmania species, displaying an in vivo activity equivalent to the currently used drug, glucantime, in a mouse model of L. amazonensis infection. Overall, these data validate IPCS as an antileishmanial drug target and indicate that clemastine fumarate is a candidate for repurposing for the treatment of leishmaniasis.
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Affiliation(s)
- John G. M. Mina
- Departments of Chemistry, University of Durham, Science Laboratories, South Road, Durham DH1 3LE, United Kingdom
| | - Rebecca L. Charlton
- Departments of Chemistry, University of Durham, Science Laboratories, South Road, Durham DH1 3LE, United Kingdom
- Institute of Biophysics Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Edubiel Alpizar-Sosa
- Department of Biosciences, University of Durham, South Road, Durham DH1 3LE, United Kingdom
- Wellcome Centre for Integrative Parasitology and Glasgow Polyomics, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Douglas O. Escrivani
- Departments of Chemistry, University of Durham, Science Laboratories, South Road, Durham DH1 3LE, United Kingdom
- Institute of Biophysics Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Christopher Brown
- Departments of Chemistry, University of Durham, Science Laboratories, South Road, Durham DH1 3LE, United Kingdom
| | - Amjed Alqaisi
- Department of Biosciences, University of Durham, South Road, Durham DH1 3LE, United Kingdom
- Department of Biology, College of Science, University of Baghdad, Baghdad 10071, Iraq
| | - Maria Paula G. Borsodi
- Institute of Biophysics Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudia P. Figueiredo
- School of Pharmacy, Universidade Federal do Rio de Janeiro, 21944-590 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emanuelle V. de Lima
- School of Pharmacy, Universidade Federal do Rio de Janeiro, 21944-590 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emily A. Dickie
- Wellcome Centre for Integrative Parasitology and Glasgow Polyomics, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Wenbin Wei
- Department of Biosciences, University of Durham, South Road, Durham DH1 3LE, United Kingdom
| | - Robson Coutinho-Silva
- Institute of Biophysics Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andy Merritt
- LifeArc, Open Innovation Campus, Stevenage SG1 2FX, United Kingdom
| | - Terry K. Smith
- BSRC, Schools of Biology and Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, United Kingdom
| | - Michael P. Barrett
- Wellcome Centre for Integrative Parasitology and Glasgow Polyomics, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Bartira Rossi-Bergmann
- Institute of Biophysics Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, 21941-902 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paul W. Denny
- Department of Biosciences, University of Durham, South Road, Durham DH1 3LE, United Kingdom
| | - Patrick G. Steel
- Departments of Chemistry, University of Durham, Science Laboratories, South Road, Durham DH1 3LE, United Kingdom
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22
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Cockram PE, Dickie EA, Barrett MP, Smith TK. Halogenated tryptophan derivatives disrupt essential transamination mechanisms in bloodstream form Trypanosoma brucei. PLoS Negl Trop Dis 2020; 14:e0008928. [PMID: 33275612 PMCID: PMC7744056 DOI: 10.1371/journal.pntd.0008928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 12/16/2020] [Accepted: 10/19/2020] [Indexed: 12/05/2022] Open
Abstract
Amino acid metabolism within Trypanosoma brucei, the causative agent of human African trypanosomiasis, is critical for parasite survival and virulence. Of these metabolic processes, the transamination of aromatic amino acids is one of the most important. In this study, a series of halogenated tryptophan analogues were investigated for their anti-parasitic potency. Several of these analogues showed significant trypanocidal activity. Metabolomics analysis of compound-treated parasites revealed key differences occurring within aromatic amino acid metabolism, particularly within the widely reported and essential transamination processes of this parasite.
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Affiliation(s)
- Peter E. Cockram
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Emily A. Dickie
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Michael P. Barrett
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Terry K. Smith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Scotland
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23
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Serricchio M, Hierro-Yap C, Schädeli D, Ben Hamidane H, Hemphill A, Graumann J, Zíková A, Bütikofer P. Depletion of cardiolipin induces major changes in energy metabolism in Trypanosoma brucei bloodstream forms. FASEB J 2020; 35:e21176. [PMID: 33184899 DOI: 10.1096/fj.202001579rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 01/09/2023]
Abstract
The mitochondrial inner membrane glycerophospholipid cardiolipin (CL) associates with mitochondrial proteins to regulate their activities and facilitate protein complex and supercomplex formation. Loss of CL leads to destabilized respiratory complexes and mitochondrial dysfunction. The role of CL in an organism lacking a conventional electron transport chain (ETC) has not been elucidated. Trypanosoma brucei bloodstream forms use an unconventional ETC composed of glycerol-3-phosphate dehydrogenase and alternative oxidase (AOX), while the mitochondrial membrane potential (ΔΨm) is generated by the hydrolytic action of the Fo F1 -ATP synthase (aka Fo F1 -ATPase). We now report that the inducible depletion of cardiolipin synthase (TbCls) is essential for survival of T brucei bloodstream forms. Loss of CL caused a rapid drop in ATP levels and a decline in the ΔΨm. Unbiased proteomic analyses revealed a reduction in the levels of many mitochondrial proteins, most notably of Fo F1 -ATPase subunits and AOX, resulting in a strong decline of glycerol-3-phosphate-stimulated oxygen consumption. The changes in cellular respiration preceded the observed decrease in Fo F1 -ATPase stability, suggesting that the AOX-mediated ETC is the first pathway responding to the decline in CL. Select proteins and pathways involved in glucose and amino acid metabolism were upregulated to counteract the CL depletion-induced drop in cellular ATP.
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Affiliation(s)
- Mauro Serricchio
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Carolina Hierro-Yap
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - David Schädeli
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johannes Graumann
- Weill Cornell Medicine - Qatar, Doha, State of Qatar.,Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Alena Zíková
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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24
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Giordani F, Paape D, Vincent IM, Pountain AW, Fernández-Cortés F, Rico E, Zhang N, Morrison LJ, Freund Y, Witty MJ, Peter R, Edwards DY, Wilkes JM, van der Hooft JJJ, Regnault C, Read KD, Horn D, Field MC, Barrett MP. Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs. PLoS Pathog 2020; 16:e1008932. [PMID: 33141865 PMCID: PMC7710103 DOI: 10.1371/journal.ppat.1008932] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/02/2020] [Accepted: 08/25/2020] [Indexed: 01/03/2023] Open
Abstract
Livestock diseases caused by Trypanosoma congolense, T. vivax and T. brucei, collectively known as nagana, are responsible for billions of dollars in lost food production annually. There is an urgent need for novel therapeutics. Encouragingly, promising antitrypanosomal benzoxaboroles are under veterinary development. Here, we show that the most efficacious subclass of these compounds are prodrugs activated by trypanosome serine carboxypeptidases (CBPs). Drug-resistance to a development candidate, AN11736, emerged readily in T. brucei, due to partial deletion within the locus containing three tandem copies of the CBP genes. T. congolense parasites, which possess a larger array of related CBPs, also developed resistance to AN11736 through deletion within the locus. A genome-scale screen in T. brucei confirmed CBP loss-of-function as the primary mechanism of resistance and CRISPR-Cas9 editing proved that partial deletion within the locus was sufficient to confer resistance. CBP re-expression in either T. brucei or T. congolense AN11736-resistant lines restored drug-susceptibility. CBPs act by cleaving the benzoxaborole AN11736 to a carboxylic acid derivative, revealing a prodrug activation mechanism. Loss of CBP activity results in massive reduction in net uptake of AN11736, indicating that entry is facilitated by the concentration gradient created by prodrug metabolism.
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Affiliation(s)
- Federica Giordani
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Daniel Paape
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Isabel M. Vincent
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Andrew W. Pountain
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Fernando Fernández-Cortés
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Eva Rico
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ning Zhang
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Liam J. Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Yvonne Freund
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Michael J. Witty
- Global Alliance for Livestock and Veterinary Medicine, Pentlands Science Park, Penicuik, Edinburgh, United Kingdom
| | - Rosemary Peter
- Global Alliance for Livestock and Veterinary Medicine, Pentlands Science Park, Penicuik, Edinburgh, United Kingdom
| | - Darren Y. Edwards
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jonathan M. Wilkes
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Justin J. J. van der Hooft
- Glasgow Polyomics, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Current address: Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Clément Regnault
- Glasgow Polyomics, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kevin D. Read
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - David Horn
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark C. Field
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Michael P. Barrett
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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25
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Blackburn G, Hay J, Skagen C, Paul E, Achcar F, Wilson J, Best C, Manson E, Burgess K, Barrett MP, Gill JMR. Running on Empty: A Metabolomics Approach to Investigating Changing Energy Metabolism during Fasted Exercise and Rest. Metabolites 2020; 10:metabo10100399. [PMID: 33050077 PMCID: PMC7600507 DOI: 10.3390/metabo10100399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/22/2020] [Accepted: 09/28/2020] [Indexed: 01/23/2023] Open
Abstract
Understanding the metabolic processes in energy metabolism, particularly during fasted exercise, is a growing area of research. Previous work has focused on measuring metabolites pre and post exercise. This can provide information about the final state of energy metabolism in the participants, but it does not show how these processes vary during the exercise and any subsequent post-exercise period. To address this, the work described here took fasted participants and subjected them to an exercise and rest protocol under laboratory settings, which allowed for breath and blood sampling both pre, during and post exercise. Analysis of the data produced from both the physiological measurements and the untargeted metabolomics measurements showed clear switching between glycolytic and ketolytic metabolism, with the liquid chromatography-mass spectrometry (LC-MS) data showing the separate stages of ketolytic metabolism, notably the transport, release and breakdown of long chain fatty acids. Several signals, putatively identified as short peptides, were observed to change in a pattern similar to that of the ketolytic metabolites. This work highlights the power of untargeted metabolomic methods as an investigative tool for exercise science, both to follow known processes in a more complete way and discover possible novel biomarkers.
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Affiliation(s)
- Gavin Blackburn
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK; (E.M.); (M.P.B.)
- Correspondence:
| | - Joshua Hay
- Center for Preventive Cardiology, Knight Cardiovascular Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd. Portland, OR 97239, USA;
| | - Christine Skagen
- Muscle Research Group, Department of Pharmacy, University of Oslo, Sem Sælands vei 3, 0371 Oslo, Norway;
| | - Elizabeth Paul
- BHF Glasgow Cardiovascular Research Centre (GCRC), Institute of Cardiovascular & Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK; (E.P.); (J.W.); (J.M.R.G.)
| | - Fiona Achcar
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK;
| | - John Wilson
- BHF Glasgow Cardiovascular Research Centre (GCRC), Institute of Cardiovascular & Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK; (E.P.); (J.W.); (J.M.R.G.)
| | - Cameron Best
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 126 University Place, Glasgow G12 8TA, UK;
| | - Erin Manson
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK; (E.M.); (M.P.B.)
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, The University of Edinburgh, Edinburgh EH9 3FF, UK;
| | - Michael P. Barrett
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1BD, UK; (E.M.); (M.P.B.)
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK;
| | - Jason M. R. Gill
- BHF Glasgow Cardiovascular Research Centre (GCRC), Institute of Cardiovascular & Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK; (E.P.); (J.W.); (J.M.R.G.)
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26
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Liang D, Liu Q, Zhou K, Jia W, Xie G, Chen T. IP4M: an integrated platform for mass spectrometry-based metabolomics data mining. BMC Bioinformatics 2020; 21:444. [PMID: 33028191 PMCID: PMC7542974 DOI: 10.1186/s12859-020-03786-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background Metabolomics data analyses rely on the use of bioinformatics tools. Many integrated multi-functional tools have been developed for untargeted metabolomics data processing and have been widely used. More alternative platforms are expected for both basic and advanced users. Results Integrated mass spectrometry-based untargeted metabolomics data mining (IP4M) software was designed and developed. The IP4M, has 62 functions categorized into 8 modules, covering all the steps of metabolomics data mining, including raw data preprocessing (alignment, peak de-convolution, peak picking, and isotope filtering), peak annotation, peak table preprocessing, basic statistical description, classification and biomarker detection, correlation analysis, cluster and sub-cluster analysis, regression analysis, ROC analysis, pathway and enrichment analysis, and sample size and power analysis. Additionally, a KEGG-derived metabolic reaction database was embedded and a series of ratio variables (product/substrate) can be generated with enlarged information on enzyme activity. A new method, GRaMM, for correlation analysis between metabolome and microbiome data was also provided. IP4M provides both a number of parameters for customized and refined analysis (for expert users), as well as 4 simplified workflows with few key parameters (for beginners who are unfamiliar with computational metabolomics). The performance of IP4M was evaluated and compared with existing computational platforms using 2 data sets derived from standards mixture and 2 data sets derived from serum samples, from GC–MS and LC–MS respectively. Conclusion IP4M is powerful, modularized, customizable and easy-to-use. It is a good choice for metabolomics data processing and analysis. Free versions for Windows, MAC OS, and Linux systems are provided.
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Affiliation(s)
- Dandan Liang
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Quan Liu
- Human Metabolomics Institute, Inc., Shenzhen, 518109, Guangdong, China
| | - Kejun Zhou
- Human Metabolomics Institute, Inc., Shenzhen, 518109, Guangdong, China
| | - Wei Jia
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
| | - Guoxiang Xie
- Human Metabolomics Institute, Inc., Shenzhen, 518109, Guangdong, China.
| | - Tianlu Chen
- Shanghai Key Laboratory of Diabetes Mellitus and Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
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27
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Zhu YL, Li SL, Zhu CY, Wang W, Zuo WF, Qiu XJ. Metabolomics analysis of the antidepressant prescription Danzhi Xiaoyao Powder in a rat model of Chronic Unpredictable Mild Stress (CUMS). JOURNAL OF ETHNOPHARMACOLOGY 2020; 260:112832. [PMID: 32387465 DOI: 10.1016/j.jep.2020.112832] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/24/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Danzhi Xiaoyao Powder (DZXY) is a classical prescription, that has been extensively used in traditional Chinese medicine (TMC) to treat depression for many years. However, the mechanism of DZXY is still unclear. AIM OF THE STUDY The aim was to investigate the mechanism of the antidepressant effect of DZXY on a rat model of chronic unpredictable mild stress (CUMS). MATERIALS AND METHODS Forty male SD (Sprague-Dawley) rats with similar open field test (OFT) results were randomLy divided into a control group (n = 10) and an experimental group (n = 30). A depression model was established in the experimental group using the CUMS method. After the CUMS model was established successfully, the rats were randomLy divided into a depression model group and a DZXY group. The DZXY group was fed DZXY, while the depression model group and control group were given an equal amount of 0.5% sodium carboxymethyl cellulose suspension. Intragastric administration was performed once daily for 14 consecutive days. Animal weight, the sugar preference test, the open field test and the forced swimming test were used to evaluate the modeling effect and the antidepressant effect of DZXY. After the experiment, the plasma of rats was collected and the changes in plasma metabolites were analyzed by UPLC/Q-TOF-MS. The UPLC/Q-TOF-MS spectra data were evaluated by pattern recognition analysis to determine the changes in endogenous metabolites in the rat plasma samples. RESULTS The results of the behavioral investigation showed that the rat model of depression was successfully replicated and that DZXY had an antidepressant effect. Using the UPLC-MS/MS metabolomics platform, partial least squares (PLS) and orthogonal partial least squares (OPLS), metabolic profile models (R2 and Q2 ≥ 0.5) of rat plasma were successfully constructed. The model could distinguish among the control group, the depression model group and the DZXY group. Finally, 38 differential metabolites were identified in the plasma. According to KEGG (http://www.kegg.jp) pathway analysis, amino acid metabolism, lipid metabolism, purine metabolism, the prolactin signaling pathway and bile secretion were enriched and represented the main metabolic pathways influenced in the plasma. CONCLUSIONS This study successfully established a CUMS depression model. A total of 38 differential metabolites associated with depression were identified in the plasma of rats, 24 of which were modulated by DZXY. These results suggest that DZXY can improve excitability and play an antidepressant role by regulating phenylalanine metabolism, arachidonic acid metabolism, porphyrin metabolism, D-arginine and D-ornithine metabolism, steroid hormone biosynthesis, unsaturated fatty acid biosynthesis and steroid biosynthesis.
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MESH Headings
- Animals
- Antidepressive Agents/pharmacology
- Behavior, Animal/drug effects
- Biomarkers/blood
- Chromatography, High Pressure Liquid
- Depression/blood
- Depression/drug therapy
- Depression/psychology
- Disease Models, Animal
- Drugs, Chinese Herbal/pharmacology
- Energy Metabolism/drug effects
- Exploratory Behavior/drug effects
- Food Preferences/drug effects
- Male
- Metabolomics
- Motor Activity/drug effects
- Powders
- Rats, Sprague-Dawley
- Spectrometry, Mass, Electrospray Ionization
- Stress, Psychological/blood
- Stress, Psychological/drug therapy
- Stress, Psychological/psychology
- Tandem Mass Spectrometry
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Affiliation(s)
- Yong-Liang Zhu
- Medical College of Henan University of Science and Technology, Luoyang, 471023, PR China.
| | - Shuang-Long Li
- Medical College of Henan University of Science and Technology, Luoyang, 471023, PR China.
| | - Chun-Yang Zhu
- Medical College of Henan University of Science and Technology, Luoyang, 471023, PR China.
| | - Wan Wang
- Medical College of Henan University of Science and Technology, Luoyang, 471023, PR China.
| | - Wen-Fei Zuo
- Medical College of Henan University of Science and Technology, Luoyang, 471023, PR China.
| | - Xiang-Jun Qiu
- Medical College of Henan University of Science and Technology, Luoyang, 471023, PR China.
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28
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Zoltner M, Campagnaro GD, Taleva G, Burrell A, Cerone M, Leung KF, Achcar F, Horn D, Vaughan S, Gadelha C, Zíková A, Barrett MP, de Koning HP, Field MC. Suramin exposure alters cellular metabolism and mitochondrial energy production in African trypanosomes. J Biol Chem 2020; 295:8331-8347. [PMID: 32354742 PMCID: PMC7294092 DOI: 10.1074/jbc.ra120.012355] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/21/2020] [Indexed: 12/27/2022] Open
Abstract
Introduced about a century ago, suramin remains a frontline drug for the management of early-stage East African trypanosomiasis (sleeping sickness). Cellular entry into the causative agent, the protozoan parasite Trypanosoma brucei, occurs through receptor-mediated endocytosis involving the parasite's invariant surface glycoprotein 75 (ISG75), followed by transport into the cytosol via a lysosomal transporter. The molecular basis of the trypanocidal activity of suramin remains unclear, but some evidence suggests broad, but specific, impacts on trypanosome metabolism (i.e. polypharmacology). Here we observed that suramin is rapidly accumulated in trypanosome cells proportionally to ISG75 abundance. Although we found little evidence that suramin disrupts glycolytic or glycosomal pathways, we noted increased mitochondrial ATP production, but a net decrease in cellular ATP levels. Metabolomics highlighted additional impacts on mitochondrial metabolism, including partial Krebs' cycle activation and significant accumulation of pyruvate, corroborated by increased expression of mitochondrial enzymes and transporters. Significantly, the vast majority of suramin-induced proteins were normally more abundant in the insect forms compared with the blood stage of the parasite, including several proteins associated with differentiation. We conclude that suramin has multiple and complex effects on trypanosomes, but unexpectedly partially activates mitochondrial ATP-generating activity. We propose that despite apparent compensatory mechanisms in drug-challenged cells, the suramin-induced collapse of cellular ATP ultimately leads to trypanosome cell death.
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Affiliation(s)
- Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Gustavo D Campagnaro
- Institute for Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gergana Taleva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Alana Burrell
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Michela Cerone
- Institute for Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ka-Fai Leung
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Fiona Achcar
- Wellcome Centre for Integrative Parasitology and Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - David Horn
- School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Michael P Barrett
- Wellcome Centre for Integrative Parasitology and Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Harry P de Koning
- Institute for Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom .,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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29
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Buckley J, Daly R, Cobbold CA, Burgess K, Mable BK. Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses. Proc Biol Sci 2019; 286:20192109. [PMID: 31744436 DOI: 10.1098/rspb.2019.2109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce their long-term evolutionary potential. However, appropriate short-term plastic responses to new environmental conditions might not require high levels of standing genetic variation. In this study, we tested whether mating system variation among populations, and associated changes in genetic variability, affected short-term responses to environmental challenges. We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a perennial plant, Arabidopsis lyrata, under constant growth chamber conditions and an outdoor common garden environment outside its native range. We found no effect of inbreeding on survival, flowering phenology or short-term physiological responses. Specifically, naturally occurring inbreeding had no significant effects on the plasticity of metabolome profiles, using either multivariate approaches or analysis of variation in individual metabolites, with inbreeding populations showing similar physiological responses to outbreeding populations over time in both growing environments. We conclude that low genetic diversity in naturally inbred populations may not always compromise fitness or short-term physiological capacity to respond to environmental change, which could help to explain the global success of selfing mating strategies.
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Affiliation(s)
- James Buckley
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rónán Daly
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Karl Burgess
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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30
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Lim AT, Vincent IM, Barrett MP, Gilbert IH. Small Polar Hits against S. aureus: Screening, Initial Hit Optimization, and Metabolomic Studies. ACS OMEGA 2019; 4:19199-19215. [PMID: 31763544 PMCID: PMC6869403 DOI: 10.1021/acsomega.9b02507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
The global prevalence of antibacterial resistance requires new antibacterial drugs with novel chemical scaffolds and modes of action. It is also vital to design compounds with optimal physicochemical properties to permeate the bacterial cell envelope. We described an approach of combining and integrating whole cell screening and metabolomics into early antibacterial drug discovery using a library of small polar compounds. Whole cell screening of a diverse library of small polar compounds against Staphylococcus aureus gave compound 2. Hit expansion was carried out to determine structure-activity relationships. A selection of compounds from this series, together with other screened active compounds, was subjected to an initial metabolomics study to provide a metabolic fingerprint of the mode of action. It was found that compound 2 and its analogues have a different mode of action from some of the known antibacterial compounds tested. This early study highlighted the potential of whole cell screening and metabolomics in early antibacterial drug discovery. Future works will require improving potency and performing orthogonal studies to confirm the modes of action.
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Affiliation(s)
- Andrew
S. T. Lim
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
| | - Isabel M. Vincent
- Glasgow
Polyomics, University of Glasgow, Wolfson
Wohl Cancer Research Centre, Garscube Campus, Bearsden G61 1QH, U.K.
| | - Michael P. Barrett
- Glasgow
Polyomics, University of Glasgow, Wolfson
Wohl Cancer Research Centre, Garscube Campus, Bearsden G61 1QH, U.K.
- Wellcome
Centre for Molecular Parasitology, Institute of Infection, Immunity
and Inflammation, University of Glasgow, Glasgow G12 8TA, U.K.
| | - Ian H. Gilbert
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, U.K.
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31
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Megalios A, Daly R, Burgess K. MetaboCraft: building a Minecraft plugin for metabolomics. Bioinformatics 2019; 34:2693-2694. [PMID: 29608638 PMCID: PMC6061834 DOI: 10.1093/bioinformatics/bty102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/27/2018] [Indexed: 12/02/2022] Open
Abstract
Motivation The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings. Results We have developed MetaboCraft, a Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome. Availability and implementation https://github.com/argymeg/MetaboCraft/; https://hub.docker.com/r/ronandaly/metabocraft/ Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anargyros Megalios
- Glasgow Polyomics, University of Glasgow, Glasgow, UK.,Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Karl Burgess
- Glasgow Polyomics, University of Glasgow, Glasgow, UK.,Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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32
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Cottret L, Frainay C, Chazalviel M, Cabanettes F, Gloaguen Y, Camenen E, Merlet B, Heux S, Portais JC, Poupin N, Vinson F, Jourdan F. MetExplore: collaborative edition and exploration of metabolic networks. Nucleic Acids Res 2019; 46:W495-W502. [PMID: 29718355 PMCID: PMC6030842 DOI: 10.1093/nar/gky301] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/11/2018] [Indexed: 12/16/2022] Open
Abstract
Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate hypotheses on metabolic modulations. Nevertheless, performing this kind of integrative analysis is challenging for end users with not sufficiently advanced computer skills since it requires the use of various tools and web servers. MetExplore offers an all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis. In particular, it is possible to curate and annotate metabolic networks in a collaborative environment. The network exploration is also facilitated in MetExplore by a system of interactive tables connected to a powerful network visualization module. Finally, the contextualization of metabolic elements in the network and the calculation of over-representation statistics make it possible to interpret any kind of omics data. MetExplore is a sustainable project maintained since 2010 freely available at https://metexplore.toulouse.inra.fr/metexplore2/.
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Affiliation(s)
- Ludovic Cottret
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Maxime Chazalviel
- INRA, UMR1331, Toxalim, F-31000 Toulouse, France.,MedDay Pharmaceuticals, Paris, France
| | | | - Yoann Gloaguen
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany.,Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | | | | | - Stéphanie Heux
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France.,CNRS, UMR5504, F-31400 Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France.,CNRS, UMR5504, F-31400 Toulouse, France
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33
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Giordani F, Khalaf AI, Gillingwater K, Munday JC, de Koning HP, Suckling CJ, Barrett MP, Scott FJ. Novel Minor Groove Binders Cure Animal African Trypanosomiasis in an in Vivo Mouse Model. J Med Chem 2019; 62:3021-3035. [DOI: 10.1021/acs.jmedchem.8b01847] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | - Abedawn I. Khalaf
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, Glasgow G1 1XL, U.K
| | - Kirsten Gillingwater
- Parasite Chemotherapy, Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4001, Switzerland
| | | | | | - Colin J. Suckling
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, Glasgow G1 1XL, U.K
| | | | - Fraser J. Scott
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, U.K
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34
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van der Hooft JJJ, Alghefari W, Watson E, Everest P, Morton FR, Burgess KEV, Smith DGE. Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose. Metabolomics 2018; 14:144. [PMID: 30830405 PMCID: PMC6208705 DOI: 10.1007/s11306-018-1438-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/04/2018] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Campylobacter jejuni is the leading cause of foodborne bacterial enteritis in humans, and yet little is known in regard to how genetic diversity and metabolic capabilities among isolates affect their metabolic phenotype and pathogenicity. OBJECTIVES For instance, the C. jejuni 11168 strain can utilize both L-fucose and L-glutamate as a carbon source, which provides the strain with a competitive advantage in some environments and in this study we set out to assess the metabolic response of C. jejuni 11168 to the presence of L-fucose and L-glutamate in the growth medium. METHODS To achieve this, untargeted hydrophilic liquid chromatography coupled to mass spectrometry was used to obtain metabolite profiles of supernatant extracts obtained at three different time points up to 24 h. RESULTS This study identified both the depletion and the production and subsequent release of a multitude of expected and unexpected metabolites during the growth of C. jejuni 11168 under three different conditions. A large set of standards allowed identification of a number of metabolites. Further mass spectrometry fragmentation analysis allowed the additional annotation of substrate-specific metabolites. The results show that C. jejuni 11168 upon L-fucose addition indeed produces degradation products of the fucose pathway. Furthermore, methionine was faster depleted from the medium, consistent with previously-observed methionine auxotrophy. CONCLUSIONS Moreover, a multitude of not previously annotated metabolites in C. jejuni were found to be increased specifically upon L-fucose addition. These metabolites may well play a role in the pathogenicity of this C. jejuni strain.
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Affiliation(s)
| | - Wejdan Alghefari
- King Abdulaziz University, Jeddah, 21589, Kingdom of Saudi Arabia
- Institute of Biological Chemistry, Biophysics & Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, UK
| | - Eleanor Watson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, UK
| | - Paul Everest
- School of Veterinary Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK
| | - Fraser R Morton
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Karl E V Burgess
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - David G E Smith
- Institute of Biological Chemistry, Biophysics & Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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35
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Ji H, Zhang Z, Lu H. TarMet: a reactive GUI tool for efficient and confident quantification of MS based targeted metabolic and stable isotope tracer analysis. Metabolomics 2018; 14:68. [PMID: 30830368 DOI: 10.1007/s11306-018-1363-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/16/2018] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Untargeted and targeted analyses are two classes of metabolic study. Both strategies have been advanced by high resolution mass spectrometers coupled with chromatography, which have the advantages of high mass sensitivity and accuracy. State-of-art methods for mass spectrometric data sets do not always quantify metabolites of interest in a targeted assay efficiently and accurately. OBJECTIVES TarMet can quantify targeted metabolites as well as their isotopologues through a reactive and user-friendly graphical user interface. METHODS TarMet accepts vendor-neutral data files (NetCDF, mzXML and mzML) as inputs. Then it extracts ion chromatograms, detects peak position and bounds and confirms the metabolites via the isotope patterns. It can integrate peak areas for all isotopologues automatically. RESULTS TarMet detects more isotopologues and quantify them better than state-of-art methods, and it can process isotope tracer assay well. CONCLUSION TarMet is a better tool for targeted metabolic and stable isotope tracer analyses.
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Affiliation(s)
- Hongchao Ji
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
| | - Zhimin Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China.
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China.
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36
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Rosato A, Tenori L, Cascante M, De Atauri Carulla PR, Martins Dos Santos VAP, Saccenti E. From correlation to causation: analysis of metabolomics data using systems biology approaches. Metabolomics 2018; 14:37. [PMID: 29503602 PMCID: PMC5829120 DOI: 10.1007/s11306-018-1335-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Metabolomics is a well-established tool in systems biology, especially in the top-down approach. Metabolomics experiments often results in discovery studies that provide intriguing biological hypotheses but rarely offer mechanistic explanation of such findings. In this light, the interpretation of metabolomics data can be boosted by deploying systems biology approaches. OBJECTIVES This review aims to provide an overview of systems biology approaches that are relevant to metabolomics and to discuss some successful applications of these methods. METHODS We review the most recent applications of systems biology tools in the field of metabolomics, such as network inference and analysis, metabolic modelling and pathways analysis. RESULTS We offer an ample overview of systems biology tools that can be applied to address metabolomics problems. The characteristics and application results of these tools are discussed also in a comparative manner. CONCLUSIONS Systems biology-enhanced analysis of metabolomics data can provide insights into the molecular mechanisms originating the observed metabolic profiles and enhance the scientific impact of metabolomics studies.
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Affiliation(s)
- Antonio Rosato
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy.
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marta Cascante
- CIBER de Enfermedades hepáticas y digestivas (CIBERHD, Madrid) and Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Ramon De Atauri Carulla
- CIBER de Enfermedades hepáticas y digestivas (CIBERHD, Madrid) and Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.
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37
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Misra BB. New tools and resources in metabolomics: 2016-2017. Electrophoresis 2018; 39:909-923. [PMID: 29292835 DOI: 10.1002/elps.201700441] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/17/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
Rapid advances in mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based platforms for metabolomics have led to an upsurge of data every single year. Newer high-throughput platforms, hyphenated technologies, miniaturization, and tool kits in data acquisition efforts in metabolomics have led to additional challenges in metabolomics data pre-processing, analysis, interpretation, and integration. Thanks to the informatics, statistics, and computational community, new resources continue to develop for metabolomics researchers. The purpose of this review is to provide a summary of the metabolomics tools, software, and databases that were developed or improved during 2016-2017, thus, enabling readers, developers, and researchers access to a succinct but thorough list of resources for further improvisation, implementation, and application in due course of time.
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Affiliation(s)
- Biswapriya B Misra
- Department of Internal Medicine, Section of Molecular Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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