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Ott H, Bennewitz K, Zhang X, Prianichnikova M, Sticht C, Poschet G, Kroll J. Sodium thiosulfate treatment rescues hyperglycaemia-induced pronephros damage in zebrafish by upregulating nitric oxide signalling. J Physiol 2024. [PMID: 39264236 DOI: 10.1113/jp286398] [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: 04/18/2024] [Accepted: 08/16/2024] [Indexed: 09/13/2024] Open
Abstract
Sodium thiosulfate (STS) is gaining increasing attention in research for its potential therapeutic applications across a spectrum of disease processes beyond its current uses. However, the precise mechanisms of action remain incompletely understood. We investigated the efficacy of STS in treating hyperglycaemia-induced pronephros damage in zebrafish to gain further insight into the underlying mechanisms. Hyperglycaemia was induced in zebrafish by suppressing the pdx1 transcription factor, which plays a crucial role in maintaining physiological pancreatic function. STS was administered by introducing it into the medium of zebrafish larvae. The pronephros structure was analysed at 48 h post-fertilization. Metabolomic profiling and RNA sequencing were conducted on groups exposed to various experimental conditions. Our findings reveal a downregulation of nitric oxide (NO) signalling in zebrafish with a knocked-down pdx1 gene, both metabolomically and transcriptionally. Notably, treatment with STS led to a compensatory upregulation of the NO signalling, ultimately resulting in the rescue of the pronephros structure. Our study provides compelling evidence that targeting NO metabolism by the administration of STS offers a promising strategy for addressing hyperglycaemia-induced organ damage. These findings underscore the potential of STS as a promising therapeutic agent for diabetic complications and warrant further investigation of its clinical applications. KEY POINTS: Sodium thiosulfate (STS) is increasingly drawing attention in research for its potential therapeutic applications across a spectrum of disease processes. Here, we demonstrate that STS treatment rescues hyperglycaemia-induced pronephros damage in zebrafish. We identified upregulation of nitric oxide signalling as the major driver behind STS-mediated rescue. Our data suggest that STS offers a promising strategy for addressing hyperglycaemia-induced organ damage, including diabetic nephropathy.
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Affiliation(s)
- Hannes Ott
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katrin Bennewitz
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xin Zhang
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Mariia Prianichnikova
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Jens Kroll
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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2
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Gegner HM, Naake T, Aljakouch K, Dugourd A, Kliewer G, Müller T, Schilling D, Schneider MA, Kunze-Rohrbach N, Grünewald TGP, Hell R, Saez-Rodriguez J, Huber W, Poschet G, Krijgsveld J. A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens. Clin Proteomics 2024; 21:49. [PMID: 38969985 PMCID: PMC11225228 DOI: 10.1186/s12014-024-09501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Understanding the interplay of the proteome and the metabolome helps to understand cellular regulation and response. To enable robust inferences from such multi-omics analyses, we introduced and evaluated a workflow for combined proteome and metabolome analysis starting from a single sample. Specifically, we integrated established and individually optimized protocols for metabolomic and proteomic profiling (EtOH/MTBE and autoSP3, respectively) into a unified workflow (termed MTBE-SP3), and took advantage of the fact that the protein residue of the metabolomic sample can be used as a direct input for proteome analysis. We particularly evaluated the performance of proteome analysis in MTBE-SP3, and demonstrated equivalence of proteome profiles irrespective of prior metabolite extraction. In addition, MTBE-SP3 combines the advantages of EtOH/MTBE and autoSP3 for semi-automated metabolite extraction and fully automated proteome sample preparation, respectively, thus advancing standardization and scalability for large-scale studies. We showed that MTBE-SP3 can be applied to various biological matrices (FFPE tissue, fresh-frozen tissue, plasma, serum and cells) to enable implementation in a variety of clinical settings. To demonstrate applicability, we applied MTBE-SP3 and autoSP3 to a lung adenocarcinoma cohort showing consistent proteomic alterations between tumour and non-tumour adjacent tissue independent of the method used. Integration with metabolomic data obtained from the same samples revealed mitochondrial dysfunction in tumour tissue through deregulation of OGDH, SDH family enzymes and PKM. In summary, MTBE-SP3 enables the facile and reliable parallel measurement of proteins and metabolites obtained from the same sample, benefiting from reduced sample variation and input amount. This workflow is particularly applicable for studies with limited sample availability and offers the potential to enhance the integration of metabolomic and proteomic datasets.
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Affiliation(s)
- Hagen M Gegner
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Thomas Naake
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Karim Aljakouch
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Georg Kliewer
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Torsten Müller
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Dustin Schilling
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Röntgenstraße 1, 69126, Heidelberg, Germany
- Translational Research Center Heidelberg (TLRC), Member of The German Center for Lung Research (DZL), Im Neuenheimer Feld 156, 69120, Heidelberg, Germany
| | - Nina Kunze-Rohrbach
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany.
| | - Jeroen Krijgsveld
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany.
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
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Merquiol L, Romano G, Cutignano A, D'Ambra I. Chemical markers in marine food web: A simple workflow based on methyl tert-butyl ether extraction for fatty acids and stable isotopes assessment in plankton samples. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106087. [PMID: 37473598 DOI: 10.1016/j.marenvres.2023.106087] [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: 03/26/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
Fatty acids (FAs) are used, often in combination with stable isotopes (SIs), as chemical biomarkers to assess the contribution of different prey to the diet of consumers and define food web structure and dynamics. Extraction of lipids is traditionally carried out using methanol (MeOH) combined with chloroform or dichloromethane, these latter being well-known environmental pollutant and potential carcinogenic agents. Recently, extraction protocols based on methyl tert-butyl ether (MTBE) and MeOH have been proposed as an alternative to halogenated solvents in lipidomic studies. However, no specific investigation has been performed to assess MTBE suitability in marine ecological studies including FA analysis together with SI measurements. We used an analytical workflow for qualitative and quantitative analysis of FAs and SIs in field samples of phytoplankton, zooplankton and the scyphomedusa Pelagia noctiluca, applying MTBE in comparison with chloroform- and dichloromethane-based protocols for total lipid extraction. Our analysis suggested that MTBE is a reliable substitute for lipid extraction in trophic ecology studies in marine planktonic organisms.
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Affiliation(s)
- Louise Merquiol
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Giovanna Romano
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133, Napoli, Italy
| | - Adele Cutignano
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133, Napoli, Italy; Istituto di Chimica Biomolecolare (ICB), Consiglio Nazionale delle Ricerche, via Campi Flegrei 34, 80078, Pozzuoli, Italy.
| | - Isabella D'Ambra
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
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Chromatomass-Spectrometric Method for the Quantitative Determination of Amino- and Carboxylic Acids in Biological Samples. Metabolites 2022; 13:metabo13010016. [PMID: 36676941 PMCID: PMC9863782 DOI: 10.3390/metabo13010016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
A highly sensitive method for the qualitative and quantitative determination of amino- and carboxylic acids, as well as a number of urea and methionine cycle metabolites in the studied solutions, is presented. Derivatives (esterification) were obtained for amino acids by their reaction in a solution of 3 N of hydrochloric acid in n-butanol for 15 min at 65 °C and for carboxylic acids by their reaction with phenol in ethyl acetate with 3 N of hydrochloric acid for 20 min at 65 °C. Experimental work on the determination of individual metabolites was carried out using the HPLC-MS/MS method and included the creation of a library of spectra of the analyzed compounds and their quantitative determination. Multiplex methods have been developed for the quantitative analysis of the desired metabolites in a wide range of concentrations of 3-4 orders of magnitude. The approach to the analysis of metabolites was developed based on the method of the dynamic monitoring of multiple reactions of the formation of fragments for a mass analyzer with a triple quadrupole (QQQ). The effective chromatographic separation of endogenous metabolites was carried out within 13 min. The calibration curves of the analyzed compounds were stable throughout the concentration range and had the potential to fit below empirical levels. The developed methods and obtained experimental data are of interest for a wide range of biomedical studies, as well as for monitoring the content of endogenous metabolites in biological samples under various pathological conditions. The sensitivity limit of the methods for amino acids was about 4.8 nM and about 0.5 μM for carboxylic acids. Up to 19 amino- and up to 12 carboxy acids and about 10 related metabolites can be tested in a single sample.
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Andresen C, Boch T, Gegner HM, Mechtel N, Narr A, Birgin E, Rasbach E, Rahbari N, Trumpp A, Poschet G, Hübschmann D. Comparison of extraction methods for intracellular metabolomics of human tissues. Front Mol Biosci 2022; 9:932261. [PMID: 36090025 PMCID: PMC9461704 DOI: 10.3389/fmolb.2022.932261] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Analyses of metabolic compounds inside cells or tissues provide high information content since they represent the endpoint of biological information flow and are a snapshot of the integration of many regulatory processes. However, quantification of the abundance of metabolites requires their careful extraction. We present a comprehensive study comparing ten extraction protocols in four human sample types (liver tissue, bone marrow, HL60, and HEK cells) aiming to detect and quantify up to 630 metabolites of different chemical classes. We show that the extraction efficiency and repeatability are highly variable across protocols, tissues, and chemical classes of metabolites. We used different quality metrics including the limit of detection and variability between replicates as well as the sum of concentrations as a global estimate of analytical repeatability of the extraction. The coverage of extracted metabolites depends on the used solvents, which has implications for the design of measurements of different sample types and metabolic compounds of interest. The benchmark dataset can be explored in an easy-to-use, interactive, and flexible online resource (R/shiny app MetaboExtract: http://www.metaboextract.shiny.dkfz.de) for context-specific selection of the optimal extraction method. Furthermore, data processing and conversion functionality underlying the shiny app are accessible as an R package: https://cran.r-project.org/package=MetAlyzer.
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Affiliation(s)
- Carolin Andresen
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Tobias Boch
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center, Heidelberg, Germany
- Department of Personalized Oncology, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany
| | - Hagen M. Gegner
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Nils Mechtel
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Andreas Narr
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Emrullah Birgin
- Department of Surgery, Medical Faculty Mannheim, Universitätsmedizin Mannheim, Heidelberg University, Mannheim, Germany
| | - Erik Rasbach
- Department of Surgery, Medical Faculty Mannheim, Universitätsmedizin Mannheim, Heidelberg University, Mannheim, Germany
| | - Nuh Rahbari
- Department of Surgery, Medical Faculty Mannheim, Universitätsmedizin Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, German Cancer Research Center and DKFZ-ZMBH Alliance, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Daniel Hübschmann
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- *Correspondence: Daniel Hübschmann,
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da Silva KM, Iturrospe E, van den Boom R, van de Lavoir M, Robeyns R, Vergauwen L, Knapen D, Cuykx M, Covaci A, van Nuijs ALN. Lipidomics profiling of zebrafish liver through untargeted liquid chromatography-high resolution mass spectrometry. J Sep Sci 2022; 45:2935-2945. [PMID: 35716100 DOI: 10.1002/jssc.202200214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/10/2022]
Abstract
Lipidomics analysis of zebrafish tissues has shown promising results to understand disease-related outcomes of exposure to toxic substances at molecular level. However, knowledge about their lipidome is limited, as most untargeted studies only identify the lipids that are statistically significant in their setup. In this work, liquid chromatography-high resolution mass spectrometry was used to study different aspects of the analytical workflow, i.e., extraction solvents (methanol/chloroform/water (3/2/2, v/v/v), methanol/dichloromethane/water (2/3/2, v/v/v) and methanol/methyl-tert-butyl ether/water (3/10/2.5, v/v/v), instrumental response, and strategies used for lipid annotation. The number of high-quality features (relative standard deviation of the intensity values ≤ 10% in the range 103 -107 counts) was affected by the dilution of lipid extracts, indicating that it is an important parameter for developing untargeted methods. The workflows used allowed the selection of a dilution factor to annotate 712 lipid species (507 bulk lipids) in zebrafish liver using four software (LipidMatch, LipidHunter, MS-DIAL and Lipostar). Retention time mapping was a valuable tool to filter lipid annotations obtained from automatic software annotations. The lipid profiling of zebrafish livers will help in a better understanding of the true constitution of their lipidome at the species level, as well as in the use of zebrafish in toxicological studies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Katyeny Manuela da Silva
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Elias Iturrospe
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium.,Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Campus Jette, Vrije Universiteit Brussels, Laarbeeklaan 103, Brussels, 1090, Belgium
| | - Rik van den Boom
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Maria van de Lavoir
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Rani Robeyns
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Lucia Vergauwen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Matthias Cuykx
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium.,Department of Laboratory Medicine AZ Turnhout, Rubenslaan 166, Turnhout, 2300, Belgium
| | - Adrian Covaci
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Alexander L N van Nuijs
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
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