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McCullagh J, Probert F. New analytical methods focusing on polar metabolite analysis in mass spectrometry and NMR-based metabolomics. Curr Opin Chem Biol 2024; 80:102466. [PMID: 38772215 DOI: 10.1016/j.cbpa.2024.102466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/19/2024] [Accepted: 04/26/2024] [Indexed: 05/23/2024]
Abstract
Following in the footsteps of genomics and proteomics, metabolomics has revolutionised the way we investigate and understand biological systems. Rapid development in the last 25 years has been driven largely by technical innovations in mass spectrometry and nuclear magnetic resonance spectroscopy. However, despite the modest size of metabolomes relative to proteomes and genomes, methodological capabilities for robust, comprehensive metabolite analysis remain a major challenge. Therefore, development of new methods and techniques remains vital for progress in the field. Here, we review developments in LC-MS, GC-MS and NMR methods in the last few years that have enhanced quantitative and comprehensive metabolome coverage, highlighting the techniques involved, their technical capabilities, relative performance, and potential impact.
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Affiliation(s)
- James McCullagh
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
| | - Fay Probert
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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2
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Ovbude ST, Sharmeen S, Kyei I, Olupathage H, Jones J, Bell RJ, Powers R, Hage DS. Applications of chromatographic methods in metabolomics: A review. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1239:124124. [PMID: 38640794 DOI: 10.1016/j.jchromb.2024.124124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 03/11/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
Chromatography is a robust and reliable separation method that can use various stationary phases to separate complex mixtures commonly seen in metabolomics. This review examines the types of chromatography and stationary phases that have been used in targeted or untargeted metabolomics with methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. General considerations for sample pretreatment and separations in metabolomics are considered, along with the various supports and separation formats for chromatography that have been used in such work. The types of liquid chromatography (LC) that have been most extensively used in metabolomics will be examined, such as reversed-phase liquid chromatography and hydrophilic liquid interaction chromatography. In addition, other forms of LC that have been used in more limited applications for metabolomics (e.g., ion-exchange, size-exclusion, and affinity methods) will be discussed to illustrate how these techniques may be utilized for new and future research in this field. Multidimensional LC methods are also discussed, as well as the use of gas chromatography and supercritical fluid chromatography in metabolomics. In addition, the roles of chromatography in NMR- vs. MS-based metabolomics are considered. Applications are given within the field of metabolomics for each type of chromatography, along with potential advantages or limitations of these separation methods.
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Affiliation(s)
- Susan T Ovbude
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Sadia Sharmeen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Isaac Kyei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Harshana Olupathage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Jacob Jones
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Richard J Bell
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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3
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Then CK, Paillas S, Moomin A, Misheva MD, Moir RA, Hay SM, Bremner D, Roberts Nee Nellany KS, Smith EE, Heidari Z, Sescu D, Wang X, Suárez-Bonnet A, Hay N, Murdoch SL, Saito R, Collie-Duguid ESR, Richardson S, Priestnall SL, Wilson JM, Gurumurthy M, Royle JS, Samuel LM, Ramsay G, Vallis KA, Foster KR, McCullagh JSO, Kiltie AE. Dietary fibre supplementation enhances radiotherapy tumour control and alleviates intestinal radiation toxicity. MICROBIOME 2024; 12:89. [PMID: 38745230 PMCID: PMC11092108 DOI: 10.1186/s40168-024-01804-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/02/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Non-toxic approaches to enhance radiotherapy outcomes are beneficial, particularly in ageing populations. Based on preclinical findings showing that high-fibre diets sensitised bladder tumours to irradiation by modifying the gut microbiota, along with clinical evidence of prebiotics enhancing anti-cancer immunity, we hypothesised that dietary fibre and its gut microbiota modification can radiosensitise tumours via secretion of metabolites and/or immunomodulation. We investigated the efficacy of high-fibre diets combined with irradiation in immunoproficient C57BL/6 mice bearing bladder cancer flank allografts. RESULT Psyllium plus inulin significantly decreased tumour size and delayed tumour growth following irradiation compared to 0.2% cellulose and raised intratumoural CD8+ cells. Post-irradiation, tumour control positively correlated with Lachnospiraceae family abundance. Psyllium plus resistant starch radiosensitised the tumours, positively correlating with Bacteroides genus abundance and increased caecal isoferulic acid levels, associated with a favourable response in terms of tumour control. Psyllium plus inulin mitigated the acute radiation injury caused by 14 Gy. Psyllium plus inulin increased caecal acetate, butyrate and propionate levels, and psyllium alone and psyllium plus resistant starch increased acetate levels. Human gut microbiota profiles at the phylum level were generally more like mouse 0.2% cellulose profiles than high fibre profiles. CONCLUSION These supplements may be useful in combination with radiotherapy in patients with pelvic malignancy. Video Abstract.
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Affiliation(s)
- Chee Kin Then
- Department of Oncology, University of Oxford, Oxford, UK
- Department of Radiation Oncology, Shunag Ho Hospital, Taipei Medical University, New Taipai City, Taiwan
| | - Salome Paillas
- Department of Oncology, University of Oxford, Oxford, UK
| | - Aliu Moomin
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
- Aberdeen Cancer Centre, University of Aberdeen, Aberdeen, UK
| | - Mariya D Misheva
- Chemistry Research Laboratory, Department of Chemistry, Mansfield Road, University of Oxford, Oxford, UK
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Rachel A Moir
- Department of Oncology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Susan M Hay
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
- Aberdeen Cancer Centre, University of Aberdeen, Aberdeen, UK
| | - David Bremner
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | | | - Ellen E Smith
- Centre for Genome Enabled Biology and Medicine, School of Medicine Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Zeynab Heidari
- Centre for Genome Enabled Biology and Medicine, School of Medicine Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Daniel Sescu
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Xuedan Wang
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Alejandro Suárez-Bonnet
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Nadine Hay
- NHS Grampian Biorepository, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Sarah L Murdoch
- NHS Grampian Biorepository, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Ryoichi Saito
- Lineberger Comprehensive Cancer Centre, University of North Carolina at Chapel Hill, Chapel Hill, USA
- The Department of Urology, Kyoto University, Kyoto, Japan
| | - Elaina S R Collie-Duguid
- Centre for Genome Enabled Biology and Medicine, School of Medicine Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | | | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Joan M Wilson
- NHS Grampian Biorepository, Aberdeen Royal Infirmary, Aberdeen, UK
| | | | - Justine S Royle
- Department of Urology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Leslie M Samuel
- Department of Oncology, Aberdeen Royal Infirmary, Aberdeen, UK
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - George Ramsay
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
- Health Services Research Unit, University of Aberdeen, Aberdeen, UK
| | | | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, Mansfield Road, University of Oxford, Oxford, UK
| | - Anne E Kiltie
- Department of Oncology, University of Oxford, Oxford, UK.
- The Rowett Institute, University of Aberdeen, Aberdeen, UK.
- Aberdeen Cancer Centre, University of Aberdeen, Aberdeen, UK.
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK.
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4
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Okomo Aloo S, Park S, Martins Oyinloye T, Oh DH. Rheological properties, biochemical changes, and potential health benefits of dehulled and defatted industrial hempseeds after fermentation. Food Chem 2024; 439:138086. [PMID: 38043281 DOI: 10.1016/j.foodchem.2023.138086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/11/2023] [Accepted: 11/25/2023] [Indexed: 12/05/2023]
Abstract
Dehulled hempseed (DHS), fermented dehulled hempseed (FDHS), hempseed cake (HSC), and fermented HSC (FHSC) were examined for their phytochemical composition, health benefits, and rheological characteristics. At 500 µg/mL concentration, DHS, FDHS, HSC, and FHSC extracts exhibited the ability to inhibit DPPH radicals, with 32.46 %, 47.35 %, 33.85 %, and 47.41 %, respectively. Similarly, they demonstrated potential to scavenge ABTS radicals by 13.7 %, 27.87 %, 14.40 % and 25.70 %, respectively. For lipase inhibition activity, FDHS (72.92 %) and FDHS (85.89 %) outperformed DHS (52.94 %) and HSC (43.08 %). Furthermore, FHSC enhanced the survival and reduced fat accumulation in glucose-supplemented Caenorhabditis elegans. We used HPLC and UHPLC-ESI-QTOF-MS for metabolite analysis, quantifying eight polyphenols using HPLC and identifying thirty-four metabolites with UHPLC-ESI-QTOF-MS. Generally, metabolomics indicated an improved metabolite profile after fermentation. Fermentation also showed impact on rheological characteristics, modifying viscosity, loss modulus, and storage modulus. These findings collectively demonstrate the ability of fermentation in enhancing overall value of hempseed.
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Affiliation(s)
- Simon Okomo Aloo
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - SeonJu Park
- Chuncheon Center, Korea Basic Science Institute, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Timilehin Martins Oyinloye
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea.
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5
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Westhoff P, Weber APM. The role of metabolomics in informing strategies for improving photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1696-1713. [PMID: 38158893 DOI: 10.1093/jxb/erad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.
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Affiliation(s)
- Philipp Westhoff
- CEPLAS Plant Metabolomics and Metabolism Laboratory, Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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6
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Bergmann D, Matarrita-Rodríguez J, Abdulla H. Toward a More Comprehensive Approach for Dissolved Organic Matter Chemical Characterization Using an Orbitrap Fusion Tribrid Mass Spectrometer Coupled with Ion and Liquid Chromatography Techniques. Anal Chem 2024; 96:3744-3753. [PMID: 38373907 PMCID: PMC10918622 DOI: 10.1021/acs.analchem.3c02599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Dissolved organic matter (DOM) represents one of the largest active organic carbon pools in the global carbon cycle. Although extensively studied, only <10% of DOM has been chemically characterized into individual dissolved compounds due to its molecular complexity. This study introduced a more comprehensive DOM characterization method by coupling both ion chromatography (IC) and liquid chromatography (LC) with high mass accuracy and resolution mass spectrometry. We presented a new on-the-fly mass calibration of the Orbitrap technique by utilizing the "lock mass" function in the Orbitrap Fusion Tribrid mass spectrometer (OT-FTMS), which assures high mass accuracy at every scan by a postcolumn introduction of internal labeled standards. With both IC and LC, tested unlabeled standards of amino acids, small peptides, and organic acids were consistently below 1.0 ppm mass error, giving the OT-FTMS the potential of reaching mass accuracy of the Fourier-transform ion cyclotron resonance mass spectrometer. In addition to mass accuracy, a pooled quality control sample (QC) was used to increase reproducibility by applying systematic error removal using random forest (SERRF). Using an untargeted mass spectrometry approach, estuarine DOM samples were analyzed by OT-FTMS coupled to IC in negative mode and LC in positive mode detection to cover a wide range of highly cationic to highly anionic molecules. As a proof of concept, we focused on elucidating the structures of three distinct DOM compound classes with varied acidities and basicities. In UPLC-OT-FTMS, a total of 915 compounds were detected. We putatively elucidated 44 small peptides and 33 deaminated peptides of these compounds. With IC-OT-FTMS, a total of 1432 compounds were detected. We putatively elucidated 20 peptides, 268 deaminated peptides, and 188 organic acids. Except for five compounds, all putatively elucidated compounds were uniquely detected in their corresponding chromatography technique. These results highlight the need for combining these two techniques to provide a more comprehensive method for DOM characterization. Application of the combined IC and LC techniques is not limited to DOM chemical characterization. It can analyze other complex compound mixtures, such as metabolites, and anthropogenic pollutants, such as pesticides and endocrine-disrupting chemicals, in environmental and biological samples.
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Affiliation(s)
- Daniela Bergmann
- Department
of Physical and Environmental Sciences, Texas A&M University-Corpus Christi , Corpus Christi, Texas 78412, United States
| | - Jessie Matarrita-Rodríguez
- Department
of Physical and Environmental Sciences, Texas A&M University-Corpus Christi , Corpus Christi, Texas 78412, United States
- Centro
de Investigación en Contaminación Ambiental (CICA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Hussain Abdulla
- Department
of Physical and Environmental Sciences, Texas A&M University-Corpus Christi , Corpus Christi, Texas 78412, United States
- Center
for Water Supply Studies, Texas A&M
University-Corpus Christi , Corpus Christi, Texas 78412, United States
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7
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Ikeda K, Takahashi M, Bamba T, Izumi Y. Comparison of Amine-Modified Polymeric Stationary Phases for Polar Metabolomic Analysis Based on Unified-Hydrophilic Interaction/Anion Exchange Liquid Chromatography/High-Resolution Mass Spectrometry (Unified-HILIC/AEX/HRMS). Mass Spectrom (Tokyo) 2024; 13:A0143. [PMID: 38410254 PMCID: PMC10894851 DOI: 10.5702/massspectrometry.a0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
In metabolomic analysis, one of the most commonly used techniques to support the detection sensitivity and quantitation of mass spectrometry is combining it with liquid chromatography. Recently, we developed a method that enables comprehensive single-run measurement of hydrophilic metabolites using unified-hydrophilic interaction/anion exchange liquid chromatography/high-resolution mass spectrometry (unified-HILIC/AEX/HRMS) with a polymer-based mixed amines column (Gelpack GL-HilicAex). However, the importance of stationary phase functional groups and mobile phase conditions for the separation mechanisms and sensitive detection in unified-HILIC/AEX/HRMS is not yet fully understood. This study aimed to understand the importance of the mobile and stationary phases in unified-HILIC/AEX/HRMS. Two different alkali-resistant polymer-based amines-modified columns (Gelpack GL-HilicAex, primary, secondary, tertiary, and quaternary amine-modified polyglycerol dimethacrylate gel; Asahipak NH2P-50 2D, secondary amine-modified polyvinyl alcohol gel) and two eluents (acetonitrile and ammonium bicarbonate solution, pH 9.8) were used for comparative validation. A comparison of mobile phase conditions using both columns confirmed that the two-step separation from HILIC to AEX characteristic of unified-HILIC/AEX requires a linear gradient condition from acetonitrile to nearly 50% water and AEX with up to 40 mM bicarbonate ions. We found that when alkali-resistant hydrophilic polymer packing materials are modified with amines, unified-HILIC/AEX separation can be reproduced if at least one secondary amine associated with the amine series is present in the stationary phase. Furthermore, the difference in sensitivity in the HILIC and AEX modes owing to the different columns indicates the need for further improvements in the mobile phase composition and stationary phase.
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Affiliation(s)
- Kazuki Ikeda
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatomo Takahashi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Bamba
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoshihiro Izumi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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8
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Yalaz C, Bridges E, Alham NK, Zois CE, Chen J, Bensaad K, Miar A, Pires E, Muschel RJ, McCullagh JSO, Harris AL. Cone photoreceptor phosphodiesterase PDE6H inhibition regulates cancer cell growth and metabolism, replicating the dark retina response. Cancer Metab 2024; 12:5. [PMID: 38350962 PMCID: PMC10863171 DOI: 10.1186/s40170-023-00326-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/24/2023] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND PDE6H encodes PDE6γ', the inhibitory subunit of the cGMP-specific phosphodiesterase 6 in cone photoreceptors. Inhibition of PDE6, which has been widely studied for its role in light transduction, increases cGMP levels. The purpose of this study is to characterise the role of PDE6H in cancer cell growth. METHODS From an siRNA screen for 487 genes involved in metabolism, PDE6H was identified as a controller of cell cycle progression in HCT116 cells. Role of PDE6H in cancer cell growth and metabolism was studied through the effects of its depletion on levels of cell cycle controllers, mTOR effectors, metabolite levels, and metabolic energy assays. Effect of PDE6H deletion on tumour growth was also studied in a xenograft model. RESULTS PDE6H knockout resulted in an increase of intracellular cGMP levels, as well as changes to the levels of nucleotides and key energy metabolism intermediates. PDE6H knockdown induced G1 cell cycle arrest and cell death and reduced mTORC1 signalling in cancer cell lines. Both knockdown and knockout of PDE6H resulted in the suppression of mitochondrial function. HCT116 xenografts revealed that PDE6H deletion, as well as treatment with the PDE5/6 inhibitor sildenafil, slowed down tumour growth and improved survival, while sildenafil treatment did not have an additive effect on slowing the growth of PDE6γ'-deficient tumours. CONCLUSIONS Our results indicate that the changes in cGMP and purine pools, as well as mitochondrial function which is observed upon PDE6γ' depletion, are independent of the PKG pathway. We show that in HCT116, PDE6H deletion replicates many effects of the dark retina response and identify PDE6H as a new target in preventing cancer cell proliferation and tumour growth.
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Affiliation(s)
- Ceren Yalaz
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Esther Bridges
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nasullah K Alham
- Department of Engineering Science, Institute of Biomedical Engineering (IBME), University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Christos E Zois
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jianzhou Chen
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Karim Bensaad
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana Miar
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ruth J Muschel
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - James S O McCullagh
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Adrian L Harris
- Molecular Oncology Laboratories, Department of Medical Oncology, John Radcliffe Hospital, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
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9
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Park KC, Crump NT, Louwman N, Krywawych S, Cheong YJ, Vendrell I, Gill EK, Gunadasa-Rohling M, Ford KL, Hauton D, Fournier M, Pires E, Watson L, Roseman G, Holder J, Koschinski A, Carnicer R, Curtis MK, Zaccolo M, Hulikova A, Fischer R, Kramer HB, McCullagh JSO, Trefely S, Milne TA, Swietach P. Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1221-1245. [PMID: 38500966 PMCID: PMC7615744 DOI: 10.1038/s44161-023-00365-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/15/2023] [Indexed: 03/20/2024]
Abstract
Propiogenic substrates and gut bacteria produce propionate, a post-translational protein modifier. In this study, we used a mouse model of propionic acidaemia (PA) to study how disturbances to propionate metabolism result in histone modifications and changes to gene expression that affect cardiac function. Plasma propionate surrogates were raised in PA mice, but female hearts manifested more profound changes in acyl-CoAs, histone propionylation and acetylation, and transcription. These resulted in moderate diastolic dysfunction with raised diastolic Ca2+, expanded end-systolic ventricular volume and reduced stroke volume. Propionate was traced to histone H3 propionylation and caused increased acetylation genome-wide, including at promoters of Pde9a and Mme, genes related to contractile dysfunction through downscaled cGMP signaling. The less severe phenotype in male hearts correlated with β-alanine buildup. Raising β-alanine in cultured myocytes treated with propionate reduced propionyl-CoA levels, indicating a mechanistic relationship. Thus, we linked perturbed propionate metabolism to epigenetic changes that impact cardiac function.
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Affiliation(s)
- Kyung Chan Park
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Nicholas T. Crump
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Present Address: Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Niamh Louwman
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Steve Krywawych
- Department of Chemical Pathology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Yuen Jian Cheong
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Iolanda Vendrell
- Nuffield Department of Medicine, Target Discovery Institute, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Eleanor K. Gill
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | | | - Kerrie L. Ford
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - David Hauton
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | - Lydia Watson
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Gerald Roseman
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - James Holder
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Koschinski
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Ricardo Carnicer
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - M. Kate Curtis
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Manuela Zaccolo
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Alzbeta Hulikova
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Holger B. Kramer
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Sophie Trefely
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Thomas A. Milne
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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10
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Macioszek S, Dudzik D, Biesemans M, Wozniak A, Schöffski P, Markuszewski MJ. A multiplatform metabolomics approach for comprehensive analysis of GIST xenografts with various KIT mutations. Analyst 2023; 148:3883-3891. [PMID: 37458061 DOI: 10.1039/d3an00599b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Metabolites in biological matrices belong to diverse chemical groups, ranging from non-polar long-chain fatty acids to small polar molecules. The goal of untargeted metabolomic analysis is to measure the highest number of metabolites in the sample. Nevertheless, from an analytical point of view, no single technique can measure such a broad spectrum of analytes. Therefore, we selected a method based on GC-MS and LC-MS with two types of stationary phases for the untargeted profiling of gastrointestinal stromal tumours. The procedure was applied to GIST xenograft samples (n = 71) representing four different mutation models, half of which were treated with imatinib. We aimed to verify the method coverage and advantages of applying each technique. RP-LC-MS measured most metabolites due to a significant fraction of lipid components of the tumour tissue. What is unique and worth noting is that all applied techniques were able to distinguish between different mutation models. However, for detecting imatinib-induced alterations in the GIST metabolome, RP-LC-MS and GC-MS proved to be more relevant than HILIC-LC-MS, resulting in a higher number of significantly changed metabolites in four treated models. Undoubtedly, the inclusion of all mentioned techniques makes the method more comprehensive. Nonetheless, for green chemistry and time and labour saving, we assume that RP-LC-MS and GC-MS analyses are sufficient to cover the global GIST metabolome.
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Affiliation(s)
- Szymon Macioszek
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
| | - Danuta Dudzik
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
| | - Margot Biesemans
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
| | - Agnieszka Wozniak
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, and Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Patrick Schöffski
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, and Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Michal J Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland.
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11
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Solomou G, Finch A, Asghar A, Bardella C. Mutant IDH in Gliomas: Role in Cancer and Treatment Options. Cancers (Basel) 2023; 15:cancers15112883. [PMID: 37296846 DOI: 10.3390/cancers15112883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Altered metabolism is a common feature of many cancers and, in some cases, is a consequence of mutation in metabolic genes, such as the ones involved in the TCA cycle. Isocitrate dehydrogenase (IDH) is mutated in many gliomas and other cancers. Physiologically, IDH converts isocitrate to α-ketoglutarate (α-KG), but when mutated, IDH reduces α-KG to D2-hydroxyglutarate (D2-HG). D2-HG accumulates at elevated levels in IDH mutant tumours, and in the last decade, a massive effort has been made to develop small inhibitors targeting mutant IDH. In this review, we summarise the current knowledge about the cellular and molecular consequences of IDH mutations and the therapeutic approaches developed to target IDH mutant tumours, focusing on gliomas.
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Affiliation(s)
- Georgios Solomou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Alina Finch
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Asim Asghar
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chiara Bardella
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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12
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Liu S, Lai Z, Zhang M, Tian H, Zhou J, Li Z. Facile synthesis of amino-functionalized magnetic materials for efficient enrichment of anionic metabolites from biological samples. Anal Chim Acta 2023; 1250:340977. [PMID: 36898822 DOI: 10.1016/j.aca.2023.340977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023]
Abstract
The analysis of biological samples is often affected by the background matrix. Proper sample preparation is a critical step in the analytical procedure for complex samples. In this study, a simple and efficient enrichment strategy based on Amino-functionalized Polymer-Magnetic MicroParticles (NH2-PMMPs) with coral-like porous structures was developed to enable the detection of 320 anionic metabolites, providing detailed coverage of phosphorylation metabolism. Among them, 102 polar phosphate metabolites including nucleotides, cyclic nucleotides, sugar nucleotides, phosphate sugars, and phosphates, were enriched and identified from serum, tissues, and cells. Furthermore, the detection of 34 previously unknown polar phosphate metabolites in serum samples demonstrates the advantages of this efficient enrichment method for mass spectrometric analysis. The limit of detections (LODs) were between 0.02 and 4 nmol/L for most anionic metabolites and its high sensitivity enabled the detection of 36 polar anion metabolites from 10 cell equivalent samples. This study has provided a promising tool for the efficient enrichment and analysis of anionic metabolites in biological samples with high sensitivity and broad coverage, facilitating the knowledge of the phosphorylation processes of life.
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Affiliation(s)
- Shuai Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Mo Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Hongtao Tian
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Beijing, 100871, China.
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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13
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Niu N, Ye J, Hu Z, Zhang J, Wang Y. Regulative Roles of Metabolic Plasticity Caused by Mitochondrial Oxidative Phosphorylation and Glycolysis on the Initiation and Progression of Tumorigenesis. Int J Mol Sci 2023; 24:ijms24087076. [PMID: 37108242 PMCID: PMC10139088 DOI: 10.3390/ijms24087076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
One important feature of tumour development is the regulatory role of metabolic plasticity in maintaining the balance of mitochondrial oxidative phosphorylation and glycolysis in cancer cells. In recent years, the transition and/or function of metabolic phenotypes between mitochondrial oxidative phosphorylation and glycolysis in tumour cells have been extensively studied. In this review, we aimed to elucidate the characteristics of metabolic plasticity (emphasizing their effects, such as immune escape, angiogenesis migration, invasiveness, heterogeneity, adhesion, and phenotypic properties of cancers, among others) on tumour progression, including the initiation and progression phases. Thus, this article provides an overall understanding of the influence of abnormal metabolic remodeling on malignant proliferation and pathophysiological changes in carcinoma.
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Affiliation(s)
- Nan Niu
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
- College of Physics and Optoelectronic Engineering, Canghai Campus of Shenzhen University, Shenzhen 518060, China
| | - Jinfeng Ye
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Zhangli Hu
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Junbin Zhang
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Yun Wang
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
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14
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Floros DJ, Xu K, Berthiller F, Schwartz-Zimmermann H. Comparison of chromatographic conditions for the targeted tandem mass spectrometric determination of 354 mammalian metabolites. J Chromatogr A 2023; 1697:463985. [PMID: 37062154 DOI: 10.1016/j.chroma.2023.463985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/22/2023] [Accepted: 04/08/2023] [Indexed: 04/18/2023]
Abstract
Metabolomics is becoming increasingly popular in livestock research, but no single analytical method can cover the entire metabolome. As such, we compared similar and complementary chromatographic methods with respect to analyte coverage and chromatographic properties of mammalian metabolites. We investigated 354 biologically relevant primary metabolites from 19 compound classes including amino acids, bile acids, biogenic amines, carboxylic acids, lipids, nucleotides and sugars. A total of 2063 selected reaction monitoring transitions were optimized on a triple quadrupole mass spectrometer. We then determined the retention profiles and peak parameters of our compounds using an anion exchange chromatography (AIC), three reversed-phase (RP) and three hydrophilic interaction liquid chromatography (HILIC) methods. On average, HILIC methods covered 54% of all metabolites with retention factors >1, while average RP coverage was 41%. In contrast to RP, HILIC methods could also retain polar metabolites such as amino acids and biogenic amines. Carboxylic acids, nucleotides, and sugar related compounds were best separated by AIC or zwitterionic pHILIC with alkaline eluents. Combining two complementary HILIC and RP methods increased the library coverage to 92%. By further including important short chain fatty acids, a combination of HILIC, RP and AIC methods achieved a coverage of 97%. The resulting dataset of LC and MS/MS parameters will facilitate the development of tailor-made quantitative targeted LC-MS/MS methods to investigate the mammalian metabolome.
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Affiliation(s)
- Dimitrios J Floros
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Kangkang Xu
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Franz Berthiller
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria.
| | - Heidi Schwartz-Zimmermann
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
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15
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Lin YT, Chan SA, Chen YJ, Chung KP, Kuo CH. Using an In-Sample Addition of Medronic Acid for the Analysis of Purine- and Pyrimidine-Related Derivatives and Its Application in the Study of Lung Adenocarcinoma A549 Cell Lines by LC-MS/MS. J Proteome Res 2023; 22:1434-1445. [PMID: 36930966 DOI: 10.1021/acs.jproteome.2c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Intracellular purine- and pyrimidine-related derivatives are vital molecules for preserving genetic information and are essential for cellular bioenergetics and signal transduction. This study developed a practical liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantifying intracellular purine- and pyrimidine-related derivatives. To solve the distorted peak shape related to di- and triphosphate nucleotides, in-sample addition of medronic acid and ammonium phosphate was performed. Using the BEH-amide column, the results showed that adding 0.5 mM medronic acid to the sample significantly improved the peak shape without causing an obvious ion suppressive effect. Method validation confirmed that the coefficients of determination (R2) values for linearity evaluation were above 0.94 for all analytes. The intraday and interday accuracies ranged from 85.1 to 128.4%, with the precision below 16.6%. The validated method was successfully applied in characterizing the alterations of purine- and pyrimidine-related derivatives in the A549 cell line with perturbed mitochondrial fission or blockade of the electron transport chain. Collectively, this study demonstrates that the strategy of in-sample medronic acid addition is effective in improving the quantification of intracellular purine- and pyrimidine-related derivatives. We believe that our proposed platform can facilitate the development of novel drugs targeting purine and pyrimidine metabolism in the future.
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Affiliation(s)
- Ya-Ting Lin
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan.,The Metabolomics Core Laboratory, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 100, Taiwan
| | | | - Yi-Jung Chen
- Department of Laboratory Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Kuei-Pin Chung
- Department of Laboratory Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Ching-Hua Kuo
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan.,The Metabolomics Core Laboratory, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 100, Taiwan.,Department of Pharmacy, National Taiwan University Hospital, Taipei 100, Taiwan
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16
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Agudo-Jurado FJ, Reveglia P, Rubiales D, Evidente A, Barilli E. Status of Phytotoxins Isolated from Necrotrophic Fungi Causing Diseases on Grain Legumes. Int J Mol Sci 2023; 24:ijms24065116. [PMID: 36982189 PMCID: PMC10049004 DOI: 10.3390/ijms24065116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
Fungal phytotoxins can be defined as secondary metabolites toxic to host plants and are believed to be involved in the symptoms developed of a number of plant diseases by targeting host cellular machineries or interfering with host immune responses. As any crop, legumes can be affected by a number of fungal diseases, causing severe yield losses worldwide. In this review, we report and discuss the isolation, chemical, and biological characterization of fungal phytotoxins produced by the most important necrotrophic fungi involved in legume diseases. Their possible role in plant-pathogen interaction and structure-toxicity relationship studies have also been reported and discussed. Moreover, multidisciplinary studies on other prominent biological activity conducted on reviewed phytotoxins are described. Finally, we explore the challenges in the identification of new fungal metabolites and their possible applications in future experiments.
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Affiliation(s)
| | - Pierluigi Reveglia
- Plant Breeding Department, Institute for Sustainable Agriculture (CSIC), 14004 Córdoba, Spain
| | - Diego Rubiales
- Plant Breeding Department, Institute for Sustainable Agriculture (CSIC), 14004 Córdoba, Spain
| | - Antonio Evidente
- Department of Chemical Sciences, University of Naples Federico II (UNINA), 80138 Naples, Italy
- Institute of Sciences of Food Production, National Research Council, 70126 Bari, Italy
| | - Eleonora Barilli
- Plant Breeding Department, Institute for Sustainable Agriculture (CSIC), 14004 Córdoba, Spain
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17
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Van Bergen NJ, Gunanayagam K, Bournazos AM, Walvekar AS, Warmoes MO, Semcesen LN, Lunke S, Bommireddipalli S, Sikora T, Patraskaki M, Jones DL, Garza D, Sebire D, Gooley S, McLean CA, Naidoo P, Rajasekaran M, Stroud DA, Linster CL, Wallis M, Cooper ST, Christodoulou J. Severe NAD(P)HX Dehydratase (NAXD) Neurometabolic Syndrome May Present in Adulthood after Mild Head Trauma. Int J Mol Sci 2023; 24:ijms24043582. [PMID: 36834994 PMCID: PMC9963268 DOI: 10.3390/ijms24043582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
We have previously reported that pathogenic variants in a key metabolite repair enzyme NAXD cause a lethal neurodegenerative condition triggered by episodes of fever in young children. However, the clinical and genetic spectrum of NAXD deficiency is broadening as our understanding of the disease expands and as more cases are identified. Here, we report the oldest known individual succumbing to NAXD-related neurometabolic crisis, at 32 years of age. The clinical deterioration and demise of this individual were likely triggered by mild head trauma. This patient had a novel homozygous NAXD variant [NM_001242882.1:c.441+3A>G:p.?] that induces the mis-splicing of the majority of NAXD transcripts, leaving only trace levels of canonically spliced NAXD mRNA, and protein levels below the detection threshold by proteomic analysis. Accumulation of damaged NADH, the substrate of NAXD, could be detected in the fibroblasts of the patient. In agreement with prior anecdotal reports in paediatric patients, niacin-based treatment also partly alleviated some clinical symptoms in this adult patient. The present study extends our understanding of NAXD deficiency by uncovering shared mitochondrial proteomic signatures between the adult and our previously reported paediatric NAXD cases, with reduced levels of respiratory complexes I and IV as well as the mitoribosome, and the upregulation of mitochondrial apoptotic pathways. Importantly, we highlight that head trauma in adults, in addition to paediatric fever or illness, may precipitate neurometabolic crises associated with pathogenic NAXD variants.
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Affiliation(s)
- Nicole J. Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3002, Australia
- Correspondence: (N.J.V.B.); (J.C.)
| | - Karen Gunanayagam
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Adam M. Bournazos
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- The Children’s Medical Research Institute, 214 Hawkesbury Road, Westmead, Sydney, NSW 2145, Australia
| | - Adhish S. Walvekar
- Enzymology and Metabolism Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Marc O. Warmoes
- Enzymology and Metabolism Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Liana N. Semcesen
- Department of Biochemistry & Pharmacology, Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, VIC 3002, Australia
| | - Sebastian Lunke
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3002, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- The Children’s Medical Research Institute, 214 Hawkesbury Road, Westmead, Sydney, NSW 2145, Australia
| | - Tim Sikora
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
| | - Myrto Patraskaki
- Enzymology and Metabolism Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Dean L. Jones
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS 7000, Australia
- School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Denisse Garza
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Dale Sebire
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Samuel Gooley
- Department of Neurology, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Catriona A. McLean
- Department of Anatomical Pathology, Alfred Hospital, Melbourne, VIC 3002, Australia
| | - Parm Naidoo
- Department of Medical Imaging, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Mugil Rajasekaran
- Department of Medical Imaging, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - David A. Stroud
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
- Department of Biochemistry & Pharmacology, Bio21 Molecular Science & Biotechnology Institute, University of Melbourne, Melbourne, VIC 3002, Australia
| | - Carole L. Linster
- Enzymology and Metabolism Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Mathew Wallis
- School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Sandra T. Cooper
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
- The Children’s Medical Research Institute, 214 Hawkesbury Road, Westmead, Sydney, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, NSW 2006, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3002, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, Melbourne, VIC 3002, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, NSW 2006, Australia
- Correspondence: (N.J.V.B.); (J.C.)
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18
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Zapata-Restrepio LM, Hauton C, Hudson MD, Williams ID, Hauton D. Toxicity of tributyltin to the European flat oyster Ostrea edulis: Metabolomic responses indicate impacts to energy metabolism, biochemical composition and reproductive maturation. PLoS One 2023; 18:e0280777. [PMID: 36745593 PMCID: PMC9901812 DOI: 10.1371/journal.pone.0280777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/10/2023] [Indexed: 02/07/2023] Open
Abstract
Tri-Butyl Tin (TBT) remains as a legacy pollutant in the benthic environments. Although the toxic impacts and endocrine disruption caused by TBT to gastropod molluscs have been established, the changes in energy reserves allocated to maintenance, growth, reproduction and survival of European oysters Ostrea edulis, a target species of concerted benthic habitat restoration projects, have not been explored. This study was designed to evaluate the effect of TBT chloride (TBTCl) on potential ions and relevant metabolomic pathways and its association with changes in physiological, biochemical and reproductive parameters in O. edulis exposed to environmental relevant concentrations of TBTCl. Oysters were exposed to TBTCl 20 ng/L (n = 30), 200 ng/L (n = 30) and 2000 ng/L (n = 30) for nine weeks. At the end of the exposure, gametogenic stage, sex, energy reserve content and metabolomic profiling analysis were conducted to elucidate the metabolic alterations that occur in individuals exposed to those compounds. Metabolite analysis showed significant changes in the digestive gland biochemistry in oysters exposed to TBTCl, decreasing tissue ATP concentrations through a combination of the disruption of the TCA cycle and other important molecular pathways involved in homeostasis, mitochondrial metabolism and antioxidant response. TBTCl exposure increased mortality and caused changes in the gametogenesis with cycle arrest in stages G0 and G1. Sex determination was affected by TBTCl exposure, increasing the proportion of oysters identified as males in O. edulis treated at 20ng/l TBTCl, and with an increased proportion of inactive stages in oysters treated with 2000 ng/l TBTCl. The presence and persistence of environmental pollutants, such as TBT, could represent an additional threat to the declining O. edulis populations and related taxa around the world, by increasing mortality, changing reproductive maturation, and disrupting metabolism. Our findings identify the need to consider additional factors (e.g. legacy pollution) when identifying coastal locations for shellfish restoration.
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Affiliation(s)
- Lina M. Zapata-Restrepio
- School of Geography and Environmental Sciences, University of Southampton, Highfield Campus, Southampton, United Kingdom
- * E-mail:
| | - Chris Hauton
- Ocean and Earth Sciences, National Oceanography Centre, University of Southampton, Southampton, Hampshire, United Kingdom
| | - Malcolm D. Hudson
- School of Geography and Environmental Sciences, University of Southampton, Highfield Campus, Southampton, United Kingdom
| | - Ian D. Williams
- Faculty of Engineering and Physical Sciences, University of Southampton, Highfield Campus, Southampton, United Kingdom
| | - David Hauton
- Metabolomics Research Group, Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
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19
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Su M, Serafimov K, Li P, Knappe C, Lämmerhofer M. Isomer selectivity of one- and two-dimensional approaches of mixed-mode and hydrophilic interaction liquid chromatography coupled to tandem mass spectrometry for sugar phosphates of glycolysis and pentose phosphate pathways. J Chromatogr A 2023; 1688:463727. [PMID: 36566570 DOI: 10.1016/j.chroma.2022.463727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/23/2022]
Abstract
In this study, the chromatographic behavior of mixed-mode and hydrophilic interaction liquid chromatography (HILIC) with the mixed-mode HILIC/strong anion-exchange (SAX) column HILICpak VT-50 2D and the two HILIC columns Atlantis Premier BEH Z-HILIC and Acquity Premier BEH Amide was assessed with regard to their separation capability of the metabolites from the glycolysis and pentose phosphate pathways. Chromatographic conditions were evaluated with the aim of achieving separation of the isomeric glycolytic phosphorylated carbohydrate metabolites free from isomeric interferences and thus allowing for selective targeted analysis by liquid chromatography with tandem mass spectrometry (MS/MS) using multiple reaction monitoring acquisition. The effects of pH values (8.0/9.0/10.0) of the ammonium bicarbonate buffer and gradient time were investigated during HILIC-MS/MS analysis, with the optimal conditions found at pH = 10.0. Separation of the pentose phosphate isomers (ribose 5- and 1-phosphate, xylulose 5-phosphate and ribulose 5-phosphate) was achieved on the mixed-mode HILIC/SAX (HILICpak VT-50 2D) column and HILIC BEH Amide column. Column performance was evaluated based on the direct comparison of chromatographic parameters, i.e. peak width at 50% and peak tailing factors of the individual metabolites. Parity plots were generated allowing a direct comparison between the normalized retention times and assessment of orthogonality of all 3 stationary phases evaluated. Separation of 7 biologically relevant hexose monophosphates metabolites turned out to be challenging by HILIC-MS/MS, with the BEH Amide providing the best individual results for such a separation. However, fructose 6-phosphate and glucose 1-phosphate co-eluted. Therefore, an on-line heart-cutting HILIC-Mixed Mode 2D-LC-QToF experiment was conducted, allowing the separation of this critical isomer pair. In this setup, the BEH Amide column in the 1D separated the majority of target metabolites, while a heart-cut of the peak from totally coeluted fructose 6-phosphate and glucose 1-phosphate was separated in the 2D with HILICpak VT50-2D column, thus allowing undisturbed determination of the glycolytic phosphorylated carbohydrate metabolites due to their chromatographic separation from hexose monophosphate metabolites. The assay specificity towards 7 common hexose monophosphates was characterized (glucose 1- and 6-phosphate, galactose 1- and 6-phosphate, fructose 6-phosphate, mannose 1- and 6-phosphate). The selectivity of some rare hexose monophosphates (allose 6-phosphate, tagatose 6-phosphate, sorbose 1-phosphate) was also tested.
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Affiliation(s)
- Min Su
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Kristian Serafimov
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Peng Li
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany.
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20
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Ngere J, Ebrahimi KH, Williams R, Pires E, Walsby-Tickle J, McCullagh JSO. Ion-Exchange Chromatography Coupled to Mass Spectrometry in Life Science, Environmental, and Medical Research. Anal Chem 2023; 95:152-166. [PMID: 36625129 PMCID: PMC9835059 DOI: 10.1021/acs.analchem.2c04298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Judith
B. Ngere
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kourosh H. Ebrahimi
- Institute
of Pharmaceutical Science, King’s
College London, London SE1 9NH, U.K.
| | - Rachel Williams
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Elisabete Pires
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - John Walsby-Tickle
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - James S. O. McCullagh
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,
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21
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Smith EN, Ratcliffe RG, Kruger NJ. Isotopically non-stationary metabolic flux analysis of heterotrophic Arabidopsis thaliana cell cultures. FRONTIERS IN PLANT SCIENCE 2023; 13:1049559. [PMID: 36699846 PMCID: PMC9868915 DOI: 10.3389/fpls.2022.1049559] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Fluxes are the ultimate phenotype of metabolism and their accurate quantification is fundamental to any understanding of metabolic networks. Steady state metabolic flux analysis has been the method of choice for quantifying fluxes in heterotrophic cells, but it is unable to measure fluxes during short-lived metabolic states, such as a transient oxidative load. Isotopically non-stationary metabolic flux analysis (INST-MFA) can be performed over shorter timescales (minutes - hours) and might overcome this limitation. INST-MFA has recently been applied to photosynthesising leaves, but agriculturally important tissues such as roots and storage organs, or plants during the night are heterotrophic. Here we outline the application of INST-MFA to heterotrophic plant cells. Using INST-MFA we were able to identify changes in the fluxes supported by phosphoenolpyruvate carboxylase and malic enzyme under oxidative load, highlighting the potential of INST-MFA to measure fluxes during short-lived metabolic states. We discuss the challenges in applying INST-MFA, and highlight further development required before it can be routinely used to quantify fluxes in heterotrophic plant cells.
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Affiliation(s)
- Edward N. Smith
- Molecular Plant Biology, Department of Biology, University of Oxford, Oxford, United Kingdom
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - R. George Ratcliffe
- Molecular Plant Biology, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Nicholas J. Kruger
- Molecular Plant Biology, Department of Biology, University of Oxford, Oxford, United Kingdom
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22
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Chung YH, Hung TH, Yu CF, Tsai CK, Weng CC, Jhang F, Chen FH, Lin G. Glycolytic Plasticity of Metastatic Lung Cancer Captured by Noninvasive 18F-FDG PET/CT and Serum 1H-NMR Analysis: An Orthotopic Murine Model Study. Metabolites 2023; 13:metabo13010110. [PMID: 36677035 PMCID: PMC9866275 DOI: 10.3390/metabo13010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 12/31/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
We aim to establish a noninvasive diagnostic platform to capture early phenotypic transformation for metastasis using 18F-FDG PET and 1H-NMR-based serum metabolomics. Mice with implantation of NCI-H460 cells grew only primary lung tumors in the localized group and had both primary and metastatic lung tumors in the metastatic group. The serum metabolites were analyzed using 1H-NMR at the time of PET/CT scan. The glycolysis status and cell proliferation were validated by Western blotting and staining. A receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic accuracy of SUVmean and serum metabolites in metastasis. In the metastatic mice, the SUVmean of metastatic tumors was significantly higher than that of primary lung tumors in PET images, which was supported by elevated glycolytic protein expression of HK2 and PKM2. The serum pyruvate level in the metastatic group was significantly lower than that in the localized group, corresponding to increased pyruvate-catalyzed enzyme and proliferation rates in metastatic tumors. In diagnosing localized or metastatic tumors, the areas under the ROC curves of SUVmean and pyruvate were 0.92 and 0.91, respectively, with p < 0.05. In conclusion, the combination of 18F-FDG PET and 1H-NMR-based serum metabolomics demonstrated the feasibility of a glycolytic platform for diagnosing metastatic lung cancers.
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Affiliation(s)
- Yi-Hsiu Chung
- Department of Medical Research and Development, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
| | - Tsai-Hsien Hung
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
| | - Ching-Fang Yu
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan 333323, Taiwan
| | - Cheng-Kun Tsai
- Clinical Metabolomics Core Lab, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
| | - Chi-Chang Weng
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan 333323, Taiwan
| | - Fujie Jhang
- Department of Medical Research and Development, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
| | - Fang-Hsin Chen
- Institute of Nuclear Engineering and Science, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Gigin Lin
- Clinical Metabolomics Core Lab, Chang Gung Memorial Hospital at Linkou, Taoyuan 333423, Taiwan
- Department of Medical Imaging and Intervention, Institute for Radiological Research, Chang Gung Memorial Hospital at Linkou, Chang Gung University, Taoyuan 333323, Taiwan
- Correspondence:
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23
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The mechanisms underlying montelukast's neuropsychiatric effects - new insights from a combined metabolic and multiomics approach. Life Sci 2022; 310:121056. [DOI: 10.1016/j.lfs.2022.121056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
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24
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Advances in capillary electrophoresis mass spectrometry for metabolomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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25
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Haythorne E, Lloyd M, Walsby-Tickle J, Tarasov AI, Sandbrink J, Portillo I, Exposito RT, Sachse G, Cyranka M, Rohm M, Rorsman P, McCullagh J, Ashcroft FM. Altered glycolysis triggers impaired mitochondrial metabolism and mTORC1 activation in diabetic β-cells. Nat Commun 2022; 13:6754. [PMID: 36376280 PMCID: PMC9663558 DOI: 10.1038/s41467-022-34095-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Chronic hyperglycaemia causes a dramatic decrease in mitochondrial metabolism and insulin content in pancreatic β-cells. This underlies the progressive decline in β-cell function in diabetes. However, the molecular mechanisms by which hyperglycaemia produces these effects remain unresolved. Using isolated islets and INS-1 cells, we show here that one or more glycolytic metabolites downstream of phosphofructokinase and upstream of GAPDH mediates the effects of chronic hyperglycemia. This metabolite stimulates marked upregulation of mTORC1 and concomitant downregulation of AMPK. Increased mTORC1 activity causes inhibition of pyruvate dehydrogenase which reduces pyruvate entry into the tricarboxylic acid cycle and partially accounts for the hyperglycaemia-induced reduction in oxidative phosphorylation and insulin secretion. In addition, hyperglycaemia (or diabetes) dramatically inhibits GAPDH activity, thereby impairing glucose metabolism. Our data also reveal that restricting glucose metabolism during hyperglycaemia prevents these changes and thus may be of therapeutic benefit. In summary, we have identified a pathway by which chronic hyperglycaemia reduces β-cell function.
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Affiliation(s)
- Elizabeth Haythorne
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.
| | - Matthew Lloyd
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Andrei I Tarasov
- School of Biomedical Sciences, Ulster University, Coleraine, BT52 1SA, Northern Ireland, UK
| | - Jonas Sandbrink
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - Idoia Portillo
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - Raul Terron Exposito
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.,Institute for Diabetes and Cancer (IDC), Helmholtz Center, Munich, Neuherberg, 85764, Germany
| | - Gregor Sachse
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.,Brandenburg Medical School (Theodor Fontane), ZTM-BB, Brandenburg a. d. H, 14770, Germany
| | - Malgorzata Cyranka
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - Maria Rohm
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.,Institute for Diabetes and Cancer (IDC), Helmholtz Center, Munich, Neuherberg, 85764, Germany
| | - Patrik Rorsman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - James McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Frances M Ashcroft
- Department of Physiology, Anatomy and Genetics and OXION, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.
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26
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Reinbold R, Hvinden IC, Rabe P, Herold RA, Finch A, Wood J, Morgan M, Staudt M, Clifton IJ, Armstrong FA, McCullagh JSO, Redmond J, Bardella C, Abboud MI, Schofield CJ. Resistance to the isocitrate dehydrogenase 1 mutant inhibitor ivosidenib can be overcome by alternative dimer-interface binding inhibitors. Nat Commun 2022; 13:4785. [PMID: 35970853 PMCID: PMC9378673 DOI: 10.1038/s41467-022-32436-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/25/2022] [Indexed: 12/02/2022] Open
Abstract
Ivosidenib, an inhibitor of isocitrate dehydrogenase 1 (IDH1) R132C and R132H variants, is approved for the treatment of acute myeloid leukaemia (AML). Resistance to ivosidenib due to a second site mutation of IDH1 R132C, leading to IDH1 R132C/S280F, has emerged. We describe biochemical, crystallographic, and cellular studies on the IDH1 R132C/S280F and R132H/S280F variants that inform on the mechanism of second-site resistance, which involves both modulation of inhibitor binding at the IDH1 dimer-interface and alteration of kinetic properties, which enable more efficient 2-HG production relative to IDH1 R132C and IDH1 R132H. Importantly, the biochemical and cellular results demonstrate that it should be possible to overcome S280F mediated resistance in AML patients by using alternative inhibitors, including some presently in phase 2 clinical trials.
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Affiliation(s)
- Raphael Reinbold
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield, Oxford, OX1 3TA, UK
| | - Ingvild C Hvinden
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield, Oxford, OX1 3TA, UK
| | - Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield, Oxford, OX1 3TA, UK
| | - Ryan A Herold
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Alina Finch
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - James Wood
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Melissa Morgan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Maximillian Staudt
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104, Freiburg, Germany
| | - Ian J Clifton
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield, Oxford, OX1 3TA, UK
| | | | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield, Oxford, OX1 3TA, UK
| | - Jo Redmond
- GlaxoSmithKline, Gunnels Wood Rd, Stevenage, SG1 2NY, UK
| | - Chiara Bardella
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield, Oxford, OX1 3TA, UK.
- Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield, Oxford, OX1 3TA, UK.
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27
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Targeted analysis of sugar phosphates from glycolysis pathway by phosphate methylation with liquid chromatography coupled to tandem mass spectrometry. Anal Chim Acta 2022; 1221:340099. [DOI: 10.1016/j.aca.2022.340099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022]
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28
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A rapid and robust method for amino acid quantification using a simple N-hydroxysuccinimide ester derivatization and liquid chromatography-ion mobility-mass spectrometry. Anal Bioanal Chem 2022; 414:5549-5559. [PMID: 35338375 DOI: 10.1007/s00216-022-03993-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/01/2022]
Abstract
The vast majority of mass spectrometry (MS)-based metabolomics studies employ reversed-phase liquid chromatography (RPLC) to separate analytes prior to MS detection. Highly polar metabolites, such as amino acids (AAs), are poorly retained by RPLC, making quantitation of these key species challenging across the broad concentration ranges typically observed in biological specimens, such as cell extracts. To improve the detection and quantitation of AAs in microglial cell extracts, the implementation of a 4-dimethylaminobenzoylamido acetic acid N-hydroxysuccinimide ester (DBAA-NHS) derivatization agent was explored for its ability to improve both analyte retention and detection limits in RPLC-MS. In addition to the introduction of the DBAA-NHS labeling reagent, a uniformly (U) 13C-labeled yeast extract was also introduced during the sample preparation workflow as an internal standard (IS) to eliminate artifacts and to enable targeted quantitation of AAs, as well as untargeted amine submetabolome profiling. To improve method sensitivity and selectivity, multiplexed drift-tube ion mobility (IM) was integrated into the LC-MS workflow, facilitating the separation of isomeric metabolites, and improving the structural identification of unknown metabolites. Implementation of the U-13C-labeled yeast extract during the multiplexed LC-IM-MS analysis enabled the quantitation of 19 of the 20 common AAs, supporting a linear dynamic range spanning up to three orders of magnitude in concentration for microglial cell extracts, in addition to reducing the required cell count for reliable quantitation from 10 to 5 million cells per sample.
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29
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Bigard A, Cardinael P, Agasse V. Anion Exchange Chromatography Coupled to Electrospray-Mass Spectrometry: An Efficient Tool for Food, Environment, and Biological Analysis. Crit Rev Anal Chem 2022; 53:1591-1603. [PMID: 35147465 DOI: 10.1080/10408347.2022.2036942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
For over 50 years, ion chromatography has been demonstrated to be a successful technique used to quantify a wide range of ions and ionizable compounds, either organic or inorganic, in various matrices using conductimetric or electrochemical detection. It was only since 1996 that ion chromatography was coupled to electrospray-mass spectrometry, opening the field to new applications in complex matrices and the detection of compounds at trace levels. This review covers the recent developments of ion exchange chromatography and mass spectrometry. It focuses on the choice of mobile phases, column geometry, suppressors, make-up solvents and type of ionization sources reported in the literature. A brief overview of a large range of applications in food analysis, environmental analysis and bioanalysis is presented, and performances are discussed.
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Affiliation(s)
- Adeline Bigard
- Normandie Univ, Laboratoire SMS-EA3233, FR3038 INC3M, UNIROUEN, Mont-Saint-Aignan, France
| | - Pascal Cardinael
- Normandie Univ, Laboratoire SMS-EA3233, FR3038 INC3M, UNIROUEN, Mont-Saint-Aignan, France
| | - Valérie Agasse
- Normandie Univ, Laboratoire SMS-EA3233, FR3038 INC3M, UNIROUEN, Mont-Saint-Aignan, France
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30
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Green CJ, Marjot T, Walsby-Tickle J, Charlton C, Cornfield T, Westcott F, Pinnick KE, Moolla A, Hazlehurst JM, McCullagh J, Tomlinson JW, Hodson L. Metformin maintains intrahepatic triglyceride content through increased hepatic de novo lipogenesis. Eur J Endocrinol 2022; 186:367-377. [PMID: 35038311 PMCID: PMC8859923 DOI: 10.1530/eje-21-0850] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/17/2022] [Indexed: 12/05/2022]
Abstract
OBJECTIVE Metformin is a first-line pharmacotherapy in the treatment of type 2 diabetes, a condition closely associated with non-alcoholic fatty liver disease (NAFLD). Although metformin promotes weight loss and improves insulin sensitivity, its effect on intrahepatic triglyceride (IHTG) remains unclear. We investigated the effect of metformin on IHTG, hepatic de novo lipogenesis (DNL), and fatty acid (FA) oxidation in vivo in humans. DESIGN AND METHODS Metabolic investigations, using stable-isotope tracers, were performed in ten insulin-resistant, overweight/obese human participants with NAFLD who were treatment naïve before and after 12 weeks of metformin treatment. The effect of metformin on markers of s.c. adipose tissue FA metabolism and function, along with the plasma metabolome, was investigated. RESULTS Twelve weeks of treatment with metformin resulted in a significant reduction in body weight and improved insulin sensitivity, but IHTG content and FA oxidation remained unchanged. Metformin treatment was associated with a significant decrease in VLDL-triglyceride (TG) concentrations and a significant increase in the relative contribution of DNL-derived FAs to VLDL-TG. There were subtle and relatively few changes in s.c. adipose tissue FA metabolism and the plasma metabolome with metformin treatment. CONCLUSIONS We demonstrate the mechanisms of action of metformin whereby it improves insulin sensitivity and promotes weight loss, without improvement in IHTG; these observations are partly explained through increased hepatic DNL and a lack of change in FA oxidation.
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Affiliation(s)
- Charlotte J Green
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Thomas Marjot
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Catriona Charlton
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Thomas Cornfield
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Felix Westcott
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Katherine E Pinnick
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Ahmad Moolla
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Jonathan M Hazlehurst
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, UK
| | - James McCullagh
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Jeremy W Tomlinson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospital Trusts, Oxford, UK
| | - Leanne Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospital Trusts, Oxford, UK
- Correspondence should be addressed to L Hodson;
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31
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Rasmussen JA, Villumsen KR, Ernst M, Hansen M, Forberg T, Gopalakrishnan S, Gilbert MTP, Bojesen AM, Kristiansen K, Limborg MT. A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss). MICROBIOME 2022; 10:21. [PMID: 35094708 PMCID: PMC8802455 DOI: 10.1186/s40168-021-01221-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/27/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism. RESULTS Our findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid related Candidatus Mycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence of Candidatus Mycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites. CONCLUSION Our results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments. Video Abstract.
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Affiliation(s)
- Jacob Agerbo Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark.
| | - Kasper Rømer Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - Madeleine Ernst
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, 2300, Copenhagen, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Aarhus, Denmark
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
- University Museum NTNU, Trondheim, Norway
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Morten Tønsberg Limborg
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark.
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32
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Vaughan-Jackson A, Stodolak S, Ebrahimi KH, Johnson E, Reardon PK, Dupont M, Zhang S, McCullagh JSO, James WS. Density dependent regulation of inflammatory responses in macrophages. Front Immunol 2022; 13:895488. [PMID: 36591218 PMCID: PMC9800520 DOI: 10.3389/fimmu.2022.895488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Macrophage distribution density is tightly regulated within the body, yet the importance of macrophage crowding during in vitro culture is largely unstudied. Using a human induced pluripotent stem cell (iPSC)-derived macrophage model of tissue resident macrophages, we characterize how increasing macrophage culture density changes their morphology and phenotype before and after inflammatory stimulation. In particular, density drives changes in macrophage inflammatory cytokine and chemokine secretion in both resting and activated states. This density regulated inflammatory state is also evident in blood monocyte derived-macrophages, the human monocytic THP-1 immortalized cell line, and iPSC-derived microglia. Density-dependent changes appear to be driven by a transferable soluble factor, yet the precise mechanism remains unknown. Our findings highlight cell plating density as an important but frequently overlooked consideration of in vitro macrophage research relevant to a variety of fields ranging from basic macrophage cell biology to disease studies.
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Affiliation(s)
- Alun Vaughan-Jackson
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- *Correspondence: Alun Vaughan-Jackson, ; William S. James,
| | - Szymon Stodolak
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Paul K. Reardon
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Maeva Dupont
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Shengpan Zhang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - William S. James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- *Correspondence: Alun Vaughan-Jackson, ; William S. James,
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Hvinden IC, Cadoux-Hudson T, Schofield CJ, McCullagh JS. Metabolic adaptations in cancers expressing isocitrate dehydrogenase mutations. Cell Rep Med 2021; 2:100469. [PMID: 35028610 PMCID: PMC8714851 DOI: 10.1016/j.xcrm.2021.100469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The most frequently mutated metabolic genes in human cancer are those encoding the enzymes isocitrate dehydrogenase 1 (IDH1) and IDH2; these mutations have so far been identified in more than 20 tumor types. Since IDH mutations were first reported in glioma over a decade ago, extensive research has revealed their association with altered cellular processes. Mutations in IDH lead to a change in enzyme function, enabling efficient conversion of 2-oxoglutarate to R-2-hydroxyglutarate (R-2-HG). It is proposed that elevated cellular R-2-HG inhibits enzymes that regulate transcription and metabolism, subsequently affecting nuclear, cytoplasmic, and mitochondrial biochemistry. The significance of these biochemical changes for tumorigenesis and potential for therapeutic exploitation remains unclear. Here we comprehensively review reported direct and indirect metabolic changes linked to IDH mutations and discuss their clinical significance. We also review the metabolic effects of first-generation mutant IDH inhibitors and highlight the potential for combination treatment strategies and new metabolic targets.
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Affiliation(s)
- Ingvild Comfort Hvinden
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
- Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - James S.O. McCullagh
- Chemistry Research Laboratory, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
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34
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Harrieder EM, Kretschmer F, Böcker S, Witting M. Current state-of-the-art of separation methods used in LC-MS based metabolomics and lipidomics. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1188:123069. [PMID: 34879285 DOI: 10.1016/j.jchromb.2021.123069] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/10/2021] [Accepted: 11/24/2021] [Indexed: 12/23/2022]
Abstract
Metabolomics deals with the large-scale analysis of metabolites, belonging to numerous compound classes and showing an extremely high chemical diversity and complexity. Lipidomics, being a subcategory of metabolomics, analyzes the cellular lipid species. Both require state-of-the-art analytical methods capable of accessing the underlying chemical complexity. One of the major techniques used for the analysis of metabolites and lipids is Liquid Chromatography-Mass Spectrometry (LC-MS), offering both different selectivities in LC separation and high sensitivity in MS detection. Chromatography can be divided into different modes, based on the properties of the employed separation system. The most popular ones are Reversed-Phase (RP) separation for non- to mid-polar molecules and Hydrophilic Interaction Liquid Chromatography (HILIC) for polar molecules. So far, no single analysis method exists that can cover the entire range of metabolites or lipids, due to the huge chemical diversity. Consequently, different separation methods have been used for different applications and research questions. In this review, we explore the current use of LC-MS in metabolomics and lipidomics. As a proxy, we examined the use of chromatographic methods in the public repositories EBI MetaboLights and NIH Metabolomics Workbench. We extracted 1484 method descriptions, collected separation metadata and generated an overview on the current use of columns, eluents, etc. Based on this overview, we reviewed current practices and identified potential future trends as well as required improvements that may allow us to increase metabolite coverage, throughput or both simultaneously.
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Affiliation(s)
- Eva-Maria Harrieder
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Fleming Kretschmer
- Chair of Bioinformatics, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Sebastian Böcker
- Chair of Bioinformatics, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Metabolomics and Proteomics Core, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University of Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany.
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35
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Liu S, Abboud MI, John T, Mikhailov V, Hvinden I, Walsby-Tickle J, Liu X, Pettinati I, Cadoux-Hudson T, McCullagh JSO, Schofield CJ. Roles of metal ions in the selective inhibition of oncogenic variants of isocitrate dehydrogenase 1. Commun Biol 2021; 4:1243. [PMID: 34725432 PMCID: PMC8560763 DOI: 10.1038/s42003-021-02743-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/04/2021] [Indexed: 12/29/2022] Open
Abstract
Cancer linked isocitrate dehydrogenase (IDH) 1 variants, notably R132H IDH1, manifest a 'gain-of-function' to reduce 2-oxoglutarate to 2-hydroxyglutarate. High-throughput screens have enabled clinically useful R132H IDH1 inhibitors, mostly allosteric binders at the dimer interface. We report investigations on roles of divalent metal ions in IDH substrate and inhibitor binding that rationalise this observation. Mg2+/Mn2+ ions enhance substrate binding to wt IDH1 and R132H IDH1, but with the former manifesting lower Mg2+/Mn2+ KMs. The isocitrate-Mg2+ complex is the preferred wt IDH1 substrate; with R132H IDH1, separate and weaker binding of 2-oxoglutarate and Mg2+ is preferred. Binding of R132H IDH1 inhibitors at the dimer interface weakens binding of active site Mg2+ complexes; their potency is affected by the Mg2+ concentration. Inhibitor selectivity for R132H IDH1 over wt IDH1 substantially arises from different stabilities of wt and R132H IDH1 substrate-Mg2+ complexes. The results reveal the importance of substrate-metal ion complexes in wt and R132H IDH1 catalysis and the basis for selective R132H IDH1 inhibition. Further studies on roles of metal ion complexes in TCA cycle and related metabolism, including from an evolutionary perspective, are of interest.
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Affiliation(s)
- Shuang Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ingvild Hvinden
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Xiao Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ilaria Pettinati
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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Skaripa-Koukelli I, Hauton D, Walsby-Tickle J, Thomas E, Owen J, Lakshminarayanan A, Able S, McCullagh J, Carlisle RC, Vallis KA. 3-Bromopyruvate-mediated MCT1-dependent metabolic perturbation sensitizes triple negative breast cancer cells to ionizing radiation. Cancer Metab 2021; 9:37. [PMID: 34649623 PMCID: PMC8515664 DOI: 10.1186/s40170-021-00273-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 09/18/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) poses a serious clinical challenge as it is an aggressive form of the disease that lacks estrogen receptor, progesterone receptor, and ERBB2 (formerly HER2) gene amplification, which limits the treatment options. The Warburg phenotype of upregulated glycolysis in the presence of oxygen has been shown to be prevalent in TNBC. Elevated glycolysis satisfies the energy requirements of cancer cells, contributes to resistance to treatment by maintaining redox homeostasis and generating nucleotide precursors required for cell proliferation and DNA repair. Expression of the monocarboxylate transporter 1 (MCT1), which is responsible for the bidirectional transport of lactate, correlates with an aggressive phenotype and poor outcome in several cancer types, including breast cancer. In this study, 3-bromopyruvate (3BP), a lactate/pyruvate analog, was used to selectively target TNBC cells that express MCT1. METHODS The cytotoxicity of 3BP was tested in MTT assays using human TNBC cell lines: BT20 (MCT1+/MCT4-), MDA-MB-23 (MCT1-/MCT4+), and BT20 in which MCT1 was knocked down (siMCT1-BT20). The metabolite profile of 3BP-treated and 3BP-untreated cells was investigated using LC-MS/MS. The extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) of BT20 and MDA-MB-231 cells treated with 3BP were measured using a Seahorse XF96 extracellular flux analyzer. The impact of ionizing radiation on cell survival, alone or in combination with 3BP pre-treatment, was evaluated using clonogenic assays. RESULTS Metabolomic analyses showed that 3BP causes inhibition of glycolysis, disturbance of redox homeostasis, decreased nucleotide synthesis, and was accompanied by a reduction in medium acidification. In addition, 3BP potentiated the cytotoxic effect of ionizing radiation, a treatment that is frequently used in the management of TNBC. CONCLUSIONS Overall, MCT1-mediated metabolic perturbation in combination with radiotherapy is shown to be a promising strategy for the treatment of glycolytic tumors such as TNBC, overcoming the selectivity challenges of targeting glycolysis with glucose analogs.
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Affiliation(s)
- Irini Skaripa-Koukelli
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - David Hauton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - John Walsby-Tickle
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Eloïse Thomas
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Joshua Owen
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Abirami Lakshminarayanan
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sarah Able
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - James McCullagh
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Robert C Carlisle
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Katherine A Vallis
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7DQ, UK.
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37
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da Silva JL, Delfino JR, Stradiotto NR. Underivatized amino acids detection by anion-exchange chromatography coupled to a nanostructured detector. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1174:122733. [PMID: 33991824 DOI: 10.1016/j.jchromb.2021.122733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/13/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
This work reports the development of a fast and reliable amperometric sensor for the detection of amino acids. The detector was constructed using copper nanoparticles (CuNPs) supported on reduced graphene oxide (RGO) modified glassy carbon electrode (CuNPs-RGO/GCE) and based on the application of high performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). Under optimized isocratic HPAEC-PAD conditions (using 40 mmol L-1 NaOH as mobile phase, flow rate of 0.30 mL min-1 and detection potential of 0.45 V vs. Pd/PdO), the linear dynamic ranges of the concentration of amino acids obtained were 0.50-50 µmol L-1 for lysine, 1.0-100 µmol L-1 for alanine, glycine and serine, and 5.0-100 µmol L-1 for leucine. The limits of detection (S/N = 3) obtained ranged from 0.10 (for lysine and leucine) to 0.50 µmol L-1 (for alanine, glycine and serine) and sensitivity varied from 6.1 (for leucine) to 21.5 nA µmol-1 L (for serine). The average recovery percentages ranged from 97% (for glycine) to 102% (for leucine and serine). The results obtained showed that the CuNPs-RGO/GCE has good long-term stability, repeatability and reproducibility; this makes the device suitable for application as an electrochemical detector. The successful application of the proposed method for the analysis of sugarcane vinasse demonstrates its suitability for separation and determination of amino acids in complex matrices.
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Affiliation(s)
- José Luiz da Silva
- Analytical Chemistry Department, Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-060, São Paulo State, Brazil; Bioenergy Research Institute, São Paulo State University (UNESP), Araraquara 14800-060, São Paulo State, Brazil.
| | - José Rodrigues Delfino
- Analytical Chemistry Department, Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-060, São Paulo State, Brazil; Bioenergy Research Institute, São Paulo State University (UNESP), Araraquara 14800-060, São Paulo State, Brazil
| | - Nelson Ramos Stradiotto
- Analytical Chemistry Department, Institute of Chemistry, São Paulo State University (UNESP), Araraquara 14800-060, São Paulo State, Brazil; Bioenergy Research Institute, São Paulo State University (UNESP), Araraquara 14800-060, São Paulo State, Brazil
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38
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Crump NT, Hadjinicolaou AV, Xia M, Walsby-Tickle J, Gileadi U, Chen JL, Setshedi M, Olsen LR, Lau IJ, Godfrey L, Quek L, Yu Z, Ballabio E, Barnkob MB, Napolitani G, Salio M, Koohy H, Kessler BM, Taylor S, Vyas P, McCullagh JSO, Milne TA, Cerundolo V. Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation. Cell Rep 2021; 35:109101. [PMID: 33979616 PMCID: PMC8131582 DOI: 10.1016/j.celrep.2021.109101] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 03/01/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Depleting the microenvironment of important nutrients such as arginine is a key strategy for immune evasion by cancer cells. Many tumors overexpress arginase, but it is unclear how these cancers, but not T cells, tolerate arginine depletion. In this study, we show that tumor cells synthesize arginine from citrulline by upregulating argininosuccinate synthetase 1 (ASS1). Under arginine starvation, ASS1 transcription is induced by ATF4 and CEBPβ binding to an enhancer within ASS1. T cells cannot induce ASS1, despite the presence of active ATF4 and CEBPβ, as the gene is repressed. Arginine starvation drives global chromatin compaction and repressive histone methylation, which disrupts ATF4/CEBPβ binding and target gene transcription. We find that T cell activation is impaired in arginine-depleted conditions, with significant metabolic perturbation linked to incomplete chromatin remodeling and misregulation of key genes. Our results highlight a T cell behavior mediated by nutritional stress, exploited by cancer cells to enable pathological immune evasion.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Andreas V Hadjinicolaou
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Meng Xia
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Uzi Gileadi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ji-Li Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mashiko Setshedi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lars R Olsen
- Section for Bioinformatics, DTU Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - I-Jun Lau
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lynn Quek
- School of Cancer and Pharmaceutical Sciences, King's College London, SGDP Centre, Memory Lane, London SE5 8AF, UK
| | - Zhanru Yu
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Erica Ballabio
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mike B Barnkob
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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Ling Q, Sadali NM, Soufi Z, Zhou Y, Huang B, Zeng Y, Rodriguez-Concepcion M, Jarvis RP. The chloroplast-associated protein degradation pathway controls chromoplast development and fruit ripening in tomato. NATURE PLANTS 2021; 7:655-666. [PMID: 34007040 DOI: 10.1038/s41477-021-00916-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The maturation of green fleshy fruit to become colourful and flavoursome is an important strategy for plant reproduction and dispersal. In tomato (Solanum lycopersicum) and many other species, fruit ripening is intimately linked to the biogenesis of chromoplasts, the plastids that are abundant in ripe fruit and specialized for the accumulation of carotenoid pigments. Chromoplasts develop from pre-existing chloroplasts in the fruit, but the mechanisms underlying this transition are poorly understood. Here, we reveal a role for the chloroplast-associated protein degradation (CHLORAD) proteolytic pathway in chromoplast differentiation. Knockdown of the plastid ubiquitin E3 ligase SP1, or its homologue SPL2, delays tomato fruit ripening, whereas overexpression of SP1 accelerates ripening, as judged by colour changes. We demonstrate that SP1 triggers broader effects on fruit ripening, including fruit softening, and gene expression and metabolism changes, by promoting the chloroplast-to-chromoplast transition. Moreover, we show that tomato SP1 and SPL2 regulate leaf senescence, revealing conserved functions of CHLORAD in plants. We conclude that SP1 homologues control plastid transitions during fruit ripening and leaf senescence by enabling reconfiguration of the plastid protein import machinery to effect proteome reorganization. The work highlights the critical role of chromoplasts in fruit ripening, and provides a theoretical basis for engineering crop improvements.
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Affiliation(s)
- Qihua Ling
- Department of Plant Sciences, University of Oxford, Oxford, UK
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Najiah Mohd Sadali
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Ziad Soufi
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Yuan Zhou
- Department of Plant Sciences, University of Oxford, Oxford, UK
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Binquan Huang
- Department of Plant Sciences, University of Oxford, Oxford, UK
- School of Agriculture, Yunnan University, Kunming, China
| | - Yunliu Zeng
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Manuel Rodriguez-Concepcion
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, Spain
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford, UK.
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Savic D, Ball V, Holzner L, Hauton D, Timm KN, Curtis MK, Heather LC, Tyler DJ. Hyperpolarized magnetic resonance shows that the anti-ischemic drug meldonium leads to increased flux through pyruvate dehydrogenase in vivo resulting in improved post-ischemic function in the diabetic heart. NMR IN BIOMEDICINE 2021; 34:e4471. [PMID: 33458907 PMCID: PMC8609426 DOI: 10.1002/nbm.4471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/20/2020] [Accepted: 12/20/2020] [Indexed: 05/07/2023]
Abstract
The diabetic heart has a decreased ability to metabolize glucose. The anti-ischemic drug meldonium may provide a route to counteract this by reducing l-carnitine levels, resulting in improved cardiac glucose utilization. Therefore, the aim of this study was to use the novel technique of hyperpolarized magnetic resonance to investigate the in vivo effects of treatment with meldonium on cardiac metabolism and function in control and diabetic rats. Thirty-six male Wistar rats were injected either with vehicle, or with streptozotocin (55 mg/kg) to induce a model of type 1 diabetes. Daily treatment with either saline or meldonium (100 mg/kg/day) was undertaken for three weeks. in vivo cardiac function and metabolism were assessed with CINE MRI and hyperpolarized magnetic resonance respectively. Isolated perfused hearts were challenged with low-flow ischemia/reperfusion to assess the impact of meldonium on post-ischemic recovery. Meldonium had no significant effect on blood glucose concentrations or on baseline cardiac function. However, hyperpolarized magnetic resonance revealed that meldonium treatment elevated pyruvate dehydrogenase flux by 3.1-fold and 1.2-fold in diabetic and control animals, respectively, suggesting an increase in cardiac glucose oxidation. Hyperpolarized magnetic resonance further demonstrated that meldonium reduced the normalized acetylcarnitine signal by 2.1-fold in both diabetic and control animals. The increase in pyruvate dehydrogenase flux in vivo was accompanied by an improvement in post-ischemic function ex vivo, as meldonium elevated the rate pressure product by 1.3-fold and 1.5-fold in the control and diabetic animals, respectively. In conclusion, meldonium improves in vivo pyruvate dehydrogenase flux in the diabetic heart, contributing to improved cardiac recovery after ischemia.
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Affiliation(s)
- Dragana Savic
- Cardiac Metabolism Research Group (CMRG), Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
- Oxford Centre for Clinical Magnetic Resonance Research (OCMR), Division of Cardiovascular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Vicky Ball
- Cardiac Metabolism Research Group (CMRG), Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Lorenz Holzner
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - David Hauton
- Cardiac Metabolism Research Group (CMRG), Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
- Metabolomics Research Group, Department of ChemistryUniversity of OxfordOxfordUK
| | - Kerstin N. Timm
- Cardiac Metabolism Research Group (CMRG), Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - M. Kate Curtis
- Cardiac Metabolism Research Group (CMRG), Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Lisa C. Heather
- Cardiac Metabolism Research Group (CMRG), Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Damian J. Tyler
- Cardiac Metabolism Research Group (CMRG), Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
- Oxford Centre for Clinical Magnetic Resonance Research (OCMR), Division of Cardiovascular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
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Savic D, Ball V, Curtis MK, Sousa Fialho MDL, Timm KN, Hauton D, West J, Griffin J, Heather LC, Tyler DJ. L-Carnitine Stimulates In Vivo Carbohydrate Metabolism in the Type 1 Diabetic Heart as Demonstrated by Hyperpolarized MRI. Metabolites 2021; 11:metabo11030191. [PMID: 33806953 PMCID: PMC8004902 DOI: 10.3390/metabo11030191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/15/2021] [Accepted: 03/19/2021] [Indexed: 01/25/2023] Open
Abstract
The diabetic heart is energetically and metabolically abnormal, with increased fatty acid oxidation and decreased glucose oxidation. One factor contributing to the metabolic dysfunction in diabetes may be abnormal handling of acetyl and acyl groups by the mitochondria. L-carnitine is responsible for their transfer across the mitochondrial membrane, therefore, supplementation with L-carnitine may provide a route to improve the metabolic state of the diabetic heart. The primary aim of this study was to use hyperpolarized magnetic resonance imaging (MRI) to investigate the effects of L-carnitine supplementation on the in vivo metabolism of [1-13C]pyruvate in diabetes. Male Wistar rats were injected with either vehicle or streptozotocin (55 mg/kg) to induce type-1 diabetes. Three weeks of daily i.p. treatment with either saline or L-carnitine (3 g/kg/day) was subsequently undertaken. In vivo cardiac function and metabolism were assessed with CINE and hyperpolarized MRI, respectively. L-carnitine supplementation prevented the progression of hyperglycemia, which was observed in untreated streptozotocin injected animals and led to reductions in plasma triglyceride and ß-hydroxybutyrate concentrations. Hyperpolarized MRI revealed that L-carnitine treatment elevated pyruvate dehydrogenase flux by 3-fold in the diabetic animals, potentially through increased buffering of excess acetyl-CoA units in the mitochondria. Improved functional recovery following ischemia was also observed in the L-carnitine treated diabetic animals.
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Affiliation(s)
- Dragana Savic
- Cardiac Metabolism Research Group, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; (V.B.); (M.K.C.); (M.d.L.S.F.); (K.N.T.); (D.H.); (L.C.H.); (D.J.T.)
- Oxford Centre for Clinical Magnetic Resonance Research (OCMR), Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX1 3PT, UK
- Correspondence:
| | - Vicky Ball
- Cardiac Metabolism Research Group, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; (V.B.); (M.K.C.); (M.d.L.S.F.); (K.N.T.); (D.H.); (L.C.H.); (D.J.T.)
| | - M. Kate Curtis
- Cardiac Metabolism Research Group, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; (V.B.); (M.K.C.); (M.d.L.S.F.); (K.N.T.); (D.H.); (L.C.H.); (D.J.T.)
| | - Maria da Luz Sousa Fialho
- Cardiac Metabolism Research Group, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; (V.B.); (M.K.C.); (M.d.L.S.F.); (K.N.T.); (D.H.); (L.C.H.); (D.J.T.)
| | - Kerstin N. Timm
- Cardiac Metabolism Research Group, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; (V.B.); (M.K.C.); (M.d.L.S.F.); (K.N.T.); (D.H.); (L.C.H.); (D.J.T.)
- Department of Pharmacology, University of Oxford, Oxford OX1 3PT, UK
| | - David Hauton
- Cardiac Metabolism Research Group, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; (V.B.); (M.K.C.); (M.d.L.S.F.); (K.N.T.); (D.H.); (L.C.H.); (D.J.T.)
- Metabolomics Research Group, Department of Chemistry, University of Oxford, Oxford OX1 3PT, UK
| | - James West
- Department of Medicine, University of Cambridge, Cambridge CB2 1TN, UK;
| | - Julian Griffin
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK;
| | - Lisa C. Heather
- Cardiac Metabolism Research Group, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; (V.B.); (M.K.C.); (M.d.L.S.F.); (K.N.T.); (D.H.); (L.C.H.); (D.J.T.)
| | - Damian J. Tyler
- Cardiac Metabolism Research Group, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK; (V.B.); (M.K.C.); (M.d.L.S.F.); (K.N.T.); (D.H.); (L.C.H.); (D.J.T.)
- Oxford Centre for Clinical Magnetic Resonance Research (OCMR), Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX1 3PT, UK
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Straube H, Witte CP, Herde M. Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC-MS Techniques. Cells 2021; 10:689. [PMID: 33804650 PMCID: PMC8003640 DOI: 10.3390/cells10030689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid-liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites.
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Affiliation(s)
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
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Zhang X, Wang J, Zhuang J, Liu C, Gao C, Li H, Ma X, Li J, Sun C. A Novel Glycolysis-Related Four-mRNA Signature for Predicting the Survival of Patients With Breast Cancer. Front Genet 2021; 12:606937. [PMID: 33584825 PMCID: PMC7876610 DOI: 10.3389/fgene.2021.606937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/04/2021] [Indexed: 01/02/2023] Open
Abstract
Background: Glycolysis is critical in the occurrence and development of tumors. Owing to the biological and clinical heterogeneity of patients with BRCA, the traditional predictive classification system is far from satisfactory. Survival and prognosis biomarkers related to glycolysis have broad application prospects for assessing the risk of patients and guiding their individualized treatment. Methods: The mRNA expression profiles and clinical information of patients with BRCA were obtained from TCGA database, and glycolysis-related genes were obtained by GSEA. Patients with BRCA were randomly divided into the training cohort and testing cohort. Univariate and multivariate Cox analyses were used to establish and validate a new mRNA signature for predicting the prognosis of patients with BRCA. Results: We established a four-gene breast cancer prediction signature that included PGK1, SDHC, PFKL, and NUP43. The patients with BRCA in the training cohort and testing cohort were divided into high-risk and low-risk groups based on the signature. The AUC values were 0.74 (training cohort), 0.806 (testing cohort) and 0.769 (entire cohort), thereby showing that the prediction performance of the signature is acceptable. Additionally, Cox regression analysis revealed that four-gene signature could independently predict the prognosis of BRCA patients without being affected by clinical factors. Conclusion: We constructed a four-gene signature to predict the prognosis of patients with BRCA. This signature will aid in the early diagnosis and personalized treatment of breast cancer, but the specific associated biological mechanism requires further study.
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Affiliation(s)
- Xiaolu Zhang
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jia Wang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Huayao Li
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaoran Ma
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jie Li
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
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