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Chan YH, Pathmasiri KC, Pierre-Jacques D, Hibbard MC, Tao N, Fischer JL, Yang E, Cologna SM, Gao R. Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics. Nat Commun 2024; 15:5036. [PMID: 38866734 PMCID: PMC11169460 DOI: 10.1038/s41467-024-49384-w] [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: 09/10/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
A technique capable of label-free detection, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of native biomolecules in intact specimens. However, MSI has often been precluded from single-cell applications due to the spatial resolution limit set forth by the physical and instrumental constraints of the method. By taking advantage of the reversible interaction between the analytes and a superabsorbent hydrogel, we have developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome the spatial resolution limits of modern mass spectrometers. With GAMSI, we show that the spatial resolution of MALDI-MSI can be enhanced ~3-6-fold to the sub-micrometer level without changing the existing mass spectrometry hardware or analysis pipeline. This approach will vastly enhance the accessibility of MSI-based spatial analysis at the cellular scale.
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Affiliation(s)
- Yat Ho Chan
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | - Maddison C Hibbard
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | | | - Stephanie M Cologna
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA.
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA.
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2
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Mlinac-Jerkovic K, Kalanj-Bognar S, Heffer M, Blažetić S. Methodological Pitfalls of Investigating Lipid Rafts in the Brain: What Are We Still Missing? Biomolecules 2024; 14:156. [PMID: 38397393 PMCID: PMC10886647 DOI: 10.3390/biom14020156] [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: 12/31/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The purpose of this review is to succinctly examine the methodologies used in lipid raft research in the brain and to highlight the drawbacks of some investigative approaches. Lipid rafts are biochemically and biophysically different from the bulk membrane. A specific lipid environment within membrane domains provides a harbor for distinct raftophilic proteins, all of which in concert create a specialized platform orchestrating various cellular processes. Studying lipid rafts has proved to be arduous due to their elusive nature, mobility, and constant dynamic reorganization to meet the cellular needs. Studying neuronal lipid rafts is particularly cumbersome due to the immensely complex regional molecular architecture of the central nervous system. Biochemical fractionation, performed with or without detergents, is still the most widely used method to isolate lipid rafts. However, the differences in solubilization when various detergents are used has exposed a dire need to find more reliable methods to study particular rafts. Biochemical methods need to be complemented with other approaches such as live-cell microscopy, imaging mass spectrometry, and the development of specific non-invasive fluorescent probes to obtain a more complete image of raft dynamics and to study the spatio-temporal expression of rafts in live cells.
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Affiliation(s)
| | | | - Marija Heffer
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Senka Blažetić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
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3
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Chan YH, Pathmasiri KC, Pierre-Jacques D, Cologna SM, Gao R. Gel-assisted mass spectrometry imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543480. [PMID: 37398444 PMCID: PMC10312618 DOI: 10.1101/2023.06.02.543480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Compatible with label-free detection and quantification, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of biomolecules in intact specimens. Yet, the spatial resolution of MSI is limited by the method's physical and instrumental constraints, which often preclude it from single-cell and subcellular applications. By taking advantage of the reversible interaction of analytes with superabsorbent hydrogels, we developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome these limits. With GAMSI, the spatial resolution of lipid and protein MALDI-MSI can be enhanced severalfold without changing the existing mass spectrometry hardware and analysis pipeline. This approach will further enhance the accessibility to (sub)cellular-scale MALDI-MSI-based spatial omics.
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Affiliation(s)
- Yat Ho Chan
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
| | | | | | - Stephanie M. Cologna
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago; Chicago, IL 60607, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
- Laboratory for Integrative Neuroscience, University of Illinois at Chicago; Chicago, IL 60607, USA
- Department of Biological Sciences, University of Illinois Chicago; Chicago, IL 60607, USA
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4
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Gameiro-Ros I, Noble L, Tong M, Yalcin EB, de la Monte SM. Tissue Microarray Lipidomic Imaging Mass Spectrometry Method: Application to the Study of Alcohol-Related White Matter Neurodegeneration. APPLIED BIOSCIENCES 2023; 2:173-193. [PMID: 38384722 PMCID: PMC10880182 DOI: 10.3390/applbiosci2020013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Central nervous system (CNS) white matter pathologies accompany many diseases across the lifespan, yet their biochemical bases, mechanisms, and consequences have remained poorly understood due to the complexity of myelin lipid-based research. However, recent advances in matrix-assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS) have minimized or eliminated many technical challenges that previously limited progress in CNS disease-based lipidomic research. MALDI-IMS can be used for lipid identification, semi-quantification, and the refined interpretation of histopathology. The present work illustrates the use of tissue micro-arrays (TMAs) for MALDI-IMS analysis of frontal lobe white matter biochemical lipidomic pathology in an experimental rat model of chronic ethanol feeding. The use of TMAs combines workload efficiency with the robustness and uniformity of data acquisition. The methods described for generating TMAs enable simultaneous comparisons of lipid profiles across multiple samples under identical conditions. With the methods described, we demonstrate significant reductions in phosphatidylinositol and increases in phosphatidylcholine in the frontal white matter of chronic ethanol-fed rats. Together with the use of a novel rapid peak alignment protocol, this approach facilitates reliable inter- and intra-group comparisons of MALDI-IMS data from experimental models and could be extended to human disease states, including using archival specimens.
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Affiliation(s)
- Isabel Gameiro-Ros
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Autonomous University of Madrid, 28029 Madrid, Spain
| | - Lelia Noble
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Ming Tong
- Department of Medicine, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Emine B. Yalcin
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Suzanne M. de la Monte
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI 02903, USA
- Department of Medicine, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI 02903, USA
- Departments of Neurology & Neurosurgery, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI 02903, USA
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5
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Dannhorn A, Swales JG, Hamm G, Strittmatter N, Kudo H, Maglennon G, Goodwin RJA, Takats Z. Evaluation of Formalin-Fixed and FFPE Tissues for Spatially Resolved Metabolomics and Drug Distribution Studies. Pharmaceuticals (Basel) 2022; 15:1307. [PMID: 36355479 PMCID: PMC9697942 DOI: 10.3390/ph15111307] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 08/26/2023] Open
Abstract
Fixation of samples is broadly used prior to the histological evaluation of tissue samples. Though recent reports demonstrated the ability to use fixed tissues for mass spectrometry imaging (MSI) based proteomics, glycomics and tumor classification studies, to date comprehensive evaluation of fixation-related effects for spatially resolved metabolomics and drug disposition studies is still missing. In this study we used matrix assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) MSI to investigate the effect of formalin-fixation and formalin-fixation combined with paraffin embedding on the detectable metabolome including xenobiotics. Formalin fixation was found to cause significant washout of polar molecular species, including inorganic salts, amino acids, organic acids and carnitine species, oxidation of endogenous lipids and formation of reaction products between lipids and fixative ingredients. The slow fixation kinetics under ambient conditions resulted in increased lipid hydrolysis in the tissue core, correlating with the time-dependent progression of the fixation. Paraffin embedding resulted in subsequent partial removal of structural lipids resulting in the distortion of the elucidated biodistributions.
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Affiliation(s)
- Andreas Dannhorn
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - John G. Swales
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Gregory Hamm
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Nicole Strittmatter
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Hiromi Kudo
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
| | - Gareth Maglennon
- Oncology Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Richard J. A. Goodwin
- Imaging & Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK
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6
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Maia M, McCann A, Malherbe C, Far J, Cunha J, Eiras-Dias J, Cordeiro C, Eppe G, Quinton L, Figueiredo A, De Pauw E, Sousa Silva M. Grapevine leaf MALDI-MS imaging reveals the localisation of a putatively identified sucrose metabolite associated to Plasmopara viticola development. FRONTIERS IN PLANT SCIENCE 2022; 13:1012636. [PMID: 36299787 PMCID: PMC9589281 DOI: 10.3389/fpls.2022.1012636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Despite well-established pathways and metabolites involved in grapevine-Plasmopara viticola interaction, information on the molecules involved in the first moments of pathogen contact with the leaf surface and their specific location is still missing. To understand and localise these molecules, we analysed grapevine leaf discs infected with P. viticola with MSI. Plant material preparation was optimised, and different matrices and solvents were tested. Our data shows that trichomes hamper matrix deposition and the ion signal. Results show that putatively identified sucrose presents a higher accumulation and a non-homogeneous distribution in the infected leaf discs in comparison with the controls. This accumulation was mainly on the veins, leading to the hypothesis that sucrose metabolism is being manipulated by the development structures of P. viticola. Up to our knowledge this is the first time that the localisation of a putatively identified sucrose metabolite was shown to be associated to P. viticola infection sites.
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Affiliation(s)
- Marisa Maia
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Andréa McCann
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Cédric Malherbe
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Jorge Cunha
- Estação Vitivinícola Nacional, Instituto Nacional de Investigação Agrária e Veterinária (INIAV), Torres-Vedras, Portugal
| | - José Eiras-Dias
- Estação Vitivinícola Nacional, Instituto Nacional de Investigação Agrária e Veterinária (INIAV), Torres-Vedras, Portugal
| | - Carlos Cordeiro
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Gauthier Eppe
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Andreia Figueiredo
- Grapevine Pathogen Systems Lab (GPS Lab), Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Edwin De Pauw
- Mass Spectrometry Laboratory (MolSys), University of Liège, Liège, Belgium
| | - Marta Sousa Silva
- Laboratório de FTICR e Espectrometria de Massa Estrutural, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
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7
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Beger AW, Hauther KA, Dudzik B, Woltjer RL, Wood PL. Human Brain Lipidomics: Investigation of Formalin Fixed Brains. Front Mol Neurosci 2022; 15:835628. [PMID: 35782380 PMCID: PMC9245516 DOI: 10.3389/fnmol.2022.835628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Human brain lipidomics have elucidated structural lipids and lipid signal transduction pathways in neurologic diseases. Such studies have traditionally sourced tissue exclusively from brain bank biorepositories, however, limited inventories signal that these facilities may not be able to keep pace with this growing research domain. Formalin fixed, whole body donors willed to academic institutions offer a potential supplemental tissue source, the lipid profiles of which have yet to be described. To determine the potential of these subjects in lipid analysis, the lipid levels of fresh and fixed frontal cortical gray matter of human donors were compared using high resolution electrospray ionization mass spectrometry. Results revealed commensurate levels of specific triacylglycerols, diacylglycerols, hexosyl ceramides, and hydroxy hexosyl ceramides. Baseline levels of these lipid families in human fixed tissue were identified via a broader survey study covering six brain regions: cerebellar gray matter, superior cerebellar peduncle, gray and subcortical white matter of the precentral gyrus, periventricular white matter, and internal capsule. Whole body donors may therefore serve as supplemental tissue sources for lipid analysis in a variety of clinical contexts, including Parkinson's disease, Alzheimer's disease, Lewy body dementia, multiple sclerosis, and Gaucher's disease.
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Affiliation(s)
- Aaron W. Beger
- Department of Anatomy, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, United States
| | - Kathleen A. Hauther
- Metabolomics Unit, College of Veterinary Medicine, Lincoln Memorial University, Harrogate, TN, United States
| | - Beatrix Dudzik
- Department of Anatomy, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN, United States
| | - Randall L. Woltjer
- Department of Neurology, Oregon Health Science University, Portland, OR, United States
- Portland VA Medical Center, Portland, OR, United States
| | - Paul L. Wood
- Metabolomics Unit, College of Veterinary Medicine, Lincoln Memorial University, Harrogate, TN, United States
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8
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Zhu X, Xu T, Peng C, Wu S. Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues. Front Chem 2022; 9:782432. [PMID: 35186891 PMCID: PMC8850921 DOI: 10.3389/fchem.2021.782432] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Compared with conventional optical microscopy techniques, mass spectrometry imaging (MSI) or imaging mass spectrometry (IMS) is a powerful, label-free analytical technique, which can sensitively and simultaneously detect, quantify, and map hundreds of biomolecules, such as peptides, proteins, lipid, and other organic compounds in cells and tissues. So far, although several soft ionization techniques, such as desorption electrospray ionization (DESI) and secondary ion mass spectrometry (SIMS) have been used for imaging biomolecules, matrix-assisted laser desorption/ionization (MALDI) is still the most widespread MSI scanning method. Here, we aim to provide a comprehensive review of MALDI-MSI with an emphasis on its advances of the instrumentation, methods, application, and future directions in single cell and biological tissues.
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Affiliation(s)
- Xiaoping Zhu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tianyi Xu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Shihua Wu, ; Shihua Wu,
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9
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Strnad Š, Strnadová V, Sýkora D, Cvačka J, Maletínská L, Vrkoslav V. MALDI Mass Spectrometry Imaging of Lipids on Free-Floating Brain Sections and Immunohistochemically Colocalized Markers of Neurodegeneration. Methods Mol Biol 2022; 2437:229-239. [PMID: 34902152 DOI: 10.1007/978-1-0716-2030-4_16] [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: 06/14/2023]
Abstract
In mass spectrometry imaging (MSI), the essential steps in sample preparation include collection and storage. The most widely used preservation procedure for MSI consists in freezing samples and storing them at temperatures below -80 °C. On the other hand, the most common method for preserving biological samples in clinical practice is their fixation in paraformaldehyde. The storage of free-floating sections is a particular type of the preservation of paraformaldehyde-fixed tissues that is used in immunohistochemistry. This chapter describes the approach of the multimodal imaging of free-floating brain sections using the MSI of lipids and the immunohistochemistry of neurodegeneration markers.
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Affiliation(s)
- Štěpán Strnad
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Veronika Strnadová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Sýkora
- University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lenka Maletínská
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimír Vrkoslav
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
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10
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Kotnala A, Anderson DM, Patterson NH, Cantrell LS, Messinger JD, Curcio CA, Schey KL. Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4798. [PMID: 34881479 PMCID: PMC8711642 DOI: 10.1002/jms.4798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/09/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Imaging mass spectrometry (IMS) allows the location and abundance of lipids to be mapped across tissue sections of human retina. For reproducible and accurate information, sample preparation methods need to be optimized. Paraformaldehyde fixation of a delicate multilayer structure like human retina facilitates the preservation of tissue morphology by forming methylene bridge crosslinks between formaldehyde and amine/thiols in biomolecules; however, retina sections analyzed by IMS are typically fresh-frozen. To determine if clinically significant inferences could be reliably based on fixed tissue, we evaluated the effect of fixation on analyte detection, spatial localization, and introduction of artifactual signals. Hence, we assessed the molecular identity of lipids generated by matrix-assisted laser desorption ionization (MALDI-IMS) and liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) for fixed and fresh-frozen retina tissues in positive and negative ion modes. Based on MALDI-IMS analysis, more lipid signals were observed in fixed compared with fresh-frozen retina. More potassium adducts were observed in fresh-frozen tissues than fixed as the fixation process caused displacement of potassium adducts to protonated and sodiated species in ion positive ion mode. LC-MS/MS analysis revealed an overall decrease in lipid signals due to fixation that reduced glycerophospholipids and glycerolipids and conserved most sphingolipids and cholesteryl esters. The high quality and reproducible information from untargeted lipidomics analysis of fixed retina informs on all major lipid classes, similar to fresh-frozen retina, and serves as a steppingstone towards understanding of lipid alterations in retinal diseases.
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Affiliation(s)
- Ankita Kotnala
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - David M.G. Anderson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Nathan Heath Patterson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Lee S. Cantrell
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Jeffrey D. Messinger
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - Christine A. Curcio
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - Kevin L. Schey
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
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11
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Ogrinc N, Caux PD, Robin YM, Bouchaert E, Fatou B, Ziskind M, Focsa C, Bertin D, Tierny D, Takats Z, Salzet M, Fournier I. Direct Water-Assisted Laser Desorption/Ionization Mass Spectrometry Lipidomic Analysis and Classification of Formalin-Fixed Paraffin-Embedded Sarcoma Tissues without Dewaxing. Clin Chem 2021; 67:1513-1523. [PMID: 34586394 DOI: 10.1093/clinchem/hvab160] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Formalin-fixed paraffin-embedded (FFPE) tissue has been the gold standard for routine pathology for general and cancer postoperative diagnostics. Despite robust histopathology, immunohistochemistry, and molecular methods, accurate diagnosis remains difficult for certain cases. Overall, the entire process can be time consuming, labor intensive, and does not reach over 90% diagnostic sensitivity and specificity. There is a growing need in onco-pathology for adjunct novel rapid, accurate, reliable, diagnostically sensitive, and specific methods for high-throughput biomolecular identification. Lipids have long been considered only as building blocks of cell membranes or signaling molecules, but have recently been introduced as central players in cancer. Due to sample processing, which limits their detection, lipid analysis directly from unprocessed FFPE tissues has never been reported. METHODS We present a proof-of-concept with direct analysis of tissue-lipidomic signatures from FFPE tissues without dewaxing and minimal sample preparation using water-assisted laser desorption ionization mass spectrometry and deep-learning. RESULTS On a cohort of difficult canine and human sarcoma cases, classification for canine sarcoma subtyping was possible with 99.1% accuracy using "5-fold" and 98.5% using "leave-one-patient out," and 91.2% accuracy for human sarcoma using 5-fold and 73.8% using leave-one-patient out. The developed classification model enabled stratification of blind samples in <5 min and showed >95% probability for discriminating 2 human sarcoma blind samples. CONCLUSION It is possible to create a rapid diagnostic platform to screen clinical FFPE tissues with minimal sample preparation for molecular pathology.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Pierre-Damien Caux
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Yves-Marie Robin
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, Lille, France
| | - Emmanuel Bouchaert
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,OCR (Oncovet Clinical Research), Parc Eurasante Lille Metropole, Loos, France
| | - Benoit Fatou
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Michael Ziskind
- University of Lille, CNRS, UMR 8523, PhLAM-Physique des Lasers, Atomes et Molécules, Lille, France
| | - Cristian Focsa
- University of Lille, CNRS, UMR 8523, PhLAM-Physique des Lasers, Atomes et Molécules, Lille, France
| | - Delphine Bertin
- Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, Lille, France
| | - Dominique Tierny
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,OCR (Oncovet Clinical Research), Parc Eurasante Lille Metropole, Loos, France
| | - Zoltan Takats
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France (IUF), Paris, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France (IUF), Paris, France
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12
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Zhang J, Sans M, Garza KY, Eberlin LS. MASS SPECTROMETRY TECHNOLOGIES TO ADVANCE CARE FOR CANCER PATIENTS IN CLINICAL AND INTRAOPERATIVE USE. MASS SPECTROMETRY REVIEWS 2021; 40:692-720. [PMID: 33094861 DOI: 10.1002/mas.21664] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Developments in mass spectrometry technologies have driven a widespread interest and expanded their use in cancer-related research and clinical applications. In this review, we highlight the developments in mass spectrometry methods and instrumentation applied to direct tissue analysis that have been tailored at enhancing performance in clinical research as well as facilitating translation and implementation of mass spectrometry in clinical settings, with a focus on cancer-related studies. Notable studies demonstrating the capabilities of direct mass spectrometry analysis in biomarker discovery, cancer diagnosis and prognosis, tissue analysis during oncologic surgeries, and other clinically relevant problems that have the potential to substantially advance cancer patient care are discussed. Key challenges that need to be addressed before routine clinical implementation including regulatory efforts are also discussed. Overall, the studies highlighted in this review demonstrate the transformative potential of mass spectrometry technologies to advance clinical research and care for cancer patients. © 2020 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Jialing Zhang
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Marta Sans
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Kyana Y Garza
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Livia S Eberlin
- Department of Chemistry, University of Texas at Austin, Austin, TX
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13
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Ghezellou P, Heiles S, Kadesch P, Ghassempour A, Spengler B. Venom Gland Mass Spectrometry Imaging of Saw-Scaled Viper, Echis carinatus sochureki, at High Lateral Resolution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1105-1115. [PMID: 33725446 DOI: 10.1021/jasms.1c00042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The snake venom gland is the place for the synthesis, storage, and secretion of a complex mixture of proteins and peptides, i.e., the venom. The morphology of the gland has been revealed by classical histology and microscopic studies. However, knowledge about the gland's cellular secretory and functional processes is still incomplete and has so far been neglected by the omics disciplines. We used autofocusing atmospheric-pressure matrix-assisted laser desorption/ionization (AP-SMALDI) mass spectrometry imaging (MSI) to investigate endogenous biomolecular distributions in the venom glands of the saw-scaled viper, Echis carinatus sochureki, employing different sample preparation methods. Fresh-freezing and formalin-fixation were tested for the gland to obtain intact tissue sections. Subsequently, MSI was conducted with 12 μm pixel resolution for both types of preparations, and the lateral distributions of the metabolites were identified. Experiments revealed that lipids belonging to the classes of PC, SM, PE, PS, PA, and TG are present in the venom gland. PC (32:0) and SM (36:1) were found to be specifically located in the areas where cells are present. The snake venom metalloprotease inhibitor pEKW (m/z 444.2233) was identified in the venom by top-down LC-MS/MS and localized by MALDI-MSI in the gland across secretory epithelial cells. The peptide can inhibit the venom's enzymatic activity during long-term storage within the venom gland. With a high degree of spectral similarities, we concluded that formalin-fixed tissue, in addition to its high ability to preserve tissue morphology, can be considered as an alternative method to fresh-frozen tissue in the case of lipid and peptide MS imaging in venom gland tissues.
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Affiliation(s)
- Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, 35392 Giessen, Germany
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, 35392 Giessen, Germany
| | - Patrik Kadesch
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, 35392 Giessen, Germany
| | - Alireza Ghassempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, 1983969411 Tehran, Iran
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, 35392 Giessen, Germany
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14
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Mamun A, Islam A, Eto F, Sato T, Kahyo T, Setou M. Mass spectrometry-based phospholipid imaging: methods and findings. Expert Rev Proteomics 2021; 17:843-854. [PMID: 33504247 DOI: 10.1080/14789450.2020.1880897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Imaging is a technique used for direct visualization of the internal structure or distribution of biomolecules of a living system in a two-dimensional or three-dimensional fashion. Phospholipids are important structural components of biological membranes and have been reported to be associated with various human diseases. Therefore, the visualization of phospholipids is crucial to understand the underlying mechanism of cellular and molecular processes in normal and diseased conditions. Areas covered: Mass spectrometry imaging (MSI) has enabled the label-free imaging of individual phospholipids in biological tissues and cells. The commonly used MSI techniques include matrix-assisted laser desorption ionization-MSI (MALDI-MSI), desorption electrospray ionization-MSI (DESI-MSI), and secondary ion mass spectrometry (SIMS) imaging. This special report described those methods, summarized the findings, and discussed the future development for the imaging of phospholipids. Expert opinion: Phospholipids imaging in complex biological samples has been significantly benefited from the development of MSI methods. In MALDI-MSI, novel matrix that produces homogenous crystals exclusively with polar lipids is important for phospholipids imaging with greater efficiency and higher spatial resolution. DESI-MSI has the potential of live imaging of the biological surface while SIMS is expected to image at the subcellular level in the near future.
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Affiliation(s)
- Al Mamun
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine , Hamamatsu, Shizuoka, Japan
| | - Ariful Islam
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine , Hamamatsu, Shizuoka, Japan
| | - Fumihiro Eto
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine , Hamamatsu, Shizuoka, Japan
| | - Tomohito Sato
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine , Hamamatsu, Shizuoka, Japan
| | - Tomoaki Kahyo
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine , Hamamatsu, Shizuoka, Japan
| | - Mitsutoshi Setou
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine , Hamamatsu, Shizuoka, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine , Hamamatsu, Shizuoka, Japan.,Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center , Hamamatsu, Shizuoka, Japan
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15
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Zahraei A, Guo G, Perwick RD, Donaldson PJ, Demarais NJ, Grey AC. Mapping glucose metabolites in the normal bovine lens: Evaluation and optimisation of a matrix-assisted laser desorption/ionisation imaging mass spectrometry method. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4666. [PMID: 33089566 DOI: 10.1002/jms.4666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/02/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
The spatial resolution of microdissection-based analytical methods to detect ocular lens glucose uptake, transport and metabolism are poor, whereas the multiplexing capability of fluorescence microscopy-based approaches to simultaneously detect multiple glucose metabolites is limited in comparison with mass spectrometry-based methods. To better understand lens glucose transport and metabolism, a more highly spatially resolved technique that maintains the fragile ocular lens tissue is required. In this study, a sample preparation method for matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) analysis of ocular lens glucose uptake and metabolism has been evaluated and optimised. Matrix choice, tissue preparation and normalisation strategy were determined using negative ion mode MALDI-Fourier transform-ion cyclotron resonance MS of bovine lens tissue and validation performed using gas chromatography-MS. An internal standard was applied concurrently with N-(1-naphthyl)ethylenediamine dihydrochloride (NEDC) matrix to limit cracking of the fresh frozen lens tissue sections. MALDI IMS data were collected at a variety of spatial resolutions to detect both endogenous lens metabolites and stable isotopically labelled glucose introduced by ex vivo lens culture. Using this approach, initial steps in important metabolic processes that are linked to diabetic cataract formation were spatially mapped in the bovine lens. In the future, this method can be applied to study the dynamics of glucose uptake, transport and metabolic flux to aid in the study of diabetic lens cataract pathophysiology.
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Affiliation(s)
- Ali Zahraei
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - George Guo
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Rebecca D Perwick
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Paul J Donaldson
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Nicholas J Demarais
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Angus C Grey
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
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16
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Denti V, Piga I, Guarnerio S, Clerici F, Ivanova M, Chinello C, Paglia G, Magni F, Smith A. Antigen Retrieval and Its Effect on the MALDI-MSI of Lipids in Formalin-Fixed Paraffin-Embedded Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1619-1624. [PMID: 32678590 PMCID: PMC8009503 DOI: 10.1021/jasms.0c00208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue represents the primary source of clinical tissue and is routinely used in MALDI-MSI studies. However, it is not particularly suitable for lipidomics imaging given that many species are depleted during tissue processing. Irrespective, a number of solvent-resistant lipids remain, but their extraction may be hindered by the cross-link between proteins. Therefore, an antigen retrieval step could enable the extraction of a greater number of lipids and may provide information that is complementary to that which can be obtained from other biomolecules, such as proteins. In this short communication, we aim to address the effect of performing antigen retrieval prior to MALDI-MSI of lipids in FFPE tissue. As a result, an increased number of lipid signals could be detected and may have derived from lipid species that are known to be implicated in the lipid-protein cross-linking that is formed as a result of formalin fixation. Human renal cancer tissue was used as a proof of concept to determine whether using these detected lipid signals were also able to highlight the histopathological regions that were present. These preliminary findings may highlight the potential to enhance the clinical relevance of the lipidomic information obtained from FFPE tissue.
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Affiliation(s)
- Vanna Denti
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Isabella Piga
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Sonia Guarnerio
- Biomolecular
Sciences Research Centre, Sheffield-Hallam
University, City Campus, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Francesca Clerici
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Mariia Ivanova
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Clizia Chinello
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Giuseppe Paglia
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Fulvio Magni
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Andrew Smith
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
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17
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Strnad Š, PraŽienková V, Holubová M, Sýkora D, Cvačka J, Maletínská L, Železná B, Kuneš J, Vrkoslav V. Mass spectrometry imaging of free-floating brain sections detects pathological lipid distribution in a mouse model of Alzheimer's-like pathology. Analyst 2020; 145:4595-4605. [PMID: 32436545 DOI: 10.1039/d0an00592d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry imaging (MSI) is a modern analytical technique capable of monitoring the spatial distribution of compounds within target tissues. Collection and storage are important steps in sample preparation. The recommended and most widely used preservation procedure for MSI is freezing samples in isopentane and storing them at temperatures below -80 °C. On the other hand, the most common and general method for preserving biological samples in clinical practice is fixation in paraformaldehyde. Special types of samples prepared from these fixed tissues that are used for histology and immunohistochemistry are free-floating sections. It would be very beneficial if the latter procedure could also be applicable for the samples intended for subsequent MSI analysis. In the present work, we optimized and evaluated paraformaldehyde-fixed free-floating sections for the analysis of lipids in mouse brains and used the sections for the study of lipid changes in double transgenic APP/PS1 mice, a model of Alzheimer's-like pathology. Moreover, we examined the neuroprotective properties of palm11-PrRP31, an anorexigenic and glucose-lowering analog of prolactin-releasing peptide, and liraglutide, a type 2 diabetes drug. From the free-floating sections, we obtained lipid images without interference or delocalization, and we demonstrated that free-floating sections can be used for the MSI of lipids. In the APP/PS1 mice, we observed a changed distribution of various lipids compared to the controls. The most significant changes in lipids in the brains of APP/PS1 mice compared to wild-type controls were related to gangliosides (GM2 36:1, GM3 36:1) and phosphatidylinositols (PI 38:4, 36:4) in regions where the accumulation of senile plaques occurred. In APP/PS1 mice peripherally treated with palm11-PrRP31 or liraglutide for 2 months, we found that both peptides reduced the amount and space occupied by lipids, which were linked to the senile plaques. These results indicate that palm11-PrRP31 as well as liraglutide might be potentially useful in the treatment of neurodegenerative diseases.
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Affiliation(s)
- Štěpán Strnad
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10, Prague, Czech Republic.
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18
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Boughton BA, Thomas ORB, Demarais NJ, Trede D, Swearer SE, Grey AC. Detection of small molecule concentration gradients in ocular tissues and humours. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4460. [PMID: 31654531 DOI: 10.1002/jms.4460] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/02/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
The eye is an elegant organ consisting of a number of tissues and fluids with specialised functions that together allow it to effectively transmit and transduce light input to the brain for visual perception. One key determinant of this integrated function is the spatial relationship of ocular tissues. Biomolecular distributions within the main ocular tissues cornea, lens, and retina have been studied extensively in isolation, yet the potential for metabolic communication between ocular tissues via the ocular humours has been difficult to visualise. To address this limitation, the current study presents a method to map spatial distributions of metabolites and small molecules in whole eyes, including ocular humours. Using a tape-transfer system and freeze-drying, the spatial distribution of ocular small molecules was investigated in mouse, rat, fish (black bream), and rabbit eyes using negative ion mode MALDI imaging mass spectrometry. Full-scan imaging was used for discovery experiments, while MS/MS imaging for identification and localisation was also demonstrated. In all eyes, metabolites such as glutathione and phospholipids were localised in the main ocular tissues. In addition, in rodent eyes, major metabolites were distributed relatively uniformly in ocular humours. In contrast, both uniform and spatially defined ocular metabolite distributions were observed in the black bream eye. Tissue and ocular humour distributions were reproducible, as demonstrated by the three-dimensional analysis of a mouse eye, and able to be captured with high spatial resolution analysis. The presented method could be used to further investigate the role of inter-tissue metabolism in ocular health, and to support the development of therapeutics to treat major ocular diseases.
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Affiliation(s)
- Berin A Boughton
- Metabolomics Australia, University of Melbourne, Melbourne, Australia
| | - Oliver R B Thomas
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Nicholas J Demarais
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Stephen E Swearer
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Angus C Grey
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
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19
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Harris A, Roseborough A, Mor R, Yeung KKC, Whitehead SN. Ganglioside Detection from Formalin-Fixed Human Brain Tissue Utilizing MALDI Imaging Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:479-487. [PMID: 31971797 DOI: 10.1021/jasms.9b00110] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Matrix assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is used to perform mass spectrometric analysis directly on biological samples providing visual and anatomical spatial information on molecules within tissues. A current obscuration of MALDI-IMS is that it is largely performed on fresh frozen tissue, whereas clinical tissue samples stored long-term are fixed in formalin, and the fixation process is thought to cause signal suppression for lipid molecules. Studies have shown that fresh frozen tissue sections applied with an ammonium formate (AF) wash prior to matrix application in the MALDI-IMS procedure display an increase in observed signal intensity and sensitivity for lipid molecules detected within the brain while maintaining the spatial distribution of molecules throughout the tissue. In this work, we investigate the viability of formalin-fixed tissue imaging in a clinical setting by comparing MALDI data of fresh frozen and postfixed rat brain samples, along with postfixed human brain samples washed with AF to assess the capabilities of ganglioside analysis in MALDI imaging of formalin-fixed tissue. Results herein demonstrate that MALDI-IMS spectra for gangliosides, including GM1, were significantly enhanced in fresh frozen rat brain, formalin-fixed rat brain, and formalin-fixed human brain samples through the use of an AF wash. Improvements in MALDI-IMS image quality were demonstrated, and the spatial distribution of molecules was retained. Results indicate that this method will allow for the analysis of gangliosides from formalin-fixed clinical samples, which can open additional avenues for neurodegenerative disease research.
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Affiliation(s)
- Aaron Harris
- Department of Chemistry, University of Western Ontario, London, ON, Canada N6A 5B7
- Vulnerable Brain Laboratory, Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada N6A 5C1
| | - A Roseborough
- Vulnerable Brain Laboratory, Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada N6A 5C1
| | - Rahul Mor
- Vulnerable Brain Laboratory, Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada N6A 5C1
| | - Ken K-C Yeung
- Department of Chemistry, University of Western Ontario, London, ON, Canada N6A 5B7
- Department of Biochemistry, University of Western Ontario, London, ON, Canada N6A 5C1
| | - Shawn N Whitehead
- Vulnerable Brain Laboratory, Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, Canada N6A 5C1
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20
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Holzlechner M, Eugenin E, Prideaux B. Mass spectrometry imaging to detect lipid biomarkers and disease signatures in cancer. Cancer Rep (Hoboken) 2019; 2:e1229. [PMID: 32729258 PMCID: PMC7941519 DOI: 10.1002/cnr2.1229] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Current methods to identify, classify, and predict tumor behavior mostly rely on histology, immunohistochemistry, and molecular determinants. However, better predictive markers are required for tumor diagnosis and evaluation. Due, in part, to recent technological advancements, metabolomics and lipid biomarkers have become a promising area in cancer research. Therefore, there is a necessity for novel and complementary techniques to identify and visualize these molecular markers within tumors and surrounding tissue. RECENT FINDINGS Since its introduction, mass spectrometry imaging (MSI) has proven to be a powerful tool for mapping analytes in biological tissues. By adding the label-free specificity of mass spectrometry to the detailed spatial information of traditional histology, hundreds of lipids can be imaged simultaneously within a tumor. MSI provides highly detailed lipid maps for comparing intra-tumor, tumor margin, and healthy regions to identify biomarkers, patterns of disease, and potential therapeutic targets. In this manuscript, recent advancement in sample preparation and MSI technologies are discussed with special emphasis on cancer lipid research to identify tumor biomarkers. CONCLUSION MSI offers a unique approach for biomolecular characterization of tumor tissues and provides valuable complementary information to histology for lipid biomarker discovery and tumor classification in clinical and research cancer applications.
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Affiliation(s)
- Matthias Holzlechner
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| | - Eliseo Eugenin
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| | - Brendan Prideaux
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
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21
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Kune C, McCann A, Raphaël LR, Arias AA, Tiquet M, Van Kruining D, Martinez PM, Ongena M, Eppe G, Quinton L, Far J, De Pauw E. Rapid Visualization of Chemically Related Compounds Using Kendrick Mass Defect As a Filter in Mass Spectrometry Imaging. Anal Chem 2019; 91:13112-13118. [DOI: 10.1021/acs.analchem.9b03333] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Andréa McCann
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - La Rocca Raphaël
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Anthony Arguelles Arias
- Microbial Processes and Interactions, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liege, Gembloux, Belgium
| | - Mathieu Tiquet
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Daan Van Kruining
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Pilar Martinez Martinez
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Marc Ongena
- Microbial Processes and Interactions, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liege, Gembloux, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
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22
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Carter CL, Hankey KG, Booth C, Tudor GL, Parker GA, Jones JW, Farese AM, MacVittie TJ, Kane MA. Characterizing the Natural History of Acute Radiation Syndrome of the Gastrointestinal Tract: Combining High Mass and Spatial Resolution Using MALDI-FTICR-MSI. HEALTH PHYSICS 2019; 116:454-472. [PMID: 30681424 PMCID: PMC6384159 DOI: 10.1097/hp.0000000000000948] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The acute radiation syndrome of the gastrointestinal tract has been histologically characterized, but the molecular and functional mechanisms that lead to these cellular alterations remain enigmatic. Mass spectrometry imaging is the only technique that enables the simultaneous detection and cellular or regional localization of hundreds of biomolecules in a single experiment. This current study utilized matrix-assisted laser desorption/ionization mass spectrometry imaging for the molecular characterization of the first natural history study of gastrointestinal acute radiation syndrome in the nonhuman primate. Jejunum samples were collected at days 4, 8, 11, 15, and 21 following 12-Gy partial-body irradiation with 2.5% bone marrow sparing. Mass spectrometry imaging investigations identified alterations in lipid species that further understanding of the functional alterations that occur over time in the different cellular regions of the jejunum following exposure to high doses of irradiation. Alterations in phosphatidylinositol species informed on dysfunctional epithelial cell differentiation and maturation. Differences in glycosphingolipids of the villi epithelium that would influence the absorptive capacity and functional structure of the brush border membrane were detected. Dichotomous alterations in cardiolipins indicated altered structural and functional integrity of mitochondria. Phosphatidylglycerol species, known regulators of toll-like receptors, were detected and localized to regions in the lamina propria that contained distinct immune cell populations. These results provide molecular insight that can inform on injury mechanism in a nonhuman primate model of the acute radiation syndrome of the gastrointestinal tract. Findings may contribute to the identification of therapeutic targets and the development of new medical countermeasures.
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Affiliation(s)
- Claire L. Carter
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD USA
| | - Kim G. Hankey
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD USA
| | | | | | - George A. Parker
- Charles River Laboratories, Pathology Associates, Raleigh-Durham, North Carolina, USA
| | - Jace W. Jones
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD USA
| | - Ann M. Farese
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD USA
| | - Thomas J. MacVittie
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD USA
| | - Maureen A. Kane
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD USA
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23
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Luberto C, Haley JD, Del Poeta M. Imaging with mass spectrometry, the next frontier in sphingolipid research? A discussion on where we stand and the possibilities ahead. Chem Phys Lipids 2019; 219:1-14. [PMID: 30641043 DOI: 10.1016/j.chemphyslip.2019.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 12/17/2022]
Abstract
In the last ten years, mass spectrometry (MS) has become the favored analytical technique for sphingolipid (SPL) analysis and measurements. Indeed MS has the unique ability to both acquire sensitive and quantitative measurements and to resolve the molecular complexity characteristic of SPL molecules, both across the different SPL families and within the same SPL family. Currently, two complementary MS-based approaches are used for lipid research: analysis of lipid extracts, mainly by infusion electrospray ionization (ESI), and mass spectrometry imaging (MSI) from a sample surface (i.e. intact tissue sections, cells, model membranes, thin layer chromatography plates) (Fig. 1). The first allows for sensitive and quantitative information about total lipid molecular species from a given specimen from which lipids have been extracted and chromatographically separated prior to the analysis; the second, albeit generally less quantitative and less specific in the identification of molecular species due to the complexity of the sample, allows for spatial information of lipid molecules from biological specimens. In the field of SPL research, MS analysis of lipid extracts from biological samples has been commonly utilized to implicate the role of these lipids in specific biological functions. On the other hand, the utilization of MSI in SPL research represents a more recent development that has started to provide interesting descriptive observations regarding the distribution of specific classes of SPLs within tissues. Thus, it is the aim of this review to discuss how MSI technology has been employed to extend the study of SPL metabolism and the type of information that has been obtained from model membranes, single cells and tissues. We envision this discussion as a complementary compendium to the excellent technical reviews recently published about the specifics of MSI technologies, including their application to SPL analysis (Fuchs et al., 2010; Berry et al., 2011; Ellis et al., 2013; Eberlin et al., 2011; Kraft and Klitzing, 2014).
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Affiliation(s)
- Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, United States.
| | - John D Haley
- Department of Pathology, Stony Brook University, Stony Brook, NY, United States
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, United States; Division of Infectious Diseases, Stony Brook University, Stony Brook, NY, United States; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States; Veterans Administrations Medical Center, Northport, NY, United States
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24
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Saudemont P, Quanico J, Robin YM, Baud A, Balog J, Fatou B, Tierny D, Pascal Q, Minier K, Pottier M, Focsa C, Ziskind M, Takats Z, Salzet M, Fournier I. Real-Time Molecular Diagnosis of Tumors Using Water-Assisted Laser Desorption/Ionization Mass Spectrometry Technology. Cancer Cell 2018; 34:840-851.e4. [PMID: 30344004 DOI: 10.1016/j.ccell.2018.09.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/08/2018] [Accepted: 09/21/2018] [Indexed: 11/20/2022]
Abstract
Histopathological diagnosis of biopsy samples and margin assessment of surgical specimens are challenging aspects in sarcoma. Using dog patient tissues, we assessed the performance of a recently developed technology for fast ex vivo molecular lipid-based diagnosis of sarcomas. The instrument is based on mass spectrometry (MS) molecular analysis through a laser microprobe operating under ambient conditions using excitation of endogenous water molecules. Classification models based on cancer/normal/necrotic, tumor grade, and subtypes showed a minimum of 97.63% correct classification. Specific markers of normal, cancer, and necrotic regions were identified by tandem MS and validated by MS imaging. Real-time detection capabilities were demonstrated by ex vivo analysis with direct interrogation of classification models.
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Affiliation(s)
- Philippe Saudemont
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; European Associated Laboratory Inserm-Imperial College of London, LANCET, 59655 Villeneuve d'Ascq Cedex, France; SATT-Nord, Immeuble Central Gare, 4(ème) étage, 25 Avenue Charles St Venant, 59800 Lille, France
| | - Jusal Quanico
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; European Associated Laboratory Inserm-Imperial College of London, LANCET, 59655 Villeneuve d'Ascq Cedex, France; Université de Lille, CNRS UMR 8523, Physique des Lasers Atomes et Molécules (PhLAM), 59655 Villeneuve d'Ascq Cedex, France
| | - Yves-Marie Robin
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, 3 Rue Frédéric Combemale, 59020 Lille Cedex, France
| | - Anna Baud
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; European Associated Laboratory Inserm-Imperial College of London, LANCET, 59655 Villeneuve d'Ascq Cedex, France
| | - Julia Balog
- European Associated Laboratory Inserm-Imperial College of London, LANCET, 59655 Villeneuve d'Ascq Cedex, France; Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, Praed Street, London, NW1 1SQ, UK
| | - Benoit Fatou
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; European Associated Laboratory Inserm-Imperial College of London, LANCET, 59655 Villeneuve d'Ascq Cedex, France
| | - Dominique Tierny
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Quentin Pascal
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Kevin Minier
- Oncovet, Avenue Paul Langevin, 59650 Villeneuve d'Ascq, France
| | - Mélissa Pottier
- Oncovet, Avenue Paul Langevin, 59650 Villeneuve d'Ascq, France
| | - Cristian Focsa
- Université de Lille, CNRS UMR 8523, Physique des Lasers Atomes et Molécules (PhLAM), 59655 Villeneuve d'Ascq Cedex, France
| | - Michael Ziskind
- Université de Lille, CNRS UMR 8523, Physique des Lasers Atomes et Molécules (PhLAM), 59655 Villeneuve d'Ascq Cedex, France
| | - Zoltan Takats
- European Associated Laboratory Inserm-Imperial College of London, LANCET, 59655 Villeneuve d'Ascq Cedex, France; Department of Surgery and Cancer, Imperial College London, St. Mary's Hospital, Praed Street, London, NW1 1SQ, UK.
| | - Michel Salzet
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; European Associated Laboratory Inserm-Imperial College of London, LANCET, 59655 Villeneuve d'Ascq Cedex, France.
| | - Isabelle Fournier
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Faculté des Sciences, Campus Cité Scientifique, Bât SN3, 1er étage, 59655 Villeneuve d'Ascq Cedex, France; European Associated Laboratory Inserm-Imperial College of London, LANCET, 59655 Villeneuve d'Ascq Cedex, France.
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25
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Dexter A, Race AM, Steven RT, Barnes JR, Hulme H, Goodwin RJA, Styles IB, Bunch J. Two-Phase and Graph-Based Clustering Methods for Accurate and Efficient Segmentation of Large Mass Spectrometry Images. Anal Chem 2017; 89:11293-11300. [DOI: 10.1021/acs.analchem.7b01758] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alex Dexter
- PSIBS
Doctoral Training Centre, University of Birmingham Edgbaston, Birmingham B15 2TT, United Kingdom
- National Physical
Laboratory, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Alan M. Race
- National Physical
Laboratory, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Rory T. Steven
- National Physical
Laboratory, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Jennifer R. Barnes
- AstraZeneca, Drug Safety and Metabolism, Cambridge CB4 0WG, United Kingdom
| | - Heather Hulme
- AstraZeneca, Drug Safety and Metabolism, Cambridge CB4 0WG, United Kingdom
- University
of Glasgow, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | | | - Iain B. Styles
- School
of Computer Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Josephine Bunch
- National Physical
Laboratory, Teddington, Middlesex TW11 0LW, United Kingdom
- School
of
Pharmacy, University of Nottingham, Nottingham, Nottinghamshire NG7 2RD, United Kingdom
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26
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Carter CL, Jones JW, Farese AM, MacVittie TJ, Kane MA. Lipidomic dysregulation within the lung parenchyma following whole-thorax lung irradiation: Markers of injury, inflammation and fibrosis detected by MALDI-MSI. Sci Rep 2017; 7:10343. [PMID: 28871103 PMCID: PMC5583385 DOI: 10.1038/s41598-017-10396-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/08/2017] [Indexed: 12/23/2022] Open
Abstract
Radiation-induced lung injury (RILI) is a delayed effect of acute radiation exposure that can limit curative cancer treatment therapies and cause lethality following high-dose whole-thorax lung irradiation (WTLI). To date, the exact mechanisms of injury development following insult remain ill-defined and there are no FDA approved pharmaceutical agents or medical countermeasures. Traditionally, RILI development is considered as three phases, the clinically latent period, the intermediate acute pneumonitis phase and the later fibrotic stage. Utilizing matrix-assisted laser desorption ionization mass spectrometry imaging, we identified a number of lipids that were reflective of disease state or injury. Lipids play central roles in metabolism and cell signaling, and thus reflect the phenotype of the tissue environment, making these molecules pivotal biomarkers in many disease processes. We detected decreases in specific surfactant lipids irrespective of the different pathologies that presented within each sample at 180 days post whole-thorax lung irradiation. We also detected regional increases in ether-linked phospholipids that are the precursors of PAF, and global decreases in lipids that were reflective of severe fibrosis. Taken together our results provide panels of lipids that can differentiate between naïve and irradiated samples, as well as providing potential markers of inflammation and fibrosis.
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Affiliation(s)
- Claire L Carter
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 21201, Baltimore, MD, USA
| | - Jace W Jones
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 21201, Baltimore, MD, USA
| | - Ann M Farese
- University of Maryland, School of Medicine, Department of Radiation Oncology, 21201, Baltimore, MD, USA
| | - Thomas J MacVittie
- University of Maryland, School of Medicine, Department of Radiation Oncology, 21201, Baltimore, MD, USA
| | - Maureen A Kane
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 21201, Baltimore, MD, USA.
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27
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Gussenhoven R, Ophelders DRMG, Kemp MW, Payne MS, Spiller OB, Beeton ML, Stock SJ, Cillero-Pastor B, Barré FPY, Heeren RMA, Kessels L, Stevens B, Rutten BP, Kallapur SG, Jobe AH, Kramer BW, Wolfs TGAM. The Paradoxical Effects of Chronic Intra-Amniotic Ureaplasma parvum Exposure on Ovine Fetal Brain Development. Dev Neurosci 2017; 39:472-486. [PMID: 28848098 DOI: 10.1159/000479021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/24/2017] [Indexed: 01/23/2023] Open
Abstract
Chorioamnionitis is associated with adverse neurodevelopmental outcomes in preterm infants. Ureaplasma spp. are the microorganisms most frequently isolated from the amniotic fluid of women diagnosed with chorioamnionitis. However, controversy remains concerning the role of Ureaplasma spp. in the pathogenesis of neonatal brain injury. We hypothesize that reexposure to an inflammatory trigger during the perinatal period might be responsible for the variation in brain outcomes of preterms following Ureaplasma-driven chorioamnionitis. To investigate these clinical scenarios, we performed a detailed multimodal study in which ovine neurodevelopmental outcomes were assessed following chronic intra-amniotic Ureaplasma parvum (UP) infection either alone or combined with subsequent lipopolysaccharide (LPS) exposure. We show that chronic intra-amniotic UP exposure during the second trimester provoked a decrease in astrocytes, increased oligodendrocyte numbers, and elevated 5-methylcytosine levels. In contrast, short-term LPS exposure before preterm birth induced increased microglial activation, myelin loss, elevation of 5-hydroxymethylcytosine levels, and lipid profile changes. These LPS-induced changes were prevented by chronic preexposure to UP (preconditioning). These data indicate that chronic UP exposure has dual effects on preterm brain development in utero. On the one hand, prolonged UP exposure causes detrimental cerebral changes that may predispose to adverse postnatal clinical outcomes. On the other, chronic intra-amniotic UP exposure preconditions the brain against a second inflammatory hit. This study demonstrates that microbial interactions and the timing and duration of the inflammatory insults determine the effects on the fetal brain. Therefore, this study helps to understand the complex and diverse postnatal neurological outcomes following UP driven chorioamnionitis.
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Affiliation(s)
- Ruth Gussenhoven
- Department of Pediatrics, Maastricht University Medical Center, Maastricht, The Netherlands
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28
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Park KM, Hyeon T, Kim MS, Moon JH. In Situ
Quantification and Profiling of Phosphatidylcholine in Mouse Brain Tissue by Matrix-assisted Laser Desorption Ionization with a Liquid Matrix. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Kyung Man Park
- Department of Chemistry; Seoul National University; Seoul 151-747 Korea
| | - Taeghwan Hyeon
- Center for Nanoparticle Research; Institute for Basic Science (IBS); Seoul 151-742 Korea
| | - Myung Soo Kim
- Center for Nanoparticle Research; Institute for Basic Science (IBS); Seoul 151-742 Korea
| | - Jeong Hee Moon
- Disease Target Structure Research Center; KRIBB; Daejeon 305-806 Korea
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29
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Proctor A, Sims CE, Allbritton NL. Chemical fixation to arrest phospholipid signaling for chemical cytometry. J Chromatogr A 2017; 1523:97-106. [PMID: 28528682 DOI: 10.1016/j.chroma.2017.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/28/2017] [Accepted: 05/07/2017] [Indexed: 12/18/2022]
Abstract
Chemical cytometry is a powerful tool for measuring biological processes such as enzymatic signaling at the single cell level. Among these technologies, single-cell capillary zone electrophoresis (CZE) has emerged as a powerful tool to assay a wide range of cellular metabolites. However, analysis of dynamic processes within cells remains challenging as signaling pathways are rapidly altered in response to changes in the cellular environment, including cell manipulation and storage. To address these limitations, we describe a method for chemical fixation of cells to stop the cellular reactions to preserve the integrity of key signaling molecules or reporters within the cell and to enable the cell to act as a storage reservoir for the reporter and its metabolites prior to assay by single-cell CZE. Fluorescent phosphatidylinositol 4,5-bisphosphate reporters were loaded into cells and the cells were chemically fixed and stored prior to analysis. The reporter and its metabolites were electrophoretically separated by single-cell CZE. Chemical fixation parameters such as fixative, fixation time, storage solution, storage duration, and extraction solution were optimized. When cells were loaded with a fluorescent C6- or C16-PIP2 followed by glutaraldehyde fixation and immediate analysis, 24±2% and 139±12% of the lipid was recoverable, respectively, when compared to an unfixed control. Storage of the cells for 24h yielded recoverable lipid of 61±3% (C6-PIP2) and 55±5% (C16-PIP2) when compared to cells analyzed immediately after fixation. The metabolites observed with and without fixation were identical. Measurement of phospholipase C activity in single leukemic cells in response to an agonist demonstrated the capability of chemical fixation coupled to single-cell CZE to yield an accurate snapshot of cellular reactions with the probe. This methodology enables cell assay with the reporter to be separated in space and time from reporter metabolite quantification while preserving assay integrity.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States.
| | - Christopher E Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States.
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States; Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, United States and North Carolina State University, Raleigh, NC 27695, United States.
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30
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FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry. Nat Methods 2016; 14:57-60. [PMID: 27842059 DOI: 10.1038/nmeth.4072] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023]
Abstract
High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM). We introduce a metabolite-signal match score and a target-decoy FDR estimate for spatial metabolomics.
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31
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Yoshimura Y, Goto-Inoue N, Moriyama T, Zaima N. Significant advancement of mass spectrometry imaging for food chemistry. Food Chem 2016; 210:200-11. [DOI: 10.1016/j.foodchem.2016.04.096] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/17/2016] [Accepted: 04/20/2016] [Indexed: 11/30/2022]
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32
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Schwamborn K, Kriegsmann M, Weichert W. MALDI imaging mass spectrometry - From bench to bedside. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:776-783. [PMID: 27810414 DOI: 10.1016/j.bbapap.2016.10.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/24/2016] [Accepted: 10/28/2016] [Indexed: 10/20/2022]
Abstract
Today, pathologists face many challenges in defining the precise morphomolecular diagnosis and in guiding clinicians to the optimal patients' treatment. To achieve this goal, increasingly, classical histomorphological methods have to be supplemented by high throughput molecular assays. Since MALDI imaging mass spectrometry (IMS) enables the assessment of spatial molecular arrangements in tissue sections, it goes far beyond microscopy in providing hundreds of different molecular images from a single scan without the need of target-specific reagents. Thus, this technology has the potential to uncover new markers for diagnostic purposes or markers that correlate with disease severity as well as prognosis and therapeutic response. Additionally, in the future MALDI IMS based classifiers measured with this technology in real time in the diagnostic setting might be applicable in the routine diagnostic setting. In this review, recently published studies that show the usefulness, advantages, and applicability of MALDI IMS in different fields of pathology (diagnosis, prognosis and treatment response) are highlighted. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Kristina Schwamborn
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany.
| | - Mark Kriegsmann
- University of Heidelberg, Department of Pathology, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany
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33
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Race AM, Palmer AD, Dexter A, Steven RT, Styles IB, Bunch J. SpectralAnalysis: Software for the Masses. Anal Chem 2016; 88:9451-9458. [DOI: 10.1021/acs.analchem.6b01643] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Alan M. Race
- National
Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
- PSIBS
Doctoral Training Centre, School of Chemistry, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Andrew D. Palmer
- PSIBS
Doctoral Training Centre, School of Chemistry, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Alex Dexter
- National
Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
- PSIBS
Doctoral Training Centre, School of Chemistry, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Rory T. Steven
- National
Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
| | - Iain B. Styles
- PSIBS
Doctoral Training Centre, School of Chemistry, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School
of Computer Science, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Josephine Bunch
- National
Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
- School
of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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34
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Mohammadi AS, Phan NTN, Fletcher JS, Ewing AG. Intact lipid imaging of mouse brain samples: MALDI, nanoparticle-laser desorption ionization, and 40 keV argon cluster secondary ion mass spectrometry. Anal Bioanal Chem 2016; 408:6857-68. [PMID: 27549796 PMCID: PMC5012256 DOI: 10.1007/s00216-016-9812-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/07/2016] [Accepted: 07/18/2016] [Indexed: 01/23/2023]
Abstract
We have investigated the capability of nanoparticle-assisted laser desorption ionization mass spectrometry (NP-LDI MS), matrix-assisted laser desorption ionization (MALDI) MS, and gas cluster ion beam secondary ion mass spectrometry (GCIB SIMS) to provide maximum information available in lipid analysis and imaging of mouse brain tissue. The use of Au nanoparticles deposited as a matrix for NP-LDI MS is compared to MALDI and SIMS analysis of mouse brain tissue and allows selective detection and imaging of groups of lipid molecular ion species localizing in the white matter differently from those observed using conventional MALDI with improved imaging potential. We demonstrate that high-energy (40 keV) GCIB SIMS can act as a semi-soft ionization method to extend the useful mass range of SIMS imaging to analyze and image intact lipids in biological samples, closing the gap between conventional SIMS and MALDI techniques. The GCIB SIMS allowed the detection of more intact lipid compounds in the mouse brain compared to MALDI with regular organic matrices. The 40 keV GCIB SIMS also produced peaks observed in the NP-LDI analysis, and these peaks were strongly enhanced in intensity by exposure of the sample to trifluororacetic acid (TFA) vapor prior to analysis. These MS techniques for imaging of different types of lipids create a potential overlap and cross point that can enhance the information for imaging lipids in biological tissue sections. Schematic of mass spectral imaging of a mouse brain tissue using GCIB-SIMS and MALDI techniques ![]()
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Affiliation(s)
- Amir Saeid Mohammadi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.,National Center Imaging Mass Spectrometry, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Nhu T N Phan
- National Center Imaging Mass Spectrometry, Kemivägen 10, 41296, Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296, Gothenburg, Sweden
| | - John S Fletcher
- National Center Imaging Mass Spectrometry, Kemivägen 10, 41296, Gothenburg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Andrew G Ewing
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden. .,National Center Imaging Mass Spectrometry, Kemivägen 10, 41296, Gothenburg, Sweden. .,Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296, Gothenburg, Sweden.
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35
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Pietrowska M, Gawin M, Polańska J, Widłak P. Tissue fixed with formalin and processed without paraffin embedding is suitable for imaging of both peptides and lipids by MALDI-IMS. Proteomics 2016; 16:1670-7. [DOI: 10.1002/pmic.201500424] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Monika Pietrowska
- Center for Translational Research and Molecular Biology of Cancer; Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch; Gliwice Poland
| | - Marta Gawin
- Center for Translational Research and Molecular Biology of Cancer; Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch; Gliwice Poland
- Department of Analytical Chemistry, Faculty of Chemistry; Jagiellonian University; Kraków Poland
| | - Joanna Polańska
- Faculty of Automatic Control, Electronics and Computer Science; Silesian University of Technology; Gliwice Poland
| | - Piotr Widłak
- Center for Translational Research and Molecular Biology of Cancer; Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch; Gliwice Poland
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36
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Carter CL, Jones JW, Farese AM, MacVittie TJ, Kane MA. Inflation-Fixation Method for Lipidomic Mapping of Lung Biopsies by Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging. Anal Chem 2016; 88:4788-94. [PMID: 27028398 DOI: 10.1021/acs.analchem.6b00165] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chronic respiratory diseases are among the leading causes of deaths worldwide and major contributors of morbidity and global disease burden. To appropriately investigate lung disease, the respiratory airways must be fixed in their physiological orientation and should be inflated prior to investigations. We present an inflation-fixation method that enables lipidomic investigations of whole lung samples and resected biopsy specimens by matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). Formalin-inflation enables sample preparation to parallel standard clinical and surgical procedures, in addition to greatly reducing the complexity of analysis, by decreasing the number of analytes in the MALDI plume and reducing adduct formation in the resulting mass spectra. The reduced complexity increased sensitivity and enabled high-resolution imaging acquisitions without any loss in analyte detection at 10 and 20 μm scans. We present a detailed study of over 100 lipid ions detected in positive and negative ion modes covering the conducting and respiratory airways and parts of the peripheral nervous tissue running through the lungs. By defining the resolution required for clear definition of the alveolar space and thus the respiratory airways we have provided a guideline for MSI investigations of respiratory diseases involving the airways, including the interstitium. This study has provided a detailed map of lipid species and their localization within larger mammalian lung samples, for the first time, thus categorizing the lipidome for future MALDI-MSI studies of pulmonary diseases.
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Affiliation(s)
- Claire L Carter
- University of Maryland , School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, Maryland 21201, United States
| | - Jace W Jones
- University of Maryland , School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, Maryland 21201, United States
| | - Ann M Farese
- University of Maryland , School of Medicine, Department of Radiation Oncology, 655 West Baltimore Street, Baltimore, Maryland 21201, United States
| | - Thomas J MacVittie
- University of Maryland , School of Medicine, Department of Radiation Oncology, 655 West Baltimore Street, Baltimore, Maryland 21201, United States
| | - Maureen A Kane
- University of Maryland , School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, Maryland 21201, United States
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37
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Hong JH, Kang JW, Kim DK, Baik SH, Kim KH, Shanta SR, Jung JH, Mook-Jung I, Kim KP. Global changes of phospholipids identified by MALDI imaging mass spectrometry in a mouse model of Alzheimer's disease. J Lipid Res 2015; 57:36-45. [PMID: 26538545 DOI: 10.1194/jlr.m057869] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia; however, at the present time there is no disease-modifying drug for AD. There is increasing evidence supporting the role of lipid changes in the process of normal cognitive aging and in the etiology of age-related neurodegenerative diseases. AD is characterized by the presence of intraneuronal protein clusters and extracellular aggregates of β-amyloid (Aβ). Disrupted Aβ kinetics may activate intracellular signaling pathways, including tau hyperphosphorylation and proinflammatory pathways. We analyzed and visualized the lipid profiles of mouse brains using MALDI-TOF MS. Direct tissue analysis by MALDI-TOF imaging MS (IMS) can determine the relative abundance and spatial distribution of specific lipids in different tissues. We used 5XFAD mice that almost exclusively generate and rapidly accumulate massive cerebral levels of Aβ-42 (1). Our data showed changes in lipid distribution in the mouse frontal cortex, hippocampus, and subiculum, where Aβ plaques are first generated in AD. Our results suggest that MALDI-IMS is a powerful tool for analyzing the distribution of various phospholipids and that this application might provide novel insight into the prediction of disease.
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Affiliation(s)
- Ji Hye Hong
- Department of Applied Chemistry and Institute of Natural Sciences, College of Applied Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Jeong Won Kang
- Department of Applied Chemistry and Institute of Natural Sciences, College of Applied Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Dong Kyu Kim
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Hoon Baik
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Kyung Ho Kim
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Selina Rahman Shanta
- Department of Applied Chemistry and Institute of Natural Sciences, College of Applied Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Jae Hun Jung
- Department of Applied Chemistry and Institute of Natural Sciences, College of Applied Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry and Institute of Natural Sciences, College of Applied Sciences, Kyung Hee University, Yongin, Republic of Korea
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38
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Carter CL, Jones JW, Barrow K, Kieta K, Taylor-Howell C, Kearney S, Smith CP, Gibbs A, Farese AM, MacVittie TJ, Kane MA. A MALDI-MSI Approach to the Characterization of Radiation-Induced Lung Injury and Medical Countermeasure Development. HEALTH PHYSICS 2015; 109:466-78. [PMID: 26425906 PMCID: PMC4745118 DOI: 10.1097/hp.0000000000000353] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Radiation-induced lung injury is highly complex and characterized by multiple pathologies, which occur over time and sporadically throughout the lung. This complexity makes biomarker investigations and medical countermeasure screenings challenging. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has the ability to resolve differences spatially in molecular profiles within the lung following radiation exposure and can aid in biomarker identification and pharmaceutical efficacy investigations. MALDI-MSI was applied to the investigation of a whole-thorax lung irradiation model in non-human primates (NHP) for lipidomic analysis and medical countermeasure distribution.
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Affiliation(s)
- Claire L. Carter
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences
| | - Jace W. Jones
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences
| | - Kory Barrow
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Kaitlyn Kieta
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Cheryl Taylor-Howell
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Sean Kearney
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Cassandra P. Smith
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Allison Gibbs
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Ann M. Farese
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Thomas J. MacVittie
- University of Maryland, School of Medicine, Department of Radiation Oncology, Baltimore, MD 21201
| | - Maureen A. Kane
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences
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39
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Canela N, Herrero P, Mariné S, Nadal P, Ras MR, Rodríguez MÁ, Arola L. Analytical methods in sphingolipidomics: Quantitative and profiling approaches in food analysis. J Chromatogr A 2015; 1428:16-38. [PMID: 26275862 DOI: 10.1016/j.chroma.2015.07.110] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/27/2015] [Accepted: 07/31/2015] [Indexed: 02/07/2023]
Abstract
In recent years, sphingolipidomics has emerged as an interesting omic science that encompasses the study of the full sphingolipidome characterization, content, structure and activity in cells, tissues or organisms. Like other omics, it has the potential to impact biomarker discovery, drug development and systems biology knowledge. Concretely, dietary food sphingolipids have gained considerable importance due to their extensively reported bioactivity. Because of the complexity of this lipid family and their diversity among foods, powerful analytical methodologies are needed for their study. The analytical tools developed in the past have been improved with the enormous advances made in recent years in mass spectrometry (MS) and chromatography, which allow the convenient and sensitive identification and quantitation of sphingolipid classes and form the basis of current sphingolipidomics methodologies. In addition, novel hyphenated nuclear magnetic resonance (NMR) strategies, new ionization strategies, and MS imaging are outlined as promising technologies to shape the future of sphingolipid analyses. This review traces the analytical methods of sphingolipidomics in food analysis concerning sample extraction, chromatographic separation, the identification and quantification of sphingolipids by MS and their structural elucidation by NMR.
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Affiliation(s)
- Núria Canela
- Centre for Omic Sciences, Universitat Rovira i Virgili (COS-URV), Spain
| | - Pol Herrero
- Centre for Omic Sciences, Universitat Rovira i Virgili (COS-URV), Spain
| | - Sílvia Mariné
- Centre for Omic Sciences, Universitat Rovira i Virgili (COS-URV), Spain
| | - Pedro Nadal
- Centre for Omic Sciences, Universitat Rovira i Virgili (COS-URV), Spain
| | - Maria Rosa Ras
- Centre for Omic Sciences, Universitat Rovira i Virgili (COS-URV), Spain
| | | | - Lluís Arola
- Centre for Omic Sciences, Universitat Rovira i Virgili (COS-URV), Spain.
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40
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Yalcin EB, de la Monte SM. Review of matrix-assisted laser desorption ionization-imaging mass spectrometry for lipid biochemical histopathology. J Histochem Cytochem 2015. [PMID: 26209083 DOI: 10.1369/0022155415596202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Matrix-Assisted Laser Desorption Ionization-Imaging Mass Spectrometry (MALDI-IMS) is a rapidly evolving method used for the in situ visualization and localization of molecules such as drugs, lipids, peptides, and proteins in tissue sections. Therefore, molecules such as lipids, for which antibodies and other convenient detection reagents do not exist, can be detected, quantified, and correlated with histopathology and disease mechanisms. Furthermore, MALDI-IMS has the potential to enhance our understanding of disease pathogenesis through the use of "biochemical histopathology". Herein, we review the underlying concepts, basic methods, and practical applications of MALDI-IMS, including post-processing steps such as data analysis and identification of molecules. The potential utility of MALDI-IMS as a companion diagnostic aid for lipid-related pathological states is discussed.
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Affiliation(s)
- Emine B Yalcin
- Liver Research Center, Division of Gastroenterology and Department of Medicine (EBY, SMD)
| | - Suzanne M de la Monte
- Liver Research Center, Division of Gastroenterology and Department of Medicine (EBY, SMD),Departments of Neurology, Neurosurgery, and Pathology (SMD),Rhode Island Hospital and the Alpert Medical School of Brown University, Providence, RI (EBY, SMD)
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41
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Phan NTN, Fletcher JS, Ewing AG. Lipid structural effects of oral administration of methylphenidate in Drosophila brain by secondary ion mass spectrometry imaging. Anal Chem 2015; 87:4063-71. [PMID: 25856152 DOI: 10.1021/acs.analchem.5b00555] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We use time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging to investigate the effects of orally administrated methylphenidate on lipids in the brain of Drosophila melanogaster (fruit fly), a major invertebrate model system in biological study and neuroscience. TOF-SIMS imaging was carried out using a recently designed high energy 40 keV Ar4000(+) gas cluster ion gun which demonstrated improved sensitivity for intact lipids in the fly brain compared to the 40 keV C60(+) primary ion gun. In addition, correlation of TOF-SIMS and SEM imaging on the same fly brain showed that there is specific localization that is related to biological functions of various biomolecules. Different lipids distribute in different parts of the brain, central brain, optical lobes, and proboscis, depending on the length of the carbon chain and saturation level of fatty acid (FA) branches. Furthermore, data analysis using image principal components analysis (PCA) showed that methylphenidate dramatically affected both the distribution and abundance of lipids and their derivatives, particularly fatty acids, diacylglycerides, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol in the fly brains. Our approach using TOF-SIMS imaging successfully visualizes the effects of methylphenidate on the chemical structure of the fly brain.
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Affiliation(s)
- Nhu T N Phan
- †Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.,‡National Center Imaging Mass Spectrometry, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - John S Fletcher
- †Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.,‡National Center Imaging Mass Spectrometry, Kemivägen 10, SE-412 96 Gothenburg, Sweden.,§Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Andrew G Ewing
- †Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden.,‡National Center Imaging Mass Spectrometry, Kemivägen 10, SE-412 96 Gothenburg, Sweden.,§Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden
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42
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Wang C, Wang M, Han X. Applications of mass spectrometry for cellular lipid analysis. MOLECULAR BIOSYSTEMS 2015; 11:698-713. [PMID: 25598407 PMCID: PMC4376555 DOI: 10.1039/c4mb00586d] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mass spectrometric analysis of cellular lipids is an enabling technology for lipidomics, which is a rapidly-developing research field. In this review, we briefly discuss the principles, advantages, and possible limitations of electrospray ionization (ESI) and matrix assisted laser desorption/ionization (MALDI) mass spectrometry-based methodologies for the analysis of lipid species. The applications of these methodologies to lipidomic research are also summarized.
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Affiliation(s)
- Chunyan Wang
- Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, Florida 32827, USA.
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43
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Nilsson A, Goodwin RJA, Shariatgorji M, Vallianatou T, Webborn PJH, Andrén PE. Mass Spectrometry Imaging in Drug Development. Anal Chem 2015; 87:1437-55. [DOI: 10.1021/ac504734s] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anna Nilsson
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Richard J. A. Goodwin
- Drug Safety & Metabolism, Innovative Medicines, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 OWG, U.K
| | - Mohammadreza Shariatgorji
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Theodosia Vallianatou
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
| | - Peter J. H. Webborn
- Drug Safety & Metabolism, Innovative Medicines, AstraZeneca, Darwin Building 310, Cambridge Science Park, Milton Road, Cambridge, Cambridgeshire CB4 OWG, U.K
| | - Per E. Andrén
- Biomolecular
Imaging and Proteomics, National Center for Mass Spectrometry Imaging,
Department of Pharmaceutical Biosciences, Uppsala University, P.O. Box 591 BMC, 75124 Uppsala, Sweden
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44
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Abstract
Enriched by a decade of remarkable developments, matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has witnessed a phenomenal expansion. Initially introduced for the mapping of peptides and intact proteins from mammalian tissue sections, MALDI IMS applications now extend to a wide range of molecules including peptides, lipids, metabolites and xenobiotics. Technology and methodology are quickly evolving to push the limits of the technique forward. Within a short period of time, numerous protocols and concepts have been developed and introduced in tissue section preparation, nonexhaustively including in situ tissue chemistries and solvent-free matrix depositions. Considering the past progress and current capabilities, this Review aims to cover the different aspects and challenges of tissue section preparation for MALDI IMS.
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45
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Jadoul L, Longuespée R, Noël A, De Pauw E. A spiked tissue-based approach for quantification of phosphatidylcholines in brain section by MALDI mass spectrometry imaging. Anal Bioanal Chem 2014; 407:2095-106. [PMID: 25326885 DOI: 10.1007/s00216-014-8232-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 09/28/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
Abstract
In the last few years, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has been successfully used to study the distribution of lipids within tissue sections. However, few efforts have been made to acquire reliable quantitative data regarding the localized concentrations of these molecules. Here we propose an approach based on brain homogenates for the quantification of phosphatidylcholines (PCs) in brain section by MALDI MSI. Homogenates were spiked with a range of PC(16:0 d31/18:1) concentrations. Sections from homogenates and intact brain were simultaneously prepared before being analyzed by MALDI MSI using a Fourier transform ion cyclotron resonance (FT-ICR) analyzer. Standard curves were generated from the signal intensity of the different PC(16:0 d31/18:1) ionic species ([M+H](+), [M+Na](+) and [M+K](+)) detected from the homogenate sections. Localized quantitative data were finally extracted by correlating the standard curves with the signal intensities of endogenous PC (especially PC(16:0/18:1)) ionic species detected on different areas of the brain section. They were consistent with quantitative values found in the literature. This work introduces a new method to take directly into account biological matrix effects for the quantification of lipids as well as other endogenous compounds, in tissue sections by MALDI MSI.
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Affiliation(s)
- Laure Jadoul
- Mass Spectrometry Laboratory, Department of Chemistry, GIGA-Research, University of Liège, 4000, Liège, Belgium,
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46
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Gaudin M, Panchal M, Ayciriex S, Werner E, Brunelle A, Touboul D, Boursier-Neyret C, Auzeil N, Walther B, Duyckaerts C, Laprévote O. Ultra performance liquid chromatography - mass spectrometry studies of formalin-induced alterations of human brain lipidome. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:1035-1042. [PMID: 25303393 DOI: 10.1002/jms.3424] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/20/2014] [Accepted: 06/30/2014] [Indexed: 06/04/2023]
Abstract
The development of 'omics' sciences offers new opportunities for the study of neurodegenerative diseases but increases at the same time the sample demand on brain banks that collect and store valuable human post-mortem tissue. Our study aims to evaluate in lipidomics the potential of formalin-fixed tissue compared with the cryopreservation method, considered as the gold standard for biochemical research. Two complementary liquid chromatography/mass spectrometry analytical platforms were used on the basis of hybrid quadrupole time-of-flight and triple quadrupole mass spectrometers. Untargeted fingerprinting, semitargeted profiling of specific lipid classes and targeted monitoring of lipid species were performed in formalin-fixed and cryopreserved samples to provide detailed information at the molecular level on the formalin-induced alterations of the brain tissue. In vitro incubations of lipid standards were also performed to further describe the degradation processes induced by formaldehyde. Phospholipid compounds were found to be extensively hydrolysed, whilst the sphingolipid ones were preserved. N-methylation and N-formylation of amine-containing phospholipids have also been evidenced. These findings show that the potential detrimental effect of formalin on the analytes of interest must be taken into account when analysing formalin-fixed samples.
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Affiliation(s)
- Mathieu Gaudin
- Chimie-Toxicologie Analytique et Cellulaire, UMR CNRS 8638 COMETE, Faculté des Sciences Pharmaceutiques et Biologiques de Paris, Université Paris Descartes, Sorbonne Paris Cité, 75006, Paris, France; Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, 91198, Gif-sur-Yvette, France; Technologie Servier, 45000, Orléans, France
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47
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Arafah K, Longuespée R, Desmons A, Kerdraon O, Fournier I, Salzet M. Lipidomics for clinical diagnosis: Dye-Assisted Laser Desorption/Ionization (DALDI) method for lipids detection in MALDI mass spectrometry imaging. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:487-98. [PMID: 24905741 DOI: 10.1089/omi.2013.0175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Lipid-based biomarkers for research and diagnosis are rapidly emerging to unpack the basis of person-to-person and population variations in disease susceptibility, drug and nutritional responses, to name but a few. Hence, with the advent of MALDI Mass Spectrometry Imaging, lipids have begun to be investigated intensively. However, lipids are highly mobile during tissue preparation, and are soluble in the solvent used for matrix preparation or in the fixing fluid such as formalin, resulting in substantial delocalization. In the present article, we investigated as another alternative, the possibility of using specific dyes that can absorb UV wavelengths, in order to desorb the lipids specifically from tissue sections, and are known to immobilize them in tissues. Indeed, after lipid insolubilization with chromate solution or chemical fixation with osmium tetroxide, heterocyclic-based dyes can be directly used without matrix. Taking into account the fact that some dyes have this matrix-free capability, we identified particular dyes dedicated to histological staining of lipids that could be used with MALDI mass spectrometry imaging. We stained tissue sections with either Sudan Black B, Nile Blue A, or Oil Red O. An important advantage of this assay relies on its compatibility with usual practices of histopathological investigation of lipids. As a new method, DALDI stands for Dye-Assisted Laser Desorption Ionization and allows for future clinical and histopathological applications using routine histological protocols. Additionally, this novel methodology was validated in human ovarian cancer biopsies to demonstrate its use as a suitable procedure, for histological diagnosis in lipidomics field.
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Affiliation(s)
- Karim Arafah
- 1 Laboratoire de Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM), Université de Lille 1 , Cité Scientifique, Villeneuve D'Ascq, France
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48
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Chatterji B, Pich A. MALDI imaging mass spectrometry and analysis of endogenous peptides. Expert Rev Proteomics 2014; 10:381-8. [PMID: 23992420 DOI: 10.1586/14789450.2013.814939] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In recent years, MALDI imaging mass spectrometry (MALDI-IMS) has developed as a promising tool to investigate the spatial distribution of biomolecules in intact tissue specimens. Ion densities of various molecules can be displayed as heat maps while preserving anatomical structures. In this short review, an overview of different biomolecules that can be analyzed by MALDI-IMS is given. Many reviews have covered imaging of lipids, small metabolites, whole proteins and enzymatically digested proteins in the past. However, little is known about imaging of endogenous peptides, for example, in the rat brain, and this will therefore be highlighted in this review. Furthermore, sample preparation of frozen or formalin-fixed, paraffin-embedded (FFPE) tissue is crucial for imaging experiments. Therefore, some aspects of sample preparation will be addressed, including washing and desalting, the choice of MALDI matrix and its deposition. Apart from mapping endogenous peptides, their reliable identification in situ still remains challenging and will be discussed as well.
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Affiliation(s)
- Bijon Chatterji
- Hannover Medical School, Institute of Toxicology, Core Unit Mass Spectrometry - Proteomics, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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49
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Shariatgorji M, Svenningsson P, Andrén PE. Mass spectrometry imaging, an emerging technology in neuropsychopharmacology. Neuropsychopharmacology 2014; 39:34-49. [PMID: 23966069 PMCID: PMC3857656 DOI: 10.1038/npp.2013.215] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 01/03/2023]
Abstract
Mass spectrometry imaging is a powerful tool for directly determining the distribution of proteins, peptides, lipids, neurotransmitters, metabolites and drugs in neural tissue sections in situ. Molecule-specific imaging can be achieved using various ionization techniques that are suited to different applications but which all yield data with high mass accuracies and spatial resolutions. The ability to simultaneously obtain images showing the distributions of chemical species ranging from metal ions to macromolecules makes it possible to explore the chemical organization of a sample and to correlate the results obtained with specific anatomical features. The imaging of biomolecules has provided new insights into multiple neurological diseases, including Parkinson's and Alzheimer's disease. Mass spectrometry imaging can also be used in conjunction with other imaging techniques in order to identify correlations between changes in the distribution of important chemical species and other changes in the properties of the tissue. Here we review the applications of mass spectrometry imaging in neuroscience research and discuss its potential. The results presented demonstrate that mass spectrometry imaging is a useful experimental method with diverse applications in neuroscience.
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Affiliation(s)
- Mohammadreza Shariatgorji
- Department of Pharmaceutical Biosciences, Biomolecular Imaging and Proteomics, National Laboratory for Mass Spectrometry Imaging, Uppsala University, Uppsala, Sweden
| | - Per Svenningsson
- Department of Neurology and Clinical Neuroscience, Centre for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Per E Andrén
- Department of Pharmaceutical Biosciences, Biomolecular Imaging and Proteomics, National Laboratory for Mass Spectrometry Imaging, Uppsala University, Uppsala, Sweden,Department of Pharmaceutical Biosciences, Biomolecular Imaging and Proteomics, National Laboratory for Mass Spectrometry Imaging, Uppsala University, Box 591, Husargatan 3, Uppsala SE-75124, Sweden, Tel: +46 18 471 7206, Fax: +46 70 167 9334, E-mail:
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50
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Jackson SN, Baldwin K, Muller L, Womack VM, Schultz JA, Balaban C, Woods AS. Imaging of lipids in rat heart by MALDI-MS with silver nanoparticles. Anal Bioanal Chem 2013; 406:1377-86. [PMID: 24309627 DOI: 10.1007/s00216-013-7525-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 10/14/2013] [Accepted: 11/19/2013] [Indexed: 12/21/2022]
Abstract
Lipids are a major component of heart tissue and perform several important functions such as energy storage, signaling, and as building blocks of biological membranes. The heart lipidome is quite diverse consisting of glycerophospholipids such as phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), phosphatidylinositols (PIs), phosphatidylglycerols (PGs), cardiolipins (CLs), and glycerolipids, mainly triacylglycerols (TAGs). In this study, mass spectrometry imaging (MSI) enabled by matrix implantation of ionized silver nanoparticles (AgNP) was used to map several classes of lipids in heart tissue. The use of AgNP matrix implantation was motivated by our previous work showing that implantation doses of only 10(14)/cm(2) of 2 nm gold nanoparticulates into the first 10 nm of the near surface of the tissue enabled detection of most brain lipids (including neutral lipid species such as cerebrosides) more efficiently than traditional organic MALDI matrices. Herein, a similar implantation of 500 eV AgNP(-) across the entire heart tissue section results in a quick, reproducible, solvent-free, uniform matrix concentration of 6 nm AgNP residing near the tissue surface. MALDI-MSI analysis of either positive or negative ions produce high-quality images of several heart lipid species. In negative ion mode, 24 lipid species [16 PEs, 4 PIs, 1 PG, 1 CL, 2 sphingomyelins (SMs)] were imaged. Positive ion images were also obtained from 29 lipid species (10 PCs, 5 PEs, 5 SMs, 9 TAGs) with the TAG species being heavily concentrated in vascular regions of the heart.
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Affiliation(s)
- Shelley N Jackson
- Structural Biology Unit, NIDA IRP, NIH, 333 Cassell Drive, Room 1120, Baltimore, MD, 21224, USA
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