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Yuan C, Jin Y, Zhang H, Chen S, Yi J, Xie Q, Dong J, Wu C. Strategy to Empower Nontargeted Metabolomics by Triple-Dimensional Combinatorial Derivatization with MS-TDF Software. Anal Chem 2024; 96:7634-7642. [PMID: 38691624 DOI: 10.1021/acs.analchem.4c00527] [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: 05/03/2024]
Abstract
Chemical derivatization is a widely employed strategy in metabolomics to enhance metabolite coverage by improving chromatographic behavior and increasing the ionization rates in mass spectroscopy (MS). However, derivatization might complicate MS data, posing challenges for data mining due to the lack of a corresponding benchmark database. To address this issue, we developed a triple-dimensional combinatorial derivatization strategy for nontargeted metabolomics. This strategy utilizes three structurally similar derivatization reagents and is supported by MS-TDF software for accelerated data processing. Notably, simultaneous derivatization of specific metabolite functional groups in biological samples produced compounds with stable but distinct chromatographic retention times and mass numbers, facilitating discrimination by MS-TDF, an in-house MS data processing software. In this study, carbonyl analogues in human plasma were derivatized using a combination of three hydrazide-based derivatization reagents: 2-hydrazinopyridine, 2-hydrazino-5-methylpyridine, and 2-hydrazino-5-cyanopyridine (6-hydrazinonicotinonitrile). This approach was applied to identify potential carbonyl biomarkers in lung cancer. Analysis and validation of human plasma samples demonstrated that our strategy improved the recognition accuracy of metabolites and reduced the risk of false positives, providing a useful method for nontargeted metabolomics studies. The MATLAB code for MS-TDF is available on GitHub at https://github.com/CaixiaYuan/MS-TDF.
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Affiliation(s)
- Caixia Yuan
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, China
| | - Ying Jin
- Department of Cardiology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361005, China
| | - Hairong Zhang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, China
| | - Simian Chen
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, China
| | - Jiajin Yi
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, China
| | - Qiang Xie
- Department of Cardiology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361005, China
| | - Jiyang Dong
- Department of Electronic Science, Xiamen University, Xiamen 361005, China
| | - Caisheng Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory for Clinical Efficacy and Evidence-Based Research of Traditional Chinese Medicine, Xiamen University, Xiamen 361005, China
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Karuppasamy M, English KG, Henry CA, Manzini MC, Parant JM, Wright MA, Ruparelia AA, Currie PD, Gupta VA, Dowling JJ, Maves L, Alexander MS. Standardization of zebrafish drug testing parameters for muscle diseases. Dis Model Mech 2024; 17:dmm050339. [PMID: 38235578 PMCID: PMC10820820 DOI: 10.1242/dmm.050339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
Skeletal muscular diseases predominantly affect skeletal and cardiac muscle, resulting in muscle weakness, impaired respiratory function and decreased lifespan. These harmful outcomes lead to poor health-related quality of life and carry a high healthcare economic burden. The absence of promising treatments and new therapies for muscular disorders requires new methods for candidate drug identification and advancement in animal models. Consequently, the rapid screening of drug compounds in an animal model that mimics features of human muscle disease is warranted. Zebrafish are a versatile model in preclinical studies that support developmental biology and drug discovery programs for novel chemical entities and repurposing of established drugs. Due to several advantages, there is an increasing number of applications of the zebrafish model for high-throughput drug screening for human disorders and developmental studies. Consequently, standardization of key drug screening parameters, such as animal husbandry protocols, drug compound administration and outcome measures, is paramount for the continued advancement of the model and field. Here, we seek to summarize and explore critical drug treatment and drug screening parameters in the zebrafish-based modeling of human muscle diseases. Through improved standardization and harmonization of drug screening parameters and protocols, we aim to promote more effective drug discovery programs.
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Affiliation(s)
- Muthukumar Karuppasamy
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA
| | - Katherine G. English
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA
| | - Clarissa A. Henry
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - M. Chiara Manzini
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Melissa A. Wright
- Department of Pediatrics, Section of Child Neurology, University of Colorado at Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Avnika A. Ruparelia
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria 3010, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Peter D. Currie
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria 3010, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Victorian Node, Monash University, Clayton, Victoria 3800, Australia
| | - Vandana A. Gupta
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James J. Dowling
- Division of Neurology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario M5G 1X8, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Lisa Maves
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Matthew S. Alexander
- Division of Neurology, Department of Pediatrics, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- UAB Center for Neurodegeneration and Experimental Therapeutics (CNET), Birmingham, AL 35294, USA
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White RM, Patton EE. Adult zebrafish as advanced models of human disease. Dis Model Mech 2023; 16:dmm050351. [PMID: 37522272 PMCID: PMC10655866 DOI: 10.1242/dmm.050351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
Modelling adult diseases to understand their aetiology and progression, and to develop new therapies, is a major challenge for medical biology. We are excited by new efforts in the zebrafish community to develop models of adult diseases that range from cancer to heart, infectious and age-related diseases, and those that relate to toxicology and complex social behaviours. Here, we discuss some of the advances in the field of zebrafish models of adult disease, and where we see opportunities and challenges ahead.
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Affiliation(s)
- Richard M. White
- Ludwig Cancer Institute, Nuffield Department of Medicine, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - E. Elizabeth Patton
- MRC Human Genetics Unit, CRUK Scotland Centre and Edinburgh Cancer Research, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH42XU, UK
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Skiba A, Pellegata D, Morozova V, Kozioł E, Budzyńska B, Lee SMY, Gertsch J, Skalicka-Woźniak K. Pharmacometabolic Effects of Pteryxin and Valproate on Pentylenetetrazole-Induced Seizures in Zebrafish Reveal Vagus Nerve Stimulation. Cells 2023; 12:1540. [PMID: 37296660 PMCID: PMC10252891 DOI: 10.3390/cells12111540] [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: 04/17/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Zebrafish (Danio rerio) assays provide a versatile pharmacological platform to test compounds on a wide range of behaviors in a whole organism. A major challenge lies in the lack of knowledge about the bioavailability and pharmacodynamic effects of bioactive compounds in this model organism. Here, we employed a combined methodology of LC-ESI-MS/MS analytics and targeted metabolomics with behavioral experiments to evaluate the anticonvulsant and potentially toxic effects of the angular dihydropyranocoumarin pteryxin (PTX) in comparison to the antiepileptic drug sodium valproate (VPN) in zebrafish larvae. PTX occurs in different Apiaceae plants traditionally used in Europe to treat epilepsy but has not been investigated so far. To compare potency and efficacy, the uptake of PTX and VPN into zebrafish larvae was quantified as larvae whole-body concentrations together with amino acids and neurotransmitters as proxy pharmacodynamic readout. The convulsant agent pentylenetetrazole (PTZ) acutely reduced the levels of most metabolites, including acetylcholine and serotonin. Conversely, PTX strongly reduced neutral essential amino acids in a LAT1 (SLCA5)-independent manner, but, similarly to VPN specifically increased the levels of serotonin, acetylcholine, and choline, but also ethanolamine. PTX dose and time-dependent manner inhibited PTZ-induced seizure-like movements resulting in a ~70% efficacy after 1 h at 20 µM (the equivalent of 4.28 ± 0.28 µg/g in larvae whole-body). VPN treated for 1 h with 5 mM (the equivalent of 18.17 ± 0.40 µg/g in larvae whole-body) showed a ~80% efficacy. Unexpectedly, PTX (1-20 µM) showed significantly higher bioavailability than VPN (0.1-5 mM) in immersed zebrafish larvae, possibly because VPN in the medium dissociated partially to the readily bioavailable valproic acid. The anticonvulsive effect of PTX was confirmed by local field potential (LFP) recordings. Noteworthy, both substances specifically increased and restored whole-body acetylcholine, choline, and serotonin levels in control and PTZ-treated zebrafish larvae, indicative of vagus nerve stimulation (VNS), which is an adjunctive therapeutic strategy to treat refractory epilepsy in humans. Our study demonstrates the utility of targeted metabolomics in zebrafish assays and shows that VPN and PTX pharmacologically act on the autonomous nervous system by activating parasympathetic neurotransmitters.
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Affiliation(s)
- Adrianna Skiba
- Department of Chemistry of Natural Products, Medical University of Lublin, 20-093 Lublin, Poland
| | - Daniele Pellegata
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland (V.M.)
| | - Veronika Morozova
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland (V.M.)
| | - Ewelina Kozioł
- Department of Chemistry of Natural Products, Medical University of Lublin, 20-093 Lublin, Poland
| | - Barbara Budzyńska
- Independent Laboratory of Behavioral Studies, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 519020, China;
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland (V.M.)
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Schwaiger-Haber M, Stancliffe E, Anbukumar DS, Sells B, Yi J, Cho K, Adkins-Travis K, Chheda MG, Shriver LP, Patti GJ. Using mass spectrometry imaging to map fluxes quantitatively in the tumor ecosystem. Nat Commun 2023; 14:2876. [PMID: 37208361 DOI: 10.1038/s41467-023-38403-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 04/26/2023] [Indexed: 05/21/2023] Open
Abstract
Tumors are comprised of a multitude of cell types spanning different microenvironments. Mass spectrometry imaging (MSI) has the potential to identify metabolic patterns within the tumor ecosystem and surrounding tissues, but conventional workflows have not yet fully integrated the breadth of experimental techniques in metabolomics. Here, we combine MSI, stable isotope labeling, and a spatial variant of Isotopologue Spectral Analysis to map distributions of metabolite abundances, nutrient contributions, and metabolic turnover fluxes across the brains of mice harboring GL261 glioma, a widely used model for glioblastoma. When integrated with MSI, the combination of ion mobility, desorption electrospray ionization, and matrix assisted laser desorption ionization reveals alterations in multiple anabolic pathways. De novo fatty acid synthesis flux is increased by approximately 3-fold in glioma relative to surrounding healthy tissue. Fatty acid elongation flux is elevated even higher at 8-fold relative to surrounding healthy tissue and highlights the importance of elongase activity in glioma.
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Affiliation(s)
- Michaela Schwaiger-Haber
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Ethan Stancliffe
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Dhanalakshmi S Anbukumar
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Blake Sells
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jia Yi
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Kayla Adkins-Travis
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
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First person – Madelyn Jackstadt. Dis Model Mech 2022. [PMCID: PMC9403746 DOI: 10.1242/dmm.049787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
First Person is a series of interviews with the first authors of a selection of papers published in Disease Models & Mechanisms, helping early-career researchers promote themselves alongside their papers. Madelyn Jackstadt is first author on ‘
A multidimensional metabolomics workflow to image distribution and evaluate pharmacodynamics in adult zebrafish’, published in DMM. Madelyn is a PhD student in the lab of Gary Patti at Washington University, St. Louis, MO, USA, and is interested in utilizing metabolomics, particularly isotope tracing, in zebrafish to investigate biological questions including drug effects and disease states.
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