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Linney JA, Routledge SJ, Connell SD, Larson TR, Pitt AR, Jenkinson ER, Goddard AD. Identification of membrane engineering targets for increased butanol tolerance in Clostridium saccharoperbutylacetonicum. Biochim Biophys Acta Biomembr 2023; 1865:184217. [PMID: 37648011 DOI: 10.1016/j.bbamem.2023.184217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/17/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
There is a growing interest in the use of microbial cell factories to produce butanol, an industrial solvent and platform chemical. Biobutanol can also be used as a biofuel and represents a cleaner and more sustainable alternative to the use of conventional fossil fuels. Solventogenic Clostridia are the most popular microorganisms used due to the native expression of butanol synthesis pathways. A major drawback to the wide scale implementation and development of these technologies is the toxicity of butanol. Various membrane properties and related functions are perturbed by the interaction of butanol with the cell membrane, causing lower yields and higher purification costs. This is ultimately why the technology remains underemployed. This study aimed to develop a deeper understanding of butanol toxicity at the membrane to determine future targets for membrane engineering. Changes to the lipidome in Clostridium saccharoperbutylacetonicum N1-4 (HMT) throughout butanol fermentation were investigated with thin layer chromatography and mass spectrometry. By the end of fermentation, levels of phosphatidylglycerol lipids had increased significantly, suggesting an important role of these lipid species in tolerance to butanol. Using membrane models and in vitro assays to investigate characteristics such as permeability, fluidity, and swelling, it was found that altering the composition of membrane models can convey tolerance to butanol, and that modulating membrane fluidity appears to be a key factor. Data presented here will ultimately help to inform rational strain engineering efforts to produce more robust strains capable of producing higher butanol titres.
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Affiliation(s)
- John A Linney
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Sarah J Routledge
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Simon D Connell
- School of Physics and Astronomy and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Tony R Larson
- Department of Biology, University of York, York YO10 5DD, UK
| | - Andrew R Pitt
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | | | - Alan D Goddard
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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2
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Tharmasothirajan A, Melcr J, Linney J, Gensch T, Krumbach K, Ernst KM, Brasnett C, Poggi P, Pitt AR, Goddard AD, Chatgilialoglu A, Marrink SJ, Marienhagen J. Membrane manipulation by free fatty acids improves microbial plant polyphenol synthesis. Nat Commun 2023; 14:5619. [PMID: 37699874 PMCID: PMC10497605 DOI: 10.1038/s41467-023-40947-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 08/16/2023] [Indexed: 09/14/2023] Open
Abstract
Microbial synthesis of nutraceutically and pharmaceutically interesting plant polyphenols represents a more environmentally friendly alternative to chemical synthesis or plant extraction. However, most polyphenols are cytotoxic for microorganisms as they are believed to negatively affect cell integrity and transport processes. To increase the production performance of engineered cell factories, strategies have to be developed to mitigate these detrimental effects. Here, we examine the accumulation of the stilbenoid resveratrol in the cell membrane and cell wall during its production using Corynebacterium glutamicum and uncover the membrane rigidifying effect of this stilbenoid experimentally and with molecular dynamics simulations. A screen of free fatty acid supplements identifies palmitelaidic acid and linoleic acid as suitable additives to attenuate resveratrol's cytotoxic effects resulting in a three-fold higher product titer. This cost-effective approach to counteract membrane-damaging effects of product accumulation is transferable to the microbial production of other polyphenols and may represent an engineering target for other membrane-active bioproducts.
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Affiliation(s)
- Apilaasha Tharmasothirajan
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - John Linney
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK
| | - Thomas Gensch
- Institute for Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Karin Krumbach
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Karla Marlen Ernst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Christopher Brasnett
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Paola Poggi
- Remembrane Srl, via San Francesco 40, 40026, Imola, Italy
| | - Andrew R Pitt
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, Manchester, UK
| | - Alan D Goddard
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK
| | | | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
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3
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Hällqvist J, Lane D, Shapanis A, Davis K, Heywood WE, Doykov I, Śpiewak J, Ghansah N, Keevil B, Gupta P, Jukes-Jones R, Singh R, Foley D, Vissers JPC, Pattison R, Ferries S, Wardle R, Bartlett A, Calton LJ, Anderson L, Razavi M, Pearson T, Pope M, Yip R, Ng LL, Nicholas BI, Bailey A, Noel D, Dalton RN, Heales S, Hopley C, Pitt AR, Barran P, Jones DJL, Mills K, Skipp P, Carling RS. Operation Moonshot: rapid translation of a SARS-CoV-2 targeted peptide immunoaffinity liquid chromatography-tandem mass spectrometry test from research into routine clinical use. Clin Chem Lab Med 2023; 61:302-310. [PMID: 36395058 DOI: 10.1515/cclm-2022-1000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Abstract
OBJECTIVES During 2020, the UK's Department of Health and Social Care (DHSC) established the Moonshot programme to fund various diagnostic approaches for the detection of SARS-CoV-2, the pathogen behind the COVID-19 pandemic. Mass spectrometry was one of the technologies proposed to increase testing capacity. METHODS Moonshot funded a multi-phase development programme, bringing together experts from academia, industry and the NHS to develop a state-of-the-art targeted protein assay utilising enrichment and liquid chromatography tandem mass spectrometry (LC-MS/MS) to capture and detect low levels of tryptic peptides derived from SARS-CoV-2 virus. The assay relies on detection of target peptides, ADETQALPQRK (ADE) and AYNVTQAFGR (AYN), derived from the nucleocapsid protein of SARS-CoV-2, measurement of which allowed the specific, sensitive, and robust detection of the virus from nasopharyngeal (NP) swabs. The diagnostic sensitivity and specificity of LC-MS/MS was compared with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) via a prospective study. RESULTS Analysis of NP swabs (n=361) with a median RT-qPCR quantification cycle (Cq) of 27 (range 16.7-39.1) demonstrated diagnostic sensitivity of 92.4% (87.4-95.5), specificity of 97.4% (94.0-98.9) and near total concordance with RT-qPCR (Cohen's Kappa 0.90). Excluding Cq>32 samples, sensitivity was 97.9% (94.1-99.3), specificity 97.4% (94.0-98.9) and Cohen's Kappa 0.95. CONCLUSIONS This unique collaboration between academia, industry and the NHS enabled development, translation, and validation of a SARS-CoV-2 method in NP swabs to be achieved in 5 months. This pilot provides a model and pipeline for future accelerated development and implementation of LC-MS/MS protein/peptide assays into the routine clinical laboratory.
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Affiliation(s)
- Jenny Hällqvist
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
- UCL Queen Square Institute of Neurology, London, UK
| | - Dan Lane
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- Leicester Diabetes Centre, University of Leicester, Leicester General Hospital, Leicester, UK
| | - Andrew Shapanis
- Centre for Proteomic Research, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Kayleigh Davis
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
| | - Wendy E Heywood
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Ivan Doykov
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Justyna Śpiewak
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Nana Ghansah
- Neurometabolic Unit, National Hospital, London, UK
| | - Brian Keevil
- Department of Biochemistry, Manchester University NHS Trust, Manchester, UK
| | - Pankaj Gupta
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Rebekah Jukes-Jones
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Raj Singh
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Dominic Foley
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | | | - Rebecca Pattison
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Samantha Ferries
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Robert Wardle
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Amy Bartlett
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Lisa J Calton
- Waters Corporation, Wilmslow, UK
- Waters Corporation, Milford, MA, USA
| | - Leigh Anderson
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Terry Pearson
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Matt Pope
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Richard Yip
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
- SISCAPA Assay Technologies, Inc., Victoria, BC, Canada
| | - Leong L Ng
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | | | - Alistair Bailey
- Centre for Proteomic Research, University of Southampton, Southampton, UK
| | - Dan Noel
- Biological Sciences, University of Southampton, Southampton, UK
| | - R Neil Dalton
- WellChild Laboratory, Evelina London Children's Hospital, London, UK
| | - Simon Heales
- Neurometabolic Unit, National Hospital, London, UK
| | | | - Andrew R Pitt
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Perdita Barran
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Donald J L Jones
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Kevin Mills
- University College London Translational Mass Spectrometry Research Group Unit, London, UK
| | - Paul Skipp
- Centre for Proteomic Research, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Rachel S Carling
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
- GKT School Medical Education, Kings College London, London, UK
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Lairón-Peris M, Castiglioni GL, Routledge SJ, Alonso-Del-Real J, Linney JA, Pitt AR, Melcr J, Goddard AD, Barrio E, Querol A. Adaptive response to wine selective pressures shapes the genome of a Saccharomyces interspecies hybrid. Microb Genom 2021; 7. [PMID: 34448691 PMCID: PMC8549368 DOI: 10.1099/mgen.0.000628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
During industrial processes, yeasts are exposed to harsh conditions, which eventually lead to adaptation of the strains. In the laboratory, it is possible to use experimental evolution to link the evolutionary biology response to these adaptation pressures for the industrial improvement of a specific yeast strain. In this work, we aimed to study the adaptation of a wine industrial yeast in stress conditions of the high ethanol concentrations present in stopped fermentations and secondary fermentations in the processes of champagne production. We used a commercial Saccharomyces cerevisiae × S. uvarum hybrid and assessed its adaptation in a modified synthetic must (M-SM) containing high ethanol, which also contained metabisulfite, a preservative that is used during wine fermentation as it converts to sulfite. After the adaptation process under these selected stressful environmental conditions, the tolerance of the adapted strain (H14A7-etoh) to sulfite and ethanol was investigated, revealing that the adapted hybrid is more resistant to sulfite compared to the original H14A7 strain, whereas ethanol tolerance improvement was slight. However, a trade-off in the adapted hybrid was found, as it had a lower capacity to ferment glucose and fructose in comparison with H14A7. Hybrid genomes are almost always unstable, and different signals of adaptation on H14A7-etoh genome were detected. Each subgenome present in the adapted strain had adapted differently. Chromosome aneuploidies were present in S. cerevisiae chromosome III and in S. uvarum chromosome VII–XVI, which had been duplicated. Moreover, S. uvarum chromosome I was not present in H14A7-etoh and a loss of heterozygosity (LOH) event arose on S. cerevisiae chromosome I. RNA-sequencing analysis showed differential gene expression between H14A7-etoh and H14A7, which can be easily correlated with the signals of adaptation that were found on the H14A7-etoh genome. Finally, we report alterations in the lipid composition of the membrane, consistent with conserved tolerance mechanisms.
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Affiliation(s)
- María Lairón-Peris
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Gabriel L Castiglioni
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Sarah J Routledge
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Javier Alonso-Del-Real
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - John A Linney
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Andrew R Pitt
- College of Health and Life Sciences, Aston University, Birmingham, UK.,Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, Manchester, UK
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Material, University of Groningen, Groningen, The Netherlands
| | - Alan D Goddard
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
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5
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Abstract
The tumor suppressor phosphatase and tensin homologue (PTEN) is a redox-sensitive dual specificity phosphatase with an essential role in the negative regulation of the PI3K-AKT signaling pathway, affecting metabolic and cell survival processes. PTEN is commonly mutated in cancer, and dysregulation in the metabolism of PIP3 is implicated in other diseases such as diabetes. PTEN interactors are responsible for some functional roles of PTEN beyond the negative regulation of the PI3K pathway and are thus of great importance in cell biology. Both high-data content proteomics-based approaches and low-data content PPI approaches have been used to investigate the interactome of PTEN and elucidate further functions of PTEN. While low-data content approaches rely on co-immunoprecipitation and Western blotting, and as such require previously generated hypotheses, high-data content approaches such as affinity pull-down proteomic assays or the yeast 2-hybrid system are hypothesis generating. This review provides an overview of the PTEN interactome, including redox effects, and critically appraises the methods and results of high-data content investigations into the global interactome of PTEN. The biological significance of findings from recent studies is discussed and illustrates the breadth of cellular functions of PTEN that can be discovered by these approaches.
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Affiliation(s)
- Sarah L Smith
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, U.K
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, U.K.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, U.K
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6
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Campos-Pinto I, Méndez L, Schouten J, Wilkins J, Fedorova M, Pitt AR, Davis P, Spickett CM. Epitope mapping and characterization of 4-hydroxy-2-nonenal modified-human serum albumin using two different polyclonal antibodies. Free Radic Biol Med 2019; 144:234-244. [PMID: 31075498 DOI: 10.1016/j.freeradbiomed.2019.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 12/28/2022]
Abstract
Lipids are susceptible to damage by reactive oxygen species, and from lipid oxidation reactions many short chain lipid peroxidation products can be formed. 4-Hydroxy-2-nonenal (HNE) is one of the most abundant and cytotoxic lipid oxidation products and is known to form covalent adducts with nucleophilic amino acids of proteins. HNE-modified proteins have value as biomarkers and can be detected by antibody-based techniques, but most commercially available antibodies were raised against HNE-keyhole limpet hemocyanin. We used HNE-treated human serum albumin (HSA) to raise sheep antiserum and report for the first time the use of covalently modified peptide arrays to assess epitope binding of antibodies (Abs). Peptide arrays covering the sequence of HSA and treated post peptide synthesis with HNE were used to compare the different binding patterns of a commercial polyclonal antibody (pAb) raised against HNE-treated KLH and an in-house anti-HNE enriched pAb. The results were correlated with analysis of HNE-modified HSA by high-resolution tandem mass spectrometry. Both anti-HNE pAbs were found to bind strongly to eight common peptides on the HNE-treated HSA membranes, suggesting that HNE adducts per se induced an immune response in both cases even though different immunogens were used. Both antibodies bound with the highest affinity to the peptide 365DPHECYAKVFDEFKPLV381, which contains K378 and was also shown to be modified by the mass spectrometry analysis. Overall, the commercial anti-HNE pAb showed better specificity, recognizing nine out of the eleven adducts found by MS/MS, while the in-house enriched pAb only recognizes six. Nevertheless, the in-house pAb recognized specific peptides that were not recognized by the commercial pAb, which suggests the presence of clones uniquely specific to HNE adducts on HSA.
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Affiliation(s)
- Isabel Campos-Pinto
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YA, UK; School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Lucía Méndez
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany; Institute of Marine Research, Spanish Council for Scientific Resesarch, (IIM-CSIC), Vigo, Spain
| | - James Schouten
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YA, UK
| | - John Wilkins
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YA, UK
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Paul Davis
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YA, UK
| | - Corinne M Spickett
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
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7
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Sousa BC, Ahmed T, Dann WL, Ashman J, Guy A, Durand T, Pitt AR, Spickett CM. Short-chain lipid peroxidation products form covalent adducts with pyruvate kinase and inhibit its activity in vitro and in breast cancer cells. Free Radic Biol Med 2019; 144:223-233. [PMID: 31173844 DOI: 10.1016/j.freeradbiomed.2019.05.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/10/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
Pyruvate kinase catalyses the last step in glycolysis and has been suggested to contribute to the regulation of aerobic glycolysis in cancer cells. It can be inhibited by oxidation of cysteine residues in vitro and in vivo, which is relevant to the more pro-oxidant state in cancer and proliferating tissues. These conditions also favour lipid peroxidation and the formation of electrophilic fragmentation products, including short-chain aldehydes that can covalently modify proteins. However, as yet few studies have investigated their interactions with pyruvate kinase, so we investigated the effects of three different aldehydes, acrolein, malondialdehyde and 4-hydroxy-2(E)-hexenal (HHE), on the structure and activity of the enzyme. Analysis by LC-MS/MS showed unique modification profiles for each aldehyde, but Cys152, Cys423 and Cys474 were the residues most susceptible to electrophilic modification. Analysis of enzymatic activity under these conditions showed that acrolein was the strongest inhibitor, and at incubation times longer than 2 h, pathophysiological concentrations induced significant effects. Treatment of MCF-7 cells with the aldehydes caused similar losses of pyruvate kinase activity to those observed in vitro, and at lower concentrations than those required to cause cell death, with time and dose-dependent effects; acrolein adducts on Cys152 and Cys358 were detected. Cys358 and Cys474 are located at or near the allosteric or active sites, and formation of adducts on these residues probably contributes to loss of activity at low treatment concentrations. This study provides the first detailed analysis of the structure-activity relationship of C3 and C6 aldehydes with pyruvate kinase, and suggests that reactive short-chain aldehydes generated in diseases with an oxidative aetiology or from environmental exposure such as smoking could be involved in the metabolic alterations observed in cancer cells, through alteration of pyruvate kinase activity.
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Affiliation(s)
- Bebiana C Sousa
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Tanzim Ahmed
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - William L Dann
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Jed Ashman
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Alexandre Guy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston Triangle, Aston University, B4 7ET, Birmingham, UK.
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8
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Ni Z, Sousa BC, Colombo S, Afonso CB, Melo T, Pitt AR, Spickett CM, Domingues P, Domingues MR, Fedorova M, Criscuolo A. Evaluation of air oxidized PAPC: A multi laboratory study by LC-MS/MS. Free Radic Biol Med 2019; 144:156-166. [PMID: 31212065 DOI: 10.1016/j.freeradbiomed.2019.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/29/2019] [Accepted: 06/10/2019] [Indexed: 01/18/2023]
Abstract
Oxidized LDL (oxLDL) has been shown to play a crucial role in the onset and development of cardiovascular disorders. The study of oxLDL, as an initiator of inflammatory cascades, led to the discovery of a variety of oxidized phospholipids (oxPLs) responsible for pro-inflammatory actions. Oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PAPC) is frequently used by the scientific community as a representative oxPL mixture to study the biological effects of oxidized lipids, due to the high abundance of PAPC in human tissues and the biological activities of oxidized arachidonic acids derivatives. Most studies focusing on oxPAPC effects rely on in-house prepared mixtures of oxidized species obtained by exposing PAPC to air oxidation. Here, we described a multi-laboratory evaluation of the compounds in oxPAPC by LC-MS/MS, focusing on the identification and relative quantification of the lipid peroxidation products (LPPs) formed. PAPC was air-oxidized in four laboratories using the same protocol for 0, 48, and 72 h. It was possible to identify 55 different LPPs with unique elemental composition and characterize different structural isomeric species within these. The study showed good intra-sample reproducibility and similar qualitative patterns of oxidation, as the most abundant LPPs were essentially the same between the four laboratories. However, there were substantial differences in the extent of oxidation, i.e. the amount of LPPs relative to unmodified PAPC, at specific time points. This shows the importance of characterizing air-oxidized PAPC preparations before using them for testing biological effects of oxidized lipids, and may explain some variability of effects reported in the literature.
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Affiliation(s)
- Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Germany
| | - Bebiana C Sousa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Simone Colombo
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Catarina B Afonso
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Tania Melo
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal; Department of Chemistry & CESAM & ECOMARE, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Corinne M Spickett
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Pedro Domingues
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - M Rosário Domingues
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Germany
| | - Angela Criscuolo
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Germany; Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath-Str. 11, 28199, Bremen, Germany.
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9
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Sobczak M, Pitt AR, Spickett CM, Robaszkiewicz A. PARP1 Co-Regulates EP300-BRG1-Dependent Transcription of Genes Involved in Breast Cancer Cell Proliferation and DNA Repair. Cancers (Basel) 2019; 11:E1539. [PMID: 31614656 PMCID: PMC6826995 DOI: 10.3390/cancers11101539] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/24/2019] [Accepted: 10/05/2019] [Indexed: 12/12/2022] Open
Abstract
BRG1, an active subunit of the SWI/SNF chromatin-remodeling complex, enables the EP300-dependent transcription of proliferation and DNA repair genes from their E2F/CpG-driven promoters in breast cancer cells. In the current study, we show that BRG1-EP300 complexes are accompanied by poly-ADP-ribose polymerase 1 (PARP1), which emerges as the functional component of the promoter-bound multiprotein units that are capable of controlling gene expression. This enzyme is co-distributed with BRG1 at highly acetylated promoters of genes such as CDK4, LIG1, or NEIL3, which are responsible for cancer cell growth and the removal of DNA damage. ADP-ribosylation is necessary to maintain active transcription, since it ensures an open chromatin structure that allows high acetylation and low histone density. PARP1-mediated modification of BRG1 and EP300 does not affect the association of enzymes with gene promoters; however, it does activate EP300, which acetylates nucleosomes, leading to their eviction by BRG1, thus allowing mRNA synthesis. Although PARP1 was found at BRG1 positive/H3K27ac negative promoters of highly expressed genes in a transformed breast cancer cell line, its transcriptional activity was limited to genes simultaneously controlled by BRG1 and EP300, indicating that the ADP-ribosylation of EP300 plays a dominant role in the regulation of BRG1-EP300-driven transcription. In conclusion, PARP1 directs the transcription of some proliferation and DNA repair genes in breast cancer cells by the ADP-ribosylation of EP300, thereby causing its activation and marking nucleosomes for displacement by BRG1. PARP1 in rapidly dividing cells facilitates the expression of genes that confer a cancer cell phenotype. Our study shows a new mechanism that links PARP1 with the removal of DNA damage in breast cancer cells via the regulation of BRG1-EP300-dependent transcription of genes involved in DNA repair pathways.
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Affiliation(s)
- Maciej Sobczak
- Department of General Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
| | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| | - Corinne M Spickett
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
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10
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Rossin D, Dias IHK, Solej M, Milic I, Pitt AR, Iaia N, Scoppapietra L, Devitt A, Nano M, Degiuli M, Volante M, Caccia C, Leoni V, Griffiths HR, Spickett CM, Poli G, Biasi F. Increased production of 27-hydroxycholesterol in human colorectal cancer advanced stage: Possible contribution to cancer cell survival and infiltration. Free Radic Biol Med 2019; 136:35-44. [PMID: 30910555 DOI: 10.1016/j.freeradbiomed.2019.03.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 02/08/2023]
Abstract
So far, the investigation in cancer cell lines of the modulation of cancer growth and progression by oxysterols, in particular 27-hydroxycholesterol (27HC), has yielded controversial results. The primary aim of this study was the quantitative evaluation of possible changes in 27HC levels during the different steps of colorectal cancer (CRC) progression in humans. A consistent increase in this oxysterol in CRC mass compared to the tumor-adjacent tissue was indeed observed, but only in advanced stages of progression (TNM stage III), a phase in which cancer has spread to nearby sites. To investigate possible pro-tumor properties of 27HC, its effects were studied in vitro in differentiated CaCo-2 cells. Relatively high concentrations of this oxysterol markedly increased the release of pro-inflammatory interleukins 6 and 8, monocyte chemoattractant protein-1, vascular endothelial growth factor, as well as matrix metalloproteinases 2 and 9. The up-regulation of all these molecules, which are potentially able to favor cancer progression, appeared to be dependent upon a net stimulation of Akt signaling exerted by supra-physiological amounts of 27HC.
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Affiliation(s)
- D Rossin
- Dept. of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
| | - I H K Dias
- Aston Research Centre for Healthy Ageing, School of Life and Health Sciences, Aston University, Birmingham, UK.
| | - M Solej
- Dept. of Oncology, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
| | - I Milic
- Aston Research Centre for Healthy Ageing, School of Life and Health Sciences, Aston University, Birmingham, UK.
| | - A R Pitt
- Aston Research Centre for Healthy Ageing, School of Life and Health Sciences, Aston University, Birmingham, UK.
| | - N Iaia
- Dept. of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
| | - L Scoppapietra
- Dept. of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
| | - A Devitt
- Aston Research Centre for Healthy Ageing, School of Life and Health Sciences, Aston University, Birmingham, UK.
| | - M Nano
- Dept. of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
| | - M Degiuli
- Dept. of Oncology, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
| | - M Volante
- Dept. of Oncology, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
| | - C Caccia
- Genetics of Neurodegenerative and Metabolic Diseases, Dept. of Applied Diagnostic, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - V Leoni
- Department of Laboratory Medicine, University of Milano-Bicocca, School of Medicine, Hospital of Desio, Desio, Milan, Italy.
| | - H R Griffiths
- Health and Medical Sciences, University of Surrey, Guildford, UK.
| | - C M Spickett
- Aston Research Centre for Healthy Ageing, School of Life and Health Sciences, Aston University, Birmingham, UK.
| | - G Poli
- Dept. of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
| | - F Biasi
- Dept. of Clinical and Biological Sciences, San Luigi Hospital, University of Turin, Orbassano, Turin, Italy.
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11
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Khalaf AI, Pitt AR, Scobie M, Suckling CJ, Urwin J, Waigh RD, Fishleigh RV, Young SC. Synthesis of Novel Dna Binding Agents: Indole-Containing Analogues of Bis-Netropsin. Journal of Chemical Research 2019. [DOI: 10.3184/030823400103167444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Molecular modelling studies showed that indole dicarboxylic acids are potential linkers for the synthesis of bis-netropsin analogues with a good fit to the minor groove of DNA. To test this hypothesis, 2-carboxyindole-6-acetic acid, indole-2,6-dicarboxylic acid, 6-(2-carboxyethyl)indole-2-carboxylic acid, 6-(2-carboxy-1-ethenyl)indole-2-carboxylic acid were prepared and coupled to 3-[1-methyl-4-(1-methyl-4-aminopyrrole-2-carboxamido)pyrrole-2-carboxamido]dimethylaminopropane. Similarly indole-2,5-dicarboxylic acid was prepared and coupled to 3-[1-methyl-4-(1-methyl-4-aminopyrrple-2-carboxamido)pyrrole-2-carboxamido]propionamidine hydrochloride. The derivatives of 26–28 showed especially strong binding to AT rich regions as shown by footprinting studies.
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Affiliation(s)
- Abedawn I Khalaf
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Andrew R. Pitt
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Martin Scobie
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Colin J. Suckling
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - John Urwin
- Deparment of Pharmaceutical Sciences, Strathclyde Institute for Biomedical Sciences, 27 Taylor Street, Glasgow G4 0NR, UK
| | - Roger D. Waigh
- Deparment of Pharmaceutical Sciences, Strathclyde Institute for Biomedical Sciences, 27 Taylor Street, Glasgow G4 0NR, UK
| | - Robert V. Fishleigh
- Proteus International, Proteus House, Lyme Green Business Park, Macclesfield, Cheshire, UK
| | - Stephen C. Young
- Proteus International, Proteus House, Lyme Green Business Park, Macclesfield, Cheshire, UK
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12
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Teo ACK, Lee SC, Pollock NL, Stroud Z, Hall S, Thakker A, Pitt AR, Dafforn TR, Spickett CM, Roper DI. Analysis of SMALP co-extracted phospholipids shows distinct membrane environments for three classes of bacterial membrane protein. Sci Rep 2019; 9:1813. [PMID: 30755655 PMCID: PMC6372662 DOI: 10.1038/s41598-018-37962-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/05/2018] [Indexed: 11/24/2022] Open
Abstract
Biological characterisation of membrane proteins lags behind that of soluble proteins. This reflects issues with the traditional use of detergents for extraction, as the surrounding lipids are generally lost, with adverse structural and functional consequences. In contrast, styrene maleic acid (SMA) copolymers offer a detergent-free method for biological membrane solubilisation to produce SMA-lipid particles (SMALPs) containing membrane proteins together with their surrounding lipid environment. We report the development of a reverse-phase LC-MS/MS method for bacterial phospholipids and the first comparison of the profiles of SMALP co-extracted phospholipids from three exemplar bacterial membrane proteins with different topographies: FtsA (associated membrane protein), ZipA (single transmembrane helix), and PgpB (integral membrane protein). The data showed that while SMA treatment per se did not preferentially extract specific phospholipids from the membrane, SMALP-extracted ZipA showed an enrichment in phosphatidylethanolamines and depletion in cardiolipins compared to the bulk membrane lipid. Comparison of the phospholipid profiles of the 3 SMALP-extracted proteins revealed distinct lipid compositions for each protein: ZipA and PgpB were similar, but in FtsA samples longer chain phosphatidylglycerols and phosphatidylethanolamines were more abundant. This method offers novel information on the phospholipid interactions of these membrane proteins.
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Affiliation(s)
- Alvin C K Teo
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry, CV4 7AL, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Naomi L Pollock
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Zoe Stroud
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stephen Hall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alpesh Thakker
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - David I Roper
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry, CV4 7AL, UK.
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13
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Knight AR, Taylor EL, Lukaszewski R, Jensen KT, Jones HE, Carré JE, Isupov MN, Littlechild JA, Bailey SJ, Brewer E, McDonald TJ, Pitt AR, Spickett CM, Winyard PG. A high-sensitivity electrochemiluminescence-based ELISA for the measurement of the oxidative stress biomarker, 3-nitrotyrosine, in human blood serum and cells. Free Radic Biol Med 2018; 120:246-254. [PMID: 29555590 DOI: 10.1016/j.freeradbiomed.2018.03.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 02/02/2023]
Abstract
The generation of 3-nitrotyrosine, within proteins, is a post-translational modification resulting from oxidative or nitrative stress. It has been suggested that this modification could be used as a biomarker for inflammatory diseases. Despite the superiority of mass spectrometry-based determinations of nitrotyrosine, in a high-throughput clinical setting the measurement of nitrotyrosine by an enzyme-linked immunosorbent assay (ELISA) is likely to be more cost-effective. ELISAs offer an alternative means to detect nitrotyrosine, but many commercially available ELISAs are insufficiently sensitive to detect nitrotyrosine in healthy human serum. Here, we report the development, validation and clinical application of a novel electrochemiluminescence-based ELISA for nitrotyrosine which provides superior sensitivity (e.g. a 50-fold increase in sensitivity compared with one of the tested commercial colorimetric ELISAs). This nitrotyrosine ELISA has the following characteristics: a lower limit of quantitation of 0.04 nM nitrated albumin equivalents; intra- and inter-assay coefficients of variation of 6.5% and 11.3%, respectively; a mean recovery of 106 ± 3% and a mean linearity of 0.998 ± 0.001. Far higher nitration levels were measured in normal human blood cell populations when compared to plasma. Mass spectrometry was used to validate the new ELISA method. The analysis of the same set of chemically modified albumin samples using the ELISA method and mass spectrometry showed good agreement for the relative levels of nitration present in each sample. The assay was applied to serum samples from patients undergoing elective surgery which induces the human inflammatory response. Matched samples were collected before and one day after surgery. An increase in nitration was detected following surgery (median (IQR): 0.59 (0.00-1.34) and 0.97 (0.00-1.70) nitrotyrosine (fmol of nitrated albumin equivalents/mg protein) for pre- and post-surgery respectively. The reported assay is suitable for nitrotyrosine determination in patient serum samples, and may also be applicable as a means to determine oxidative stress in primary and cultured cell populations.
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Affiliation(s)
- Annie R Knight
- University of Exeter Medical School, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - Emma L Taylor
- University of Exeter Medical School, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | | | - Karina Tveen Jensen
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Helen E Jones
- CBR Division, Dstl, Porton Down, Salisbury SP4 0JQ, UK
| | - Jane E Carré
- University of Exeter Medical School, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Stephen J Bailey
- Sport and Health Sciences, Richards Building, University of Exeter, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK
| | - Emily Brewer
- Clinical Chemistry, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy J McDonald
- Clinical Chemistry, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Corinne M Spickett
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Paul G Winyard
- University of Exeter Medical School, St Luke's Campus, Magdalen Road, Exeter EX1 2LU, UK.
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14
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Afonso CB, Sousa BC, Pitt AR, Spickett CM. A mass spectrometry approach for the identification and localization of small aldehyde modifications of proteins. Arch Biochem Biophys 2018; 646:38-45. [PMID: 29580947 DOI: 10.1016/j.abb.2018.03.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 12/29/2022]
Abstract
Lipids containing polyunsaturated fatty acids are primary targets of oxidation, which produces reactive short-chain aldehydes that can covalently modify proteins, a process called lipoxidation. Improved mass spectrometry (MS) methods for the analysis of these adducts in complex biological systems are needed. Lysozyme and human serum albumin (HSA) were used as model proteins to investigate lipoxidation products formed by two short-chain aldehydes, acrolein and pentanal, which are unsaturated and saturated aldehydes respectively. The adducts formed were stabilized by NaBH4 or NaBH3CN reduction and analysed by MS. Analysis of intact modified lysozyme showed a pentanal modification resulting from Schiff's base formation (+70 Da), and up to 8 acrolein adducts, all resulting from Michael addition (+58 Da). Analysis of tryptic digests identified specific histidine, cysteine and lysine residues modified in both lysozyme and HSA, and determined characteristic amino acid-specific fragmentations. Eight different internal fragment ions were found that could be used as general diagnostic ions for pentanal- and acrolein-modified amino acids. The combined use of intact protein analysis and LC-MS/MS methods provided a powerful tool for the identification and localization of aldehyde-protein adducts, and the diagnostic ions will facilitate the development of targeted MS methods for analysis of adducts in more complex samples.
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Affiliation(s)
- Catarina B Afonso
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham, UK
| | - Bebiana C Sousa
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham, UK
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham, UK.
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15
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Verrastro I, Tveen-Jensen K, Spickett CM, Pitt AR. The effect of HOCl-induced modifications on phosphatase and tensin homologue (PTEN) structure and function. Free Radic Res 2018; 52:232-247. [DOI: 10.1080/10715762.2018.1424333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ivan Verrastro
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | | | | | - Andrew R. Pitt
- School of Life and Health Sciences, Aston University, Birmingham, UK
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16
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Egea J, Fabregat I, Frapart YM, Ghezzi P, Görlach A, Kietzmann T, Kubaichuk K, Knaus UG, Lopez MG, Olaso-Gonzalez G, Petry A, Schulz R, Vina J, Winyard P, Abbas K, Ademowo OS, Afonso CB, Andreadou I, Antelmann H, Antunes F, Aslan M, Bachschmid MM, Barbosa RM, Belousov V, Berndt C, Bernlohr D, Bertrán E, Bindoli A, Bottari SP, Brito PM, Carrara G, Casas AI, Chatzi A, Chondrogianni N, Conrad M, Cooke MS, Costa JG, Cuadrado A, My-Chan Dang P, De Smet B, Debelec-Butuner B, Dias IHK, Dunn JD, Edson AJ, El Assar M, El-Benna J, Ferdinandy P, Fernandes AS, Fladmark KE, Förstermann U, Giniatullin R, Giricz Z, Görbe A, Griffiths H, Hampl V, Hanf A, Herget J, Hernansanz-Agustín P, Hillion M, Huang J, Ilikay S, Jansen-Dürr P, Jaquet V, Joles JA, Kalyanaraman B, Kaminskyy D, Karbaschi M, Kleanthous M, Klotz LO, Korac B, Korkmaz KS, Koziel R, Kračun D, Krause KH, Křen V, Krieg T, Laranjinha J, Lazou A, Li H, Martínez-Ruiz A, Matsui R, McBean GJ, Meredith SP, Messens J, Miguel V, Mikhed Y, Milisav I, Milković L, Miranda-Vizuete A, Mojović M, Monsalve M, Mouthuy PA, Mulvey J, Münzel T, Muzykantov V, Nguyen ITN, Oelze M, Oliveira NG, Palmeira CM, Papaevgeniou N, Pavićević A, Pedre B, Peyrot F, Phylactides M, Pircalabioru GG, Pitt AR, Poulsen HE, Prieto I, Rigobello MP, Robledinos-Antón N, Rodríguez-Mañas L, Rolo AP, Rousset F, Ruskovska T, Saraiva N, Sasson S, Schröder K, Semen K, Seredenina T, Shakirzyanova A, Smith GL, Soldati T, Sousa BC, Spickett CM, Stancic A, Stasia MJ, Steinbrenner H, Stepanić V, Steven S, Tokatlidis K, Tuncay E, Turan B, Ursini F, Vacek J, Vajnerova O, Valentová K, Van Breusegem F, Varisli L, Veal EA, Yalçın AS, Yelisyeyeva O, Žarković N, Zatloukalová M, Zielonka J, Touyz RM, Papapetropoulos A, Grune T, Lamas S, Schmidt HHHW, Di Lisa F, Daiber A. Corrigendum to "European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS)" [Redox Biol. 13 (2017) 94-162]. Redox Biol 2017; 14:694-696. [PMID: 29107648 PMCID: PMC5975209 DOI: 10.1016/j.redox.2017.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- J Egea
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine, Univerisdad Autonoma de Madrid, Spain
| | - I Fabregat
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | - Y M Frapart
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - P Ghezzi
- Brighton & Sussex Medical School, Brighton, UK
| | - A Görlach
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - T Kietzmann
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - K Kubaichuk
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - U G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - M G Lopez
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine, Univerisdad Autonoma de Madrid, Spain
| | | | - A Petry
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - R Schulz
- Institute of Physiology, JLU Giessen, Giessen, Germany
| | - J Vina
- Department of Physiology, University of Valencia, Spain
| | - P Winyard
- University of Exeter Medical School, St Luke's Campus, Exeter EX1 2LU, UK
| | - K Abbas
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - O S Ademowo
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - C B Afonso
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - I Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - H Antelmann
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - F Antunes
- Departamento de Química e Bioquímica and Centro de Química e Bioquímica, Faculdade de Ciências, Portugal
| | - M Aslan
- Department of Medical Biochemistry, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - M M Bachschmid
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - R M Barbosa
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - V Belousov
- Molecular technologies laboratory, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - C Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - D Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, USA
| | - E Bertrán
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | - A Bindoli
- Institute of Neuroscience (CNR), Padova, Italy
| | - S P Bottari
- GETI, Institute for Advanced Biosciences, INSERM U1029, CNRS UMR 5309, Grenoble-Alpes University and Radio-analysis Laboratory, CHU de Grenoble, Grenoble, France
| | - P M Brito
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; Faculdade de Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - G Carrara
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - A I Casas
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - A Chatzi
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - N Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - M Conrad
- Helmholtz Center Munich, Institute of Developmental Genetics, Neuherberg, Germany
| | - M S Cooke
- Helmholtz Center Munich, Institute of Developmental Genetics, Neuherberg, Germany
| | - J G Costa
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - A Cuadrado
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - P My-Chan Dang
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - B De Smet
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy; Pharmahungary Group, Szeged, Hungary
| | - B Debelec-Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir 35100, Turkey
| | - I H K Dias
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - J D Dunn
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - A J Edson
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - M El Assar
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain
| | - J El-Benna
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - P Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - A S Fernandes
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - K E Fladmark
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - U Förstermann
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - R Giniatullin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Z Giricz
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - A Görbe
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - H Griffiths
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK; Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - V Hampl
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - A Hanf
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - J Herget
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - P Hernansanz-Agustín
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - M Hillion
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - J Huang
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - S Ilikay
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - P Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - V Jaquet
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - J A Joles
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | | | - D Kaminskyy
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - M Karbaschi
- Oxidative Stress Group, Dept. Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA
| | - M Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - L O Klotz
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - B Korac
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - K S Korkmaz
- Department of Bioengineering, Cancer Biology Laboratory, Faculty of Engineering, Ege University, Bornova, 35100 Izmir, Turkey
| | - R Koziel
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - D Kračun
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - K H Krause
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - V Křen
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - T Krieg
- Department of Medicine, University of Cambridge, UK
| | - J Laranjinha
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - A Lazou
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - H Li
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - A Martínez-Ruiz
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - R Matsui
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - G J McBean
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - S P Meredith
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - J Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - V Miguel
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Y Mikhed
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - I Milisav
- University of Ljubljana, Faculty of Medicine, Institute of Pathophysiology and Faculty of Health Sciences, Ljubljana, Slovenia
| | - L Milković
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - A Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - M Mojović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - M Monsalve
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - P A Mouthuy
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - J Mulvey
- Department of Medicine, University of Cambridge, UK
| | - T Münzel
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - V Muzykantov
- Department of Pharmacology, Center for Targeted Therapeutics & Translational Nanomedicine, ITMAT/CTSA Translational Research Center University of Pennsylvania The Perelman School of Medicine, Philadelphia, PA, USA
| | - I T N Nguyen
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | - M Oelze
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - N G Oliveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - C M Palmeira
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - N Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - A Pavićević
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - B Pedre
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - F Peyrot
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France; ESPE of Paris, Paris Sorbonne University, Paris, France
| | - M Phylactides
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - G G Pircalabioru
- The Research Institute of University of Bucharest, Bucharest, Romania
| | - A R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - H E Poulsen
- Laboratory of Clinical Pharmacology, Rigshospitalet, University Hospital Copenhagen, Denmark; Department of Clinical Pharmacology, Bispebjerg Frederiksberg Hospital, University Hospital Copenhagen, Denmark; Department Q7642, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - I Prieto
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - M P Rigobello
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/b, 35131 Padova, Italy
| | - N Robledinos-Antón
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - L Rodríguez-Mañas
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain; Servicio de Geriatría, Hospital Universitario de Getafe, Getafe, Spain
| | - A P Rolo
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - F Rousset
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - T Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, Stip, Republic of Macedonia
| | - N Saraiva
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - S Sasson
- Institute for Drug Research, Section of Pharmacology, Diabetes Research Unit, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - K Schröder
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany
| | - K Semen
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - T Seredenina
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - A Shakirzyanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - G L Smith
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - T Soldati
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - B C Sousa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - C M Spickett
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - A Stancic
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - M J Stasia
- Université Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, F38000 Grenoble, France; CDiReC, Pôle Biologie, CHU de Grenoble, Grenoble F-38043, France
| | - H Steinbrenner
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - V Stepanić
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - S Steven
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - K Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - E Tuncay
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - B Turan
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - F Ursini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - J Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | - O Vajnerova
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - K Valentová
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - F Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - L Varisli
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - E A Veal
- Institute for Cell and Molecular Biosciences, and Institute for Ageing, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - A S Yalçın
- Department of Biochemistry, School of Medicine, Marmara University, Istanbul, Turkey
| | - O Yelisyeyeva
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - N Žarković
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - M Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | - J Zielonka
- Medical College of Wisconsin, Milwaukee, USA
| | - R M Touyz
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - A Papapetropoulos
- Laboratoty of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - T Grune
- German Institute of Human Nutrition, Department of Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - S Lamas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - H H H W Schmidt
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - F Di Lisa
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy.
| | - A Daiber
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany.
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17
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Sousa BC, Pitt AR, Spickett CM. Chemistry and analysis of HNE and other prominent carbonyl-containing lipid oxidation compounds. Free Radic Biol Med 2017; 111:294-308. [PMID: 28192230 DOI: 10.1016/j.freeradbiomed.2017.02.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/28/2017] [Accepted: 02/01/2017] [Indexed: 01/02/2023]
Abstract
The process of lipid oxidation generates a diverse array of small aldehydes and carbonyl-containing compounds, which may occur in free form or esterified within phospholipids and cholesterol esters. These aldehydes mostly result from fragmentation of fatty acyl chains following radical oxidation, and the products can be subdivided into alkanals, alkenals (usually α,β-unsaturated), γ-substituted alkenals and bis-aldehydes. Isolevuglandins are non-fragmented di-carbonyl compounds derived from H2-isoprostanes, and oxidation of the ω-3-fatty acid docosahexenoic acid yield analogous 22 carbon neuroketals. Non-radical oxidation by hypochlorous acid can generate α-chlorofatty aldehydes from plasmenyl phospholipids. Most of these compounds are reactive and have generally been considered as toxic products of a deleterious process. The reactivity is especially high for the α,β-unsaturated alkenals, such as acrolein and crotonaldehyde, and for γ-substituted alkenals, of which 4-hydroxy-2-nonenal and 4-oxo-2-nonenal are best known. Nevertheless, in recent years several previously neglected aldehydes have been investigated and also found to have significant reactivity and biological effects; notable examples are 4-hydroxy-2-hexenal and 4-hydroxy-dodecadienal. This has led to substantial interest in the biological effects of all of these lipid oxidation products and their roles in disease, including proposals that HNE is a second messenger or signalling molecule. However, it is becoming clear that many of the effects elicited by these compounds relate to their propensity for forming adducts with nucleophilic groups on proteins, DNA and specific phospholipids. This emphasizes the need for good analytical methods, not just for free lipid oxidation products but also for the resulting adducts with biomolecules. The most informative methods are those utilizing HPLC separations and mass spectrometry, although analysis of the wide variety of possible adducts is very challenging. Nevertheless, evidence for the occurrence of lipid-derived aldehyde adducts in biological and clinical samples is building, and offers an exciting area of future research.
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Affiliation(s)
- Bebiana C Sousa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Corinne M Spickett
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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18
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Egea J, Fabregat I, Frapart YM, Ghezzi P, Görlach A, Kietzmann T, Kubaichuk K, Knaus UG, Lopez MG, Olaso-Gonzalez G, Petry A, Schulz R, Vina J, Winyard P, Abbas K, Ademowo OS, Afonso CB, Andreadou I, Antelmann H, Antunes F, Aslan M, Bachschmid MM, Barbosa RM, Belousov V, Berndt C, Bernlohr D, Bertrán E, Bindoli A, Bottari SP, Brito PM, Carrara G, Casas AI, Chatzi A, Chondrogianni N, Conrad M, Cooke MS, Costa JG, Cuadrado A, My-Chan Dang P, De Smet B, Debelec-Butuner B, Dias IHK, Dunn JD, Edson AJ, El Assar M, El-Benna J, Ferdinandy P, Fernandes AS, Fladmark KE, Förstermann U, Giniatullin R, Giricz Z, Görbe A, Griffiths H, Hampl V, Hanf A, Herget J, Hernansanz-Agustín P, Hillion M, Huang J, Ilikay S, Jansen-Dürr P, Jaquet V, Joles JA, Kalyanaraman B, Kaminskyy D, Karbaschi M, Kleanthous M, Klotz LO, Korac B, Korkmaz KS, Koziel R, Kračun D, Krause KH, Křen V, Krieg T, Laranjinha J, Lazou A, Li H, Martínez-Ruiz A, Matsui R, McBean GJ, Meredith SP, Messens J, Miguel V, Mikhed Y, Milisav I, Milković L, Miranda-Vizuete A, Mojović M, Monsalve M, Mouthuy PA, Mulvey J, Münzel T, Muzykantov V, Nguyen ITN, Oelze M, Oliveira NG, Palmeira CM, Papaevgeniou N, Pavićević A, Pedre B, Peyrot F, Phylactides M, Pircalabioru GG, Pitt AR, Poulsen HE, Prieto I, Rigobello MP, Robledinos-Antón N, Rodríguez-Mañas L, Rolo AP, Rousset F, Ruskovska T, Saraiva N, Sasson S, Schröder K, Semen K, Seredenina T, Shakirzyanova A, Smith GL, Soldati T, Sousa BC, Spickett CM, Stancic A, Stasia MJ, Steinbrenner H, Stepanić V, Steven S, Tokatlidis K, Tuncay E, Turan B, Ursini F, Vacek J, Vajnerova O, Valentová K, Van Breusegem F, Varisli L, Veal EA, Yalçın AS, Yelisyeyeva O, Žarković N, Zatloukalová M, Zielonka J, Touyz RM, Papapetropoulos A, Grune T, Lamas S, Schmidt HHHW, Di Lisa F, Daiber A. European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS). Redox Biol 2017; 13:94-162. [PMID: 28577489 PMCID: PMC5458069 DOI: 10.1016/j.redox.2017.05.007] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 12/12/2022] Open
Abstract
The European Cooperation in Science and Technology (COST) provides an ideal framework to establish multi-disciplinary research networks. COST Action BM1203 (EU-ROS) represents a consortium of researchers from different disciplines who are dedicated to providing new insights and tools for better understanding redox biology and medicine and, in the long run, to finding new therapeutic strategies to target dysregulated redox processes in various diseases. This report highlights the major achievements of EU-ROS as well as research updates and new perspectives arising from its members. The EU-ROS consortium comprised more than 140 active members who worked together for four years on the topics briefly described below. The formation of reactive oxygen and nitrogen species (RONS) is an established hallmark of our aerobic environment and metabolism but RONS also act as messengers via redox regulation of essential cellular processes. The fact that many diseases have been found to be associated with oxidative stress established the theory of oxidative stress as a trigger of diseases that can be corrected by antioxidant therapy. However, while experimental studies support this thesis, clinical studies still generate controversial results, due to complex pathophysiology of oxidative stress in humans. For future improvement of antioxidant therapy and better understanding of redox-associated disease progression detailed knowledge on the sources and targets of RONS formation and discrimination of their detrimental or beneficial roles is required. In order to advance this important area of biology and medicine, highly synergistic approaches combining a variety of diverse and contrasting disciplines are needed.
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Affiliation(s)
- Javier Egea
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine. Univerisdad Autonoma de Madrid, Spain
| | - Isabel Fabregat
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | - Yves M Frapart
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | | | - Agnes Görlach
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Kateryna Kubaichuk
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ulla G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Manuela G Lopez
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine. Univerisdad Autonoma de Madrid, Spain
| | | | - Andreas Petry
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - Rainer Schulz
- Institute of Physiology, JLU Giessen, Giessen, Germany
| | - Jose Vina
- Department of Physiology, University of Valencia, Spain
| | - Paul Winyard
- University of Exeter Medical School, St Luke's Campus, Exeter EX1 2LU, UK
| | - Kahina Abbas
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - Opeyemi S Ademowo
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Catarina B Afonso
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Ioanna Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Haike Antelmann
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Fernando Antunes
- Departamento de Química e Bioquímica and Centro de Química e Bioquímica, Faculdade de Ciências, Portugal
| | - Mutay Aslan
- Department of Medical Biochemistry, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Markus M Bachschmid
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Rui M Barbosa
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Vsevolod Belousov
- Molecular technologies laboratory, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - David Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, USA
| | - Esther Bertrán
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | | | - Serge P Bottari
- GETI, Institute for Advanced Biosciences, INSERM U1029, CNRS UMR 5309, Grenoble-Alpes University and Radio-analysis Laboratory, CHU de Grenoble, Grenoble, France
| | - Paula M Brito
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; Faculdade de Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Guia Carrara
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ana I Casas
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Afroditi Chatzi
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - Niki Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Marcus Conrad
- Helmholtz Center Munich, Institute of Developmental Genetics, Neuherberg, Germany
| | - Marcus S Cooke
- Oxidative Stress Group, Dept. Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA
| | - João G Costa
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Antonio Cuadrado
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid. Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Pham My-Chan Dang
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - Barbara De Smet
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy; Pharmahungary Group, Szeged, Hungary
| | - Bilge Debelec-Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir 35100, Turkey
| | - Irundika H K Dias
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Joe Dan Dunn
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - Amanda J Edson
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Mariam El Assar
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain
| | - Jamel El-Benna
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Ana S Fernandes
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Kari E Fladmark
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - Ulrich Förstermann
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Rashid Giniatullin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Zoltán Giricz
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Anikó Görbe
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - Helen Griffiths
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK; Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Vaclav Hampl
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Alina Hanf
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Jan Herget
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pablo Hernansanz-Agustín
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - Melanie Hillion
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Jingjing Huang
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Serap Ilikay
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - Pidder Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Vincent Jaquet
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Jaap A Joles
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | | | | | - Mahsa Karbaschi
- Oxidative Stress Group, Dept. Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Lars-Oliver Klotz
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - Bato Korac
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - Kemal Sami Korkmaz
- Department of Bioengineering, Cancer Biology Laboratory, Faculty of Engineering, Ege University, Bornova, 35100 Izmir, Turkey
| | - Rafal Koziel
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Damir Kračun
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - Karl-Heinz Krause
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Vladimír Křen
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, UK
| | - João Laranjinha
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Antigone Lazou
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Huige Li
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Antonio Martínez-Ruiz
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Reiko Matsui
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - Gethin J McBean
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Stuart P Meredith
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Joris Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Verónica Miguel
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Yuliya Mikhed
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Irina Milisav
- University of Ljubljana, Faculty of Medicine, Institute of Pathophysiology and Faculty of Health Sciences, Ljubljana, Slovenia
| | - Lidija Milković
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Miloš Mojović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - María Monsalve
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Pierre-Alexis Mouthuy
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - John Mulvey
- Department of Medicine, University of Cambridge, UK
| | - Thomas Münzel
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Vladimir Muzykantov
- Department of Pharmacology, Center for Targeted Therapeutics & Translational Nanomedicine, ITMAT/CTSA Translational Research Center University of Pennsylvania The Perelman School of Medicine, Philadelphia, PA, USA
| | - Isabel T N Nguyen
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | - Matthias Oelze
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Nuno G Oliveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos M Palmeira
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - Nikoletta Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Aleksandra Pavićević
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Brandán Pedre
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Fabienne Peyrot
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France; ESPE of Paris, Paris Sorbonne University, Paris, France
| | - Marios Phylactides
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Henrik E Poulsen
- Laboratory of Clinical Pharmacology, Rigshospitalet, University Hospital Copenhagen, Denmark; Department of Clinical Pharmacology, Bispebjerg Frederiksberg Hospital, University Hospital Copenhagen, Denmark; Department Q7642, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Ignacio Prieto
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Maria Pia Rigobello
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Natalia Robledinos-Antón
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid. Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Leocadio Rodríguez-Mañas
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain; Servicio de Geriatría, Hospital Universitario de Getafe, Getafe, Spain
| | - Anabela P Rolo
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - Francis Rousset
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, Stip, Republic of Macedonia
| | - Nuno Saraiva
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - Shlomo Sasson
- Institute for Drug Research, Section of Pharmacology, Diabetes Research Unit, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Katrin Schröder
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany
| | - Khrystyna Semen
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - Tamara Seredenina
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - Anastasia Shakirzyanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Thierry Soldati
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - Bebiana C Sousa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Corinne M Spickett
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Ana Stancic
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - Marie José Stasia
- Université Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, F38000 Grenoble, France; CDiReC, Pôle Biologie, CHU de Grenoble, Grenoble, F-38043, France
| | - Holger Steinbrenner
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - Višnja Stepanić
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Sebastian Steven
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - Kostas Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - Erkan Tuncay
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - Belma Turan
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - Fulvio Ursini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | - Olga Vajnerova
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Valentová
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lokman Varisli
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - Elizabeth A Veal
- Institute for Cell and Molecular Biosciences, and Institute for Ageing, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - A Suha Yalçın
- Department of Biochemistry, School of Medicine, Marmara University, İstanbul, Turkey
| | | | - Neven Žarković
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | | | - Rhian M Touyz
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - Andreas Papapetropoulos
- Laboratoty of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Tilman Grune
- German Institute of Human Nutrition, Department of Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Santiago Lamas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Harald H H W Schmidt
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Fabio Di Lisa
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy.
| | - Andreas Daiber
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany.
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Verrastro I, Tveen-Jensen K, Woscholski R, Spickett CM, Pitt AR. Reversible oxidation of phosphatase and tensin homolog (PTEN) alters its interactions with signaling and regulatory proteins. Free Radic Biol Med 2016; 90:24-34. [PMID: 26561776 DOI: 10.1016/j.freeradbiomed.2015.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 12/27/2022]
Abstract
Phosphatase and tensin homolog (PTEN) is involved in a number of different cellular processes including metabolism, apoptosis, cell proliferation and survival. It is a redox-sensitive dual-specificity protein phosphatase that acts as a tumor suppressor by negatively regulating the PI3K/Akt pathway. While direct evidence of redox regulation of PTEN downstream signaling has been reported, the effect of PTEN redox status on its protein-protein interactions is poorly understood. PTEN-GST in its reduced and a DTT-reversible H2O2-oxidized form was immobilized on a glutathione-sepharose support and incubated with cell lysate to capture interacting proteins. Captured proteins were analyzed by LC-MSMS and comparatively quantified using label-free methods. 97 Potential protein interactors were identified, including a significant number that are novel. The abundance of fourteen interactors was found to vary significantly with the redox status of PTEN. Altered binding to PTEN was confirmed by affinity pull-down and Western blotting for Prdx1, Trx, and Anxa2, while DDB1 was validated as a novel interactor with unaltered binding. These results suggest that the redox status of PTEN causes a functional variation in the PTEN interactome. The resin capture method developed had distinct advantages in that the redox status of PTEN could be directly controlled and measured.
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Affiliation(s)
- Ivan Verrastro
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham B4 7ET, UK
| | - Karina Tveen-Jensen
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham B4 7ET, UK
| | - Rudiger Woscholski
- Department of Chemistry and Institute of Chemical Biology, Imperial College London, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham B4 7ET, UK
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham B4 7ET, UK.
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Abstract
SIGNIFICANCE Oxidized phospholipids are now well recognized as markers of biological oxidative stress and bioactive molecules with both pro-inflammatory and anti-inflammatory effects. While analytical methods continue to be developed for studies of generic lipid oxidation, mass spectrometry (MS) has underpinned the advances in knowledge of specific oxidized phospholipids by allowing their identification and characterization, and it is responsible for the expansion of oxidative lipidomics. RECENT ADVANCES Studies of oxidized phospholipids in biological samples, from both animal models and clinical samples, have been facilitated by the recent improvements in MS, especially targeted routines that depend on the fragmentation pattern of the parent molecular ion and improved resolution and mass accuracy. MS can be used to identify selectively individual compounds or groups of compounds with common features, which greatly improves the sensitivity and specificity of detection. Application of these methods has enabled important advances in understanding the mechanisms of inflammatory diseases such as atherosclerosis, steatohepatitis, leprosy, and cystic fibrosis, and it offers potential for developing biomarkers of molecular aspects of the diseases. CRITICAL ISSUES AND FUTURE DIRECTIONS The future in this field will depend on development of improved MS technologies, such as ion mobility, novel enrichment methods and databases, and software for data analysis, owing to the very large amount of data generated in these experiments. Imaging of oxidized phospholipids in tissue MS is an additional exciting direction emerging that can be expected to advance understanding of physiology and disease.
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Affiliation(s)
- Corinne M. Spickett
- School of Life & Health Sciences, Aston University, Birmingham, United Kingdom
| | - Andrew R. Pitt
- School of Life & Health Sciences, Aston University, Birmingham, United Kingdom
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Tveen-Jensen K, Gesellchen F, Wilson R, Spickett CM, Cooper JM, Pitt AR. Interfacing low-energy SAW nebulization with Liquid Chromatography-Mass Spectrometry for the analysis of biological samples. Sci Rep 2015; 5:9736. [PMID: 25978651 PMCID: PMC4432867 DOI: 10.1038/srep09736] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/10/2015] [Indexed: 01/29/2023] Open
Abstract
Soft ionization methods for the introduction of labile biomolecules into a mass spectrometer are of fundamental importance to biomolecular analysis. Previously, electrospray ionization (ESI) and matrix assisted laser desorption-ionization (MALDI) have been the main ionization methods used. Surface acoustic wave nebulization (SAWN) is a new technique that has been demonstrated to deposit less energy into ions upon ion formation and transfer for detection than other methods for sample introduction into a mass spectrometer (MS). Here we report the optimization and use of SAWN as a nebulization technique for the introduction of samples from a low flow of liquid, and the interfacing of SAWN with liquid chromatographic separation (LC) for the analysis of a protein digest. This demonstrates that SAWN can be a viable, low-energy alternative to ESI for the LC-MS analysis of proteomic samples.
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Affiliation(s)
- Karina Tveen-Jensen
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| | - Frank Gesellchen
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Rab Wilson
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
| | - Jonathan M Cooper
- Division of Biomedical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK. G12 8LT
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, UK. B4 7ET
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Verrastro I, Pasha S, Jensen KT, Pitt AR, Spickett CM. Mass spectrometry-based methods for identifying oxidized proteins in disease: advances and challenges. Biomolecules 2015; 5:378-411. [PMID: 25874603 PMCID: PMC4496678 DOI: 10.3390/biom5020378] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/20/2015] [Accepted: 03/23/2015] [Indexed: 01/02/2023] Open
Abstract
Many inflammatory diseases have an oxidative aetiology, which leads to oxidative damage to biomolecules, including proteins. It is now increasingly recognized that oxidative post-translational modifications (oxPTMs) of proteins affect cell signalling and behaviour, and can contribute to pathology. Moreover, oxidized proteins have potential as biomarkers for inflammatory diseases. Although many assays for generic protein oxidation and breakdown products of protein oxidation are available, only advanced tandem mass spectrometry approaches have the power to localize specific oxPTMs in identified proteins. While much work has been carried out using untargeted or discovery mass spectrometry approaches, identification of oxPTMs in disease has benefitted from the development of sophisticated targeted or semi-targeted scanning routines, combined with chemical labeling and enrichment approaches. Nevertheless, many potential pitfalls exist which can result in incorrect identifications. This review explains the limitations, advantages and challenges of all of these approaches to detecting oxidatively modified proteins, and provides an update on recent literature in which they have been used to detect and quantify protein oxidation in disease.
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Affiliation(s)
- Ivan Verrastro
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Sabah Pasha
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Karina Tveen Jensen
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
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Reis A, Rudnitskaya A, Chariyavilaskul P, Dhaun N, Melville V, Goddard J, Webb DJ, Pitt AR, Spickett CM. Top-down lipidomics of low density lipoprotein reveal altered lipid profiles in advanced chronic kidney disease. J Lipid Res 2014; 56:413-22. [PMID: 25424003 DOI: 10.1194/jlr.m055624] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This study compared the molecular lipidomic profile of LDL in patients with nondiabetic advanced renal disease and no evidence of CVD to that of age-matched controls, with the hypothesis that it would reveal proatherogenic lipid alterations. LDL was isolated from 10 normocholesterolemic patients with stage 4/5 renal disease and 10 controls, and lipids were analyzed by accurate mass LC/MS. Top-down lipidomics analysis and manual examination of the data identified 352 lipid species, and automated comparative analysis demonstrated alterations in lipid profile in disease. The total lipid and cholesterol content was unchanged, but levels of triacylglycerides and N-acyltaurines were significantly increased, while phosphatidylcholines, plasmenyl ethanolamines, sulfatides, ceramides, and cholesterol sulfate were significantly decreased in chronic kidney disease (CKD) patients. Chemometric analysis of individual lipid species showed very good discrimination of control and disease sample despite the small cohorts and identified individual unsaturated phospholipids and triglycerides mainly responsible for the discrimination. These findings illustrate the point that although the clinical biochemistry parameters may not appear abnormal, there may be important underlying lipidomic changes that contribute to disease pathology. The lipidomic profile of CKD LDL offers potential for new biomarkers and novel insights into lipid metabolism and cardiovascular risk in this disease.
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Affiliation(s)
- Ana Reis
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Alisa Rudnitskaya
- Centro de Estudios do Ambiente e do Mar (CESAM), Department of Chemistry, Universidade de Aveiro, Portugal
| | - Pajaree Chariyavilaskul
- Clinical Pharmacology Unit, British Heart Foundation Centre of Research Excellence, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Neeraj Dhaun
- Clinical Pharmacology Unit, British Heart Foundation Centre of Research Excellence, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK Department of Renal Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Vanessa Melville
- Clinical Pharmacology Unit, British Heart Foundation Centre of Research Excellence, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Jane Goddard
- Department of Renal Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - David J Webb
- Clinical Pharmacology Unit, British Heart Foundation Centre of Research Excellence, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Birmingham, UK
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Rezende Valim L, Davies JA, Tveen Jensen K, Guo R, Willison KR, Spickett CM, Pitt AR, Klug DR. Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy. J Phys Chem B 2014; 118:12855-64. [PMID: 25347525 DOI: 10.1021/jp509053q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy.
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Abstract
Oxidised biomolecules in aged tissue could potentially be used as biomarkers for age-related diseases; however, it is still unclear whether they causatively contribute to ageing or are consequences of the ageing process. To assess the potential of using protein oxidation as markers of ageing, mass spectrometry (MS) was employed for the identification and quantification of oxidative modifications in obese (ob/ob) mice. Lean muscle mass and strength is reduced in obesity, representing a sarcopenic model in which the levels of oxidation can be evaluated for different muscular systems including calcium homeostasis, metabolism and contractility. Several oxidised residues were identified by tandem MS (MS/MS) in both muscle homogenate and isolated sarcoplasmic reticulum (SR), an organelle that regulates intracellular calcium levels in muscle. These modifications include oxidation of methionine, cysteine, tyrosine, and tryptophan in several proteins such as sarcoplasmic reticulum calcium ATPase (SERCA), glycogen phosphorylase, and myosin. Once modifications had been identified, multiple reaction monitoring MS (MRM) was used to quantify the percentage modification of oxidised residues within the samples. Preliminary data suggests proteins in ob/ob mice are more oxidised than the controls. For example SERCA, which constitutes 60-70% of the SR, had approximately a 2-fold increase in cysteine trioxidation of Cys561 in the obese model when compared to the control. Other obese muscle proteins have also shown a similar increase in oxidation for various residues. Further analysis with complex protein mixtures will determine the potential diagnostic use of MRM experiments for analysing protein oxidation in small biological samples such as muscle needle biopsies.
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Affiliation(s)
- Sabah Pasha
- Aston University (Birmingham), Health & Life Sciences, UK.
| | | | - Andrew R Pitt
- Aston University (Birmingham), Health & Life Sciences, UK
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Abstract
Oxidative post-translational modifications (oxPTMs) can alter the function of proteins, and are important in the redox regulation of cell behaviour. The most informative technique to detect and locate oxPTMs within proteins is mass spectrometry (MS). However, proteomic MS data are usually searched against theoretical databases using statistical search engines, and the occurrence of unspecified or multiple modifications, or other unexpected features, can lead to failure to detect the modifications and erroneous identifications of oxPTMs. We have developed a new approach for mining data from accurate mass instruments that allows multiple modifications to be examined. Accurate mass extracted ion chromatograms (XIC) for specific reporter ions from peptides containing oxPTMs were generated from standard LC-MSMS data acquired on a rapid-scanning high-resolution mass spectrometer (ABSciex 5600 Triple TOF). The method was tested using proteins from human plasma or isolated LDL. A variety of modifications including chlorotyrosine, nitrotyrosine, kynurenine, oxidation of lysine, and oxidized phospholipid adducts were detected. For example, the use of a reporter ion at 184.074Da/e, corresponding to phosphocholine, was used to identify for the first time intact oxidized phosphatidylcholine adducts on LDL. In all cases the modifications were confirmed by manual sequencing. ApoB-100 containing oxidized lipid adducts was detected even in healthy human samples, as well as LDL from patients with chronic kidney disease. The accurate mass XIC method gave a lower false positive rate than normal database searching using statistical search engines, and identified more oxidatively modified peptides. A major advantage was that additional modifications could be searched after data collection, and multiple modifications on a single peptide identified. The oxPTMs present on albumin and ApoB-100 have potential as indicators of oxidative damage in ageing or inflammatory diseases.
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Affiliation(s)
| | - Ana Reis
- Aston University (Birmingham), Life and Health Sciences, United Kingdom
| | | | - Andrew R Pitt
- Aston University (Birmingham), Life and Health Sciences, United Kingdom
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Jiwaji M, Sandison ME, Reboud J, Stevenson R, Daly R, Barkess G, Faulds K, Kolch W, Graham D, Girolami MA, Cooper JM, Pitt AR. Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells. PLoS One 2014; 9:e99458. [PMID: 24926959 PMCID: PMC4057226 DOI: 10.1371/journal.pone.0099458] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 05/13/2014] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of oligonucleotide delivery to the cell and indeed, following delivery, the characterization of the effects on the cell. METHODS In this report, we compare different transfection reagents as delivery vehicles for gold nanoparticles functionalized with DNA oligonucleotides, and quantify their relative transfection efficiencies. The inhibitory properties of small interfering RNA (siRNA), single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) sequences targeted to human metallothionein hMT-IIa are also quantified in HeLa cells. Techniques used in this study include fluorescence and confocal microscopy, qPCR and Western analysis. FINDINGS We show that the use of transfection reagents does significantly increase nanoparticle transfection efficiencies. Furthermore, siRNA, ssRNA and ssDNA sequences all have comparable inhibitory properties to ssDNA sequences immobilized onto gold nanoparticles. We also show that functionalized gold nanoparticles can co-localize with autophagosomes and illustrate other factors that can affect data collection and interpretation when performing studies with functionalized nanoparticles. CONCLUSIONS The desired outcome for biological knockdown studies is the efficient reduction of a specific target; which we demonstrate by using ssDNA inhibitory sequences targeted to human metallothionein IIa gene transcripts that result in the knockdown of both the mRNA transcript and the target protein.
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Affiliation(s)
- Meesbah Jiwaji
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
| | - Mairi E. Sandison
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Julien Reboud
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Ross Stevenson
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Rónán Daly
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Gráinne Barkess
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Karen Faulds
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Walter Kolch
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Systems Biology Ireland and the Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Duncan Graham
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Mark A. Girolami
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
- Department of Statistical Science, University College London, London, United Kingdom
| | - Jonathan M. Cooper
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Andrew R. Pitt
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
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Maciel E, Neves BM, Santinha D, Reis A, Domingues P, Teresa Cruz M, Pitt AR, Spickett CM, Domingues MRM. Detection of phosphatidylserine with a modified polar head group in human keratinocytes exposed to the radical generator AAPH. Arch Biochem Biophys 2014; 548:38-45. [DOI: 10.1016/j.abb.2014.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/24/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
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Reis A, Rudnitskaya A, Blackburn GJ, Mohd Fauzi N, Pitt AR, Spickett CM. A comparison of five lipid extraction solvent systems for lipidomic studies of human LDL. J Lipid Res 2013; 54:1812-24. [PMID: 23670529 DOI: 10.1194/jlr.m034330] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Lipidome profile of fluids and tissues is a growing field as the role of lipids as signaling molecules is increasingly understood, relying on an effective and representative extraction of the lipids present. A number of solvent systems suitable for lipid extraction are commonly in use, though no comprehensive investigation of their effectiveness across multiple lipid classes has been carried out. To address this, human LDL from normolipidemic volunteers was used to evaluate five different solvent extraction protocols [Folch, Bligh and Dyer, acidified Bligh and Dyer, methanol (MeOH)-tert-butyl methyl ether (TBME), and hexane-isopropanol] and the extracted lipids were analyzed by LC-MS in a high-resolution instrument equipped with polarity switching. Overall, more than 350 different lipid species from 19 lipid subclasses were identified. Solvent composition had a small effect on the extraction of predominant lipid classes (triacylglycerides, cholesterol esters, and phosphatidylcholines). In contrast, extraction of less abundant lipids (phosphatidylinositols, lyso-lipids, ceramides, and cholesterol sulfates) was greatly influenced by the solvent system used. Overall, the Folch method was most effective for the extraction of a broad range of lipid classes in LDL, although the hexane-isopropanol method was best for apolar lipids and the MeOH-TBME method was suitable for lactosyl ceramides.
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Affiliation(s)
- Ana Reis
- School of Life and Health Sciences, Aston University, Birmingham, UK.
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Spickett CM, Reis A, Pitt AR. Use of narrow mass-window, high-resolution extracted product ion chromatograms for the sensitive and selective identification of protein modifications. Anal Chem 2013; 85:4621-7. [PMID: 23534669 DOI: 10.1021/ac400131f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein modifications, including oxidative modifications, glycosylations, and oxidized lipid-protein adducts, are becoming increasingly important as biomarkers and in understanding disease etiology. There has been a great deal of interest in mapping these on Apo B100 from low density lipoprotein (LDL). We have used extracted ion chromatograms of product ions generated using a very narrow mass window from high-resolution tandem mass spectrometric data collected on a rapid scanning quadrupole time-of-flight (QTOF) instrument, to selectively and sensitively detect modified peptides and identify the site and nature of a number of protein modifications in parallel. We have demonstrated the utility of this method by characterizing for the first time oxidized phospholipid adducts to LDL and human serum albumin and for the detection of glycosylation and kynurenin formation from the oxidation of tryptophan residues in LDL.
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Affiliation(s)
- Corinne M Spickett
- Life and Health Sciences, Aston University, Aston Triangle, Birmingham, United Kingdom
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Tveen-Jensen K, Reis A, Mouls L, Pitt AR, Spickett CM. Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples. J Proteomics 2013; 92:71-9. [PMID: 23603107 DOI: 10.1016/j.jprot.2013.03.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/29/2013] [Accepted: 03/31/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS(3) ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run.This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine. BIOLOGICAL SIGNIFICANCE The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions.
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Jiwaji M, Daly R, Gibriel A, Barkess G, McLean P, Yang J, Pansare K, Cumming S, McLauchlan A, Kamola PJ, Bhutta MS, West AG, West KL, Kolch W, Girolami MA, Pitt AR. Unique reporter-based sensor platforms to monitor signalling in cells. PLoS One 2012; 7:e50521. [PMID: 23209767 PMCID: PMC3510088 DOI: 10.1371/journal.pone.0050521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 10/23/2012] [Indexed: 11/30/2022] Open
Abstract
Introduction In recent years much progress has been made in the development of tools for systems biology to study the levels of mRNA and protein, and their interactions within cells. However, few multiplexed methodologies are available to study cell signalling directly at the transcription factor level. Methods Here we describe a sensitive, plasmid-based RNA reporter methodology to study transcription factor activation in mammalian cells, and apply this technology to profiling 60 transcription factors in parallel. The methodology uses two robust and easily accessible detection platforms; quantitative real-time PCR for quantitative analysis and DNA microarrays for parallel, higher throughput analysis. Findings We test the specificity of the detection platforms with ten inducers and independently validate the transcription factor activation. Conclusions We report a methodology for the multiplexed study of transcription factor activation in mammalian cells that is direct and not theoretically limited by the number of available reporters.
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Affiliation(s)
- Meesbah Jiwaji
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
| | - Rónán Daly
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Abdullah Gibriel
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gráinne Barkess
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Pauline McLean
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jingli Yang
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kshama Pansare
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
| | - Sarah Cumming
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alisha McLauchlan
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Piotr J. Kamola
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Musab S. Bhutta
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Adam G. West
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Katherine L. West
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Walter Kolch
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Systems Biology Ireland and the Conway Institute, University College Dublin, Dublin, Ireland
| | - Mark A. Girolami
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
- Department of Statistical Science, University College London, London, United Kingdom
| | - Andrew R. Pitt
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
- * E-mail:
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Spickett CM, Reis A, Pitt AR. Identification of oxidized phospholipids by electrospray ionization mass spectrometry and LC-MS using a QQLIT instrument. Free Radic Biol Med 2011; 51:2133-49. [PMID: 21983435 DOI: 10.1016/j.freeradbiomed.2011.09.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Revised: 09/01/2011] [Accepted: 09/02/2011] [Indexed: 11/29/2022]
Abstract
Phospholipids are complex and varied biomolecules that are susceptible to lipid peroxidation after attack by free radicals or electrophilic oxidants and can yield a large number of different oxidation products. There are many available methods for detecting phospholipid oxidation products, but also various limitations and problems. Electrospray ionization mass spectrometry allows the simultaneous but specific analysis of multiple species with good sensitivity and has a further advantage that it can be coupled to liquid chromatography for separation of oxidation products. Here, we explain the principles of oxidized phospholipid analysis by electrospray mass spectrometry and describe fragmentation routines for surveying the structural properties of the analytes, in particular precursor ion and neutral loss scanning. These allow targeted detection of phospholipid headgroups and identification of phospholipids containing hydroperoxides and chlorine, as well as the detection of some individual oxidation products by their specific fragmentation patterns. We describe instrument protocols for carrying out these survey routines on a QTrap5500 mass spectrometer and also for interfacing with reverse-phase liquid chromatography. The article highlights critical aspects of the analysis as well as some limitations of the methodology.
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Affiliation(s)
- Corinne M Spickett
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK.
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Martino C, Zagnoni M, Sandison ME, Chanasakulniyom M, Pitt AR, Cooper JM. Intracellular protein determination using droplet-based immunoassays. Anal Chem 2011; 83:5361-8. [PMID: 21574549 DOI: 10.1021/ac200876q] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This paper describes the implementation of a sensitive, on-chip immunoassay for the analysis of intracellular proteins, developed using microdroplet technology. The system offers a number of analytical functionalities, enabling the lysis of low cell numbers, as well as protein detection and quantification, integrated within a single process flow. Cells were introduced into the device in suspension and were electrically lysed in situ. The cell lysate was subsequently encapsulated together with antibody-functionalized beads into stable, water-in-oil droplets, which were stored on-chip. The binding of intracellular proteins to the beads was monitored fluorescently. By analyzing many individual droplets and quantifying the data obtained against standard additions, we measured the level of two intracellular proteins, namely, HRas-mCitrine, expressed within HEK-293 cells, and actin-EGFP, expressed within MCF-7 cells. We determined the concentrations of these proteins over 5 orders of magnitude, from ~50 pM to 1 μM. The results from this semiautomated method were compared to those for determinations made using Western blots, and were found not only to be faster, but required a smaller number of cells.
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Affiliation(s)
- Chiara Martino
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8LT, United Kingdom
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Goodwin RJA, Pitt AR, Harrison D, Weidt SK, Langridge-Smith PRR, Barrett MP, Logan Mackay C. Matrix-free mass spectrometric imaging using laser desorption ionisation Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 2011; 25:969-72. [PMID: 21416534 PMCID: PMC3505379 DOI: 10.1002/rcm.4939] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/18/2011] [Accepted: 01/18/2011] [Indexed: 05/20/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool in metabolomics and proteomics for the spatial localization and identification of pharmaceuticals, metabolites, lipids, peptides and proteins in biological tissues. However, sample preparation remains a crucial variable in obtaining the most accurate distributions. Common washing steps used to remove salts, and solvent-based matrix application, allow analyte spreading to occur. Solvent-free matrix applications can reduce this risk, but increase the possibility of ionisation bias due to matrix adhesion to tissue sections. We report here the use of matrix-free MSI using laser desorption ionisation performed on a 12 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. We used unprocessed tissue with no post-processing following thaw-mounting on matrix-assisted laser desorption ionisation (MALDI) indium-tin oxide (ITO) target plates. The identification and distribution of a range of phospholipids in mouse brain and kidney sections are presented and compared with previously published MALDI time-of-flight (TOF) MSI distributions.
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Affiliation(s)
- Richard J A Goodwin
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, UK.
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Jiwaji M, Daly R, Pansare K, McLean P, Yang J, Kolch W, Pitt AR. The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells. BMC Mol Biol 2010; 11:103. [PMID: 21194418 PMCID: PMC3022783 DOI: 10.1186/1471-2199-11-103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 12/31/2010] [Indexed: 12/04/2022] Open
Abstract
Background The importance of appropriate normalization controls in quantitative real-time polymerase chain reaction (qPCR) experiments has become more apparent as the number of biological studies using this methodology has increased. In developing a system to study gene expression from transiently transfected plasmids, it became clear that normalization using chromosomally encoded genes is not ideal, at it does not take into account the transfection efficiency and the significantly lower expression levels of the plasmids. We have developed and validated a normalization method for qPCR using a co-transfected plasmid. Results The best chromosomal gene for normalization in the presence of the transcriptional activators used in this study, cadmium, dexamethasone, forskolin and phorbol-12-myristate 13-acetate was first identified. qPCR data was analyzed using geNorm, Normfinder and BestKeeper. Each software application was found to rank the normalization controls differently with no clear correlation. Including a co-transfected plasmid encoding the Renilla luciferase gene (Rluc) in this analysis showed that its calculated stability was not as good as the optimised chromosomal genes, most likely as a result of the lower expression levels and transfection variability. Finally, we validated these analyses by testing two chromosomal genes (B2M and ActB) and a co-transfected gene (Rluc) under biological conditions. When analyzing co-transfected plasmids, Rluc normalization gave the smallest errors compared to the chromosomal reference genes. Conclusions Our data demonstrates that transfected Rluc is the most appropriate normalization reference gene for transient transfection qPCR analysis; it significantly reduces the standard deviation within biological experiments as it takes into account the transfection efficiencies and has easily controllable expression levels. This improves reproducibility, data validity and most importantly, enables accurate interpretation of qPCR data.
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Affiliation(s)
- Meesbah Jiwaji
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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Abstract
Immunoprecipitation (IP) is one of the most widely used and selective techniques for protein purification. Here, a miniaturised, polymer-supported immunoprecipitation (µIP) method for the on-chip purification of proteins from complex mixtures is described. A 4 µl PDMS column functionalised with covalently bound antibodies was created and all critical aspects of the µIP protocol (antibody immobilisation, blocking of potential non-specific adsorption sites, sample incubation and washing conditions) were assessed and optimised. The optimised µIP method was used to obtain purified fractions of affinity-tagged protein from a bacterial lysate.
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Affiliation(s)
- Mairi E Sandison
- Integrative and Systems Biology, FBLS, University of Glasgow, Glasgow, G12 8QQ, UK.
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Goodwin RJA, Lang AM, Allingham H, Borén M, Pitt AR. Stopping the clock on proteomic degradation by heat treatment at the point of tissue excision. Proteomics 2010; 10:1751-61. [PMID: 20217868 DOI: 10.1002/pmic.200900641] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The effectiveness of rapid and controlled heating of intact tissue to inactivate native enzymatic activity and prevent proteome degradation has been evaluated. Mouse brains were bisected immediately following excision, with one hemisphere being heat treated followed by snap freezing in liquid nitrogen while the other hemisphere was snap frozen immediately. Sections were cut by cryostatic microtome and analyzed by MALDI-MS imaging and minimal label 2-D DIGE, to monitor time-dependent relative changes in intensities of protein and peptide signals. Analysis by MALDI-MS imaging demonstrated that the relative intensities of markers varied across a time course (0-5 min) when the tissues were not stabilized by heat treatment. However, the same markers were seen to be stabilized when the tissues were heat treated before snap freezing. Intensity profiles for proteins indicative of both degradation and stabilization were generated when samples of treated and nontreated tissues were analyzed by 2-D DIGE, with protein extracted before and after a 10-min warming of samples. Thus, heat treatment of tissues at the time of excision is shown to prevent subsequent uncontrolled degradation of tissues at the proteomic level before any quantitative analysis, and to be compatible with downstream proteomic analysis.
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Affiliation(s)
- Richard J A Goodwin
- Division of Integrative and Systems Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
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Goodwin RJA, Scullion P, Macintyre L, Watson DG, Pitt AR. Use of a solvent-free dry matrix coating for quantitative matrix-assisted laser desorption ionization imaging of 4-bromophenyl-1,4-diazabicyclo(3.2.2)nonane-4-carboxylate in rat brain and quantitative analysis of the drug from laser microdissected tissue regions. Anal Chem 2010; 82:3868-73. [PMID: 20380422 DOI: 10.1021/ac100398y] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A dry matrix application for matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) was used to profile the distribution of 4-bromophenyl-1,4-diazabicyclo(3.2.2)nonane-4-carboxylate, monohydrochloride (BDNC, SSR180711) in rat brain tissue sections. Matrix application involved applying layers of finely ground dry alpha-cyano-4-hydroxycinnamic acid (CHCA) to the surface of tissue sections thaw mounted onto MALDI targets. It was not possible to detect the drug when applying matrix in a standard aqueous-organic solvent solution. The drug was detected at higher concentrations in specific regions of the brain, particularly the white matter of the cerebellum. Pseudomultiple reaction monitoring imaging was used to validate that the observed distribution was the target compound. The semiquantitative data obtained from signal intensities in the imaging was confirmed by laser microdissection of specific regions of the brain directed by the imaging, followed by hydrophilic interaction chromatography in combination with a quantitative high-resolution mass spectrometry method. This study illustrates that a dry matrix coating is a valuable and complementary matrix application method for analysis of small polar drugs and metabolites that can be used for semiquantitative analysis.
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Affiliation(s)
- R J A Goodwin
- Division of Integrative and Systems Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, UK
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Goodwin RJ, Macintyre L, Watson DG, Scullion SP, Pitt AR. A solvent-free matrix application method for matrix-assisted laser desorption/ionization imaging of small molecules. Rapid Commun Mass Spectrom 2010; 24:1682-1686. [PMID: 20486266 DOI: 10.1002/rcm.4567] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Matrix application continues to be a critical step in sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI). Imaging of small molecules such as drugs and metabolites is particularly problematic because the commonly used washing steps to remove salts are usually omitted as they may also remove the analyte, and analyte spreading is more likely with conventional wet matrix application methods. We have developed a method which uses the application of matrix as a dry, finely divided powder, here referred to as dry matrix application, for the imaging of drug compounds. This appears to offer a complementary method to wet matrix application for the MALDI-MSI of small molecules, with the alternative matrix application techniques producing different ion profiles, and allows the visualization of compounds not observed using wet matrix application methods. We demonstrate its value in imaging clozapine from rat kidney and 4-bromophenyl-1,4-diazabicyclo(3.2.2)nonane-4-carboxylic acid from rat brain. In addition, exposure of the dry matrix coated sample to a saturated moist atmosphere appears to enhance the visualization of a different set of molecules.
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Affiliation(s)
- R J Goodwin
- Division of Integrative and Systems Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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Robaszkiewicz A, Greig FH, Pitt AR, Spickett CM, Bartosz G, Soszyński M. Effect of phosphatidylcholine chlorohydrins on human erythrocytes. Chem Phys Lipids 2010; 163:639-47. [PMID: 20513376 DOI: 10.1016/j.chemphyslip.2010.05.201] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 05/21/2010] [Accepted: 05/21/2010] [Indexed: 12/14/2022]
Abstract
Hypochlorite generated in vivo under pathological conditions is a known oxidant and chlorinating agent, able to react with proteins and lipids, which affects the stability of biological membranes. Reaction with unsaturated fatty acyl chains in glycerophospholipids such as phosphatidylcholine results in the formation of chlorohydrins. The aim of this study was to determine the effects of chlorohydrins formed by the reaction of hypochlorite with 1-stearoyl-2-oleoyl-, 1-stearoyl-2-linoleoyl-, and 1-stearoyl-2-arachidonylphosphatidylcholine on biophysical properties of bilayers and their effects on human erythrocytes. Using electrospray mass spectrometry we observed complete conversion of the lipids into chlorohydrins, which resulted in a decrease in the rotational correlation time and an increase in the order parameter of liposomes. Unilamellar chlorohydrin liposomes had a lower permeation coefficient for calcein than liposomes made of parent lipids. Flow cytometry demonstrated fast incorporation of uni and multilamellar chlorohydrin liposomes labeled with NBD-phosphatidylethanolamine into erythrocytes. This effect was accompanied by changes in erythrocyte shape (echinocyte formation) and aggregation. Similar but less pronounced effects were noticed for parent lipids only after longer incubation. Chlorohydrins showed also a stronger hemolytic action, proportional to the lipid:erythrocyte ratio. These results are important for understanding the effects of HOCl on mammalian cells, such as might occur in inflammatory pathology.
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Mouls L, Silajdzic E, Haroune N, Spickett CM, Pitt AR. Development of novel mass spectrometric methods for identifying HOCl-induced modifications to proteins. Proteomics 2009; 9:1617-31. [PMID: 19253297 DOI: 10.1002/pmic.200800391] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein oxidation is thought to contribute to a number of inflammatory diseases, hence the development of sensitive and specific analytical techniques to detect oxidative PTMs (oxPTMs) in biological samples is highly desirable. Precursor ion scanning for fragment ions of oxidized amino acid residues was investigated as a label-free MS approach to mapping specific oxPTMs in a complex mixture of proteins. Using HOCl-oxidized lysozyme as a model system, it was found that the immonium ions of oxidized tyrosine and tryptophan formed in MS(2) analysis could not be used as diagnostic ions, owing to the occurrence of isobaric fragment ions from unmodified peptides. Using a double quadrupole linear ion trap mass spectrometer, precursor ion scanning was combined with detection of MS(3) fragment ions from the immonium ions and collisionally-activated decomposition peptide sequencing to achieve selectivity for the oxPTMs. For chlorotyrosine, the immonium ion at 170.1 m/z fragmented to yield diagnostic ions at 153.1, 134.1, and 125.1 m/z, and the hydroxytyrosine immonium ion at 152.1 m/z gave diagnostic ions at 135.1 and 107.1 m/z. Selective MS(3) fragment ions were also identified for 2-hydroxytryptophan and 5-hydroxytryptophan. The method was used successfully to map these oxPTMs in a mixture of nine proteins that had been treated with HOCl, thereby demonstrating its potential for application to complex biological samples.
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Affiliation(s)
- Laetitia Mouls
- Faculty of Biological and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
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Burgess KEV, Lainson A, Imrie L, Fraser-Pitt D, Yaga R, Smith DGE, Swart R, Pitt AR, Inglis NF. Performance of five different electrospray ionisation sources in conjunction with rapid monolithic column liquid chromatography and fast MS/MS scanning. Proteomics 2009; 9:1720-6. [PMID: 19242933 DOI: 10.1002/pmic.200800200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The performances of five different ESI sources coupled to a polystyrene-divinylbenzene monolithic column were compared in a series of LC-ESI-MS/MS analyses of Escherichia coli outer membrane proteins. The sources selected for comparison included two different modifications of the standard electrospray source, a commercial low-flow sprayer, a stainless steel nanospray needle and a coated glass Picotip. Respective performances were judged on sensitivity and the number and reproducibility of significant protein identifications obtained through the analysis of multiple identical samples. Data quality varied between that of a ground silica capillary, with 160 total protein identifications, the lowest number of high quality peptide hits obtained (3012), and generally peaks of lower intensity; and a stainless steel nanospray needle, which resulted in increased precursor ion abundance, the highest-quality peptide fragmentation spectra (5414) and greatest number of total protein identifications (259) exhibiting the highest MASCOT scores (average increase in score of 27.5% per identified protein). The data presented show that, despite increased variability in comparative ion intensity, the stainless steel nanospray needle provides the highest overall sensitivity. However, the resulting data were less reproducible in terms of proteins identified in complex mixtures -- arguably due to an increased number of high intensity precursor ion candidates.
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Affiliation(s)
- Karl E V Burgess
- Integrative and Systems Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
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Abstract
We have used MALDI-MS imaging (MALDI-MSI) to monitor the time dependent appearance and loss of signals when tissue slices are brought rapidly to room temperature for short to medium periods of time. Sections from mouse brain were cut in a cryostat microtome, placed on a MALDI target and allowed to warm to room temperature for 30 s to 3 h. Sections were then refrozen, fixed by ethanol treatment and analysed by MALDI-MSI. The intensity of a range of markers were seen to vary across the time course, both increasing and decreasing, with the intensity of some markers changing significantly within 30 s and markers also showed tissue location specific evolution. The markers resulting from this autolysis were compared directly to those that evolved in a comparable 16 h on-tissue trypsin digest, and the markers that evolved in the two studies were seen to be substantially different. These changes offer an important additional level of location-dependent information for mapping changes and seeking disease-dependent biomarkers in the tissue. They also indicate that considerable care is required to allow comparison of biomarkers between MALDI-MSI experiments and also has implications for the standard practice of thaw-mounting multiple tissue sections onto MALDI-MS targets.
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Affiliation(s)
- Richard J A Goodwin
- Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
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Bridges DJ, Pitt AR, Hanrahan O, Brennan K, Voorheis HP, Herzyk P, de Koning HP, Burchmore RJS. Characterisation of the plasma membrane subproteome of bloodstream form Trypanosoma brucei. Proteomics 2008; 8:83-99. [PMID: 18095354 DOI: 10.1002/pmic.200700607] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteome analysis by conventional approaches is biased against hydrophobic membrane proteins, many of which are also of low abundance. We have isolated plasma membrane sheets from bloodstream forms of Trypanosoma brucei by subcellular fractionation, and then applied a battery of complementary protein separation and identification techniques to identify a large number of proteins in this fraction. The results of these analyses have been combined to generate a subproteome for the pellicular plasma membrane of bloodstream forms of T. brucei as well as a separate subproteome for the pellicular cytoskeleton. In parallel, we have used in silico approaches to predict the relative abundance of proteins potentially expressed by bloodstream form trypanosomes, and to identify likely polytopic membrane proteins, providing quality control for the experimentally defined plasma membrane subproteome. We show that the application of multiple high-resolution proteomic techniques to an enriched organelle fraction is a valuable approach for the characterisation of relatively intractable membrane proteomes. We present here the most complete analysis of a protozoan plasma membrane proteome to date and show the presence of a large number of integral membrane proteins, including 11 nucleoside/nucleobase transporters, 15 ion pumps and channels and a large number of adenylate cyclases hitherto listed as putative proteins.
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Affiliation(s)
- Daniel J Bridges
- Division of Infection and Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
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Zimmerli LU, Schiffer E, Zürbig P, Good DM, Kellmann M, Mouls L, Pitt AR, Coon JJ, Schmieder RE, Peter KH, Mischak H, Kolch W, Delles C, Dominiczak AF. Urinary Proteomic Biomarkers in Coronary Artery Disease. Mol Cell Proteomics 2008; 7:290-8. [DOI: 10.1074/mcp.m700394-mcp200] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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McMillan N, Smith LV, de la Fuente JM, Parenty ADC, Gadegaard N, Pitt AR, Thomson K, Mackenzie C, Kelly SM, Cronin L. Incorporation of N-heterocyclic cations into proteins with a highly directed chemical modification. Chem Commun (Camb) 2007:2581-3. [PMID: 17579744 DOI: 10.1039/b702575k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Heterocyclic cations are incorporated into proteins using 5-(2-bromoethyl)phenanthridinium bromide, which selectively reacts with either cysteine or lysine residues, resulting in ethylphenanthridinium (Phen) or highly stable cyclised dihydro-imidazo-phenanthridinium (DIP) adducts respectively; these modifications have been found to manipulate the observed structure of lysozyme and bovine serum albumin by AFM.
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Affiliation(s)
- Nicola McMillan
- WestCHEM, Department of Chemistry, The University of Glasgow, University Avenue, Glasgow, UK
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Abstract
The global study of the structure and dynamics of metabolic networks has been hindered by a lack of techniques that identify metabolites and their biochemical relationship in complex mixtures. The recent application of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to metabolomic analysis suggests a way to tackle the problem. A lower-cost alternative to high-field FTICR-MS, the Orbitrap mass analyzer, promises accelerated activity in this area. Here, we show how the ultra-high mass accuracy and resolution provided by this new generation of mass spectrometers can help to identify metabolites and connect them into metabolic networks. Data from perturbation studies and isotope-tracking experiments can complement this information to create metabolic maps de novo and chart unexplored areas of metabolism.
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Affiliation(s)
- Rainer Breitling
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands.
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