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Ferey J, Mervant L, Naud N, Jamin EL, Pierre F, Debrauwer L, Guéraud F. Spatial metabolomics using mass-spectrometry imaging to decipher the impact of high red meat diet on the colon metabolome in rat. Talanta 2024; 276:126230. [PMID: 38762974 DOI: 10.1016/j.talanta.2024.126230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/21/2024]
Abstract
Colorectal cancer (CRC) is the third most common cancer in the world with a higher prevalence in the developed countries, mainly caused by environmental and lifestyle factors such as diet, particularly red meat consumption. The metabolic impact of high red meat consumption on the epithelial part of the colon was investigated using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MSI), to specifically analyze the epithelial substructure. Ten colons from rats fed for 100 days high red or white meat diet were subjected to untargeted MSI analyses using two spatial resolutions (100 μm and 10 μm) to evaluate metabolite changes in the epithelial part and to visualize the distribution of metabolites of interest within the epithelium crypts. Our results suggest a specific effect of red meat diet on the colonic epithelium metabolism, as evidenced by an increase of purine catabolism products or depletion in glutathione pool, reinforcing the hypothesis of increased oxidative stress with red meat diet. This study also highlighted cholesterol sulfate as another up-regulated metabolite, interestingly localized at the top of the crypts. Altogether, this study demonstrates the feasibility and the added value of using MSI to decipher the effect of high red meat diet on the colonic epithelium.
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Affiliation(s)
- Justine Ferey
- UMR1331 Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics, MetaboHUB, Toxalim, INRAE, 31027, Toulouse, France
| | - Loïc Mervant
- UMR1331 Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics, MetaboHUB, Toxalim, INRAE, 31027, Toulouse, France; The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Nathalie Naud
- UMR1331 Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027, Toulouse, France
| | - Emilien L Jamin
- UMR1331 Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics, MetaboHUB, Toxalim, INRAE, 31027, Toulouse, France
| | - Fabrice Pierre
- UMR1331 Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027, Toulouse, France
| | - Laurent Debrauwer
- UMR1331 Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics, MetaboHUB, Toxalim, INRAE, 31027, Toulouse, France
| | - Françoise Guéraud
- UMR1331 Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, 31027, Toulouse, France
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McKinnon JC, Milioli HH, Purcell CA, Chaffer CL, Wadie B, Alexandrov T, Mitchell TW, Ellis SR. Enhancing metabolite coverage in MALDI-MSI using laser post-ionisation (MALDI-2). ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4311-4320. [PMID: 37605803 DOI: 10.1039/d3ay01046e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) of metabolites can reveal how metabolism is altered throughout heterogeneous tissues. Here negative ion mode MALDI-MSI has been coupled with laser post-ionisation (MALDI-2) and applied to the MSI of low molecular weight (LMW) metabolites (
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Affiliation(s)
- J C McKinnon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia.
| | - H H Milioli
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, UNSW Medicine, UNSW Sydney, NSW, Australia
- The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia
| | - C A Purcell
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, UNSW Medicine, UNSW Sydney, NSW, Australia
- The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia
| | - C L Chaffer
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, UNSW Medicine, UNSW Sydney, NSW, Australia
- The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia
| | - B Wadie
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - T Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - T W Mitchell
- Molecular Horizons, School of Medical, Indigenous and Health Science, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia
| | - S R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Ave, Wollongong, NSW 2522, Australia.
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3
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Stopka SA, van der Reest J, Abdelmoula WM, Ruiz DF, Joshi S, Ringel AE, Haigis MC, Agar NYR. Spatially resolved characterization of tissue metabolic compartments in fasted and high-fat diet livers. PLoS One 2022; 17:e0261803. [PMID: 36067168 PMCID: PMC9447892 DOI: 10.1371/journal.pone.0261803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
Cells adapt their metabolism to physiological stimuli, and metabolic heterogeneity exists between cell types, within tissues, and subcellular compartments. The liver plays an essential role in maintaining whole-body metabolic homeostasis and is structurally defined by metabolic zones. These zones are well-understood on the transcriptomic level, but have not been comprehensively characterized on the metabolomic level. Mass spectrometry imaging (MSI) can be used to map hundreds of metabolites directly from a tissue section, offering an important advance to investigate metabolic heterogeneity in tissues compared to extraction-based metabolomics methods that analyze tissue metabolite profiles in bulk. We established a workflow for the preparation of tissue specimens for matrix-assisted laser desorption/ionization (MALDI) MSI that can be implemented to achieve broad coverage of central carbon, nucleotide, and lipid metabolism pathways. Herein, we used this approach to visualize the effect of nutrient stress and excess on liver metabolism. Our data revealed a highly organized metabolic tissue compartmentalization in livers, which becomes disrupted under high fat diet. Fasting caused changes in the abundance of several metabolites, including increased levels of fatty acids and TCA intermediates while fatty livers had higher levels of purine and pentose phosphate-related metabolites, which generate reducing equivalents to counteract oxidative stress. This spatially conserved approach allowed the visualization of liver metabolic compartmentalization at 30 μm pixel resolution and can be applied more broadly to yield new insights into metabolic heterogeneity in vivo.
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Affiliation(s)
- Sylwia A. Stopka
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United Statees of America
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United Statees of America
| | - Jiska van der Reest
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United Statees of America
- Department of Cell Biology, Blavatnik Institute, Ludwig Center, Harvard Medical School, Boston, MA, United Statees of America
| | - Walid M. Abdelmoula
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United Statees of America
| | - Daniela F. Ruiz
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United Statees of America
- Bouvé College of Health Sciences, Northeastern University, Boston, MA, United Statees of America
| | - Shakchhi Joshi
- Department of Cell Biology, Blavatnik Institute, Ludwig Center, Harvard Medical School, Boston, MA, United Statees of America
| | - Alison E. Ringel
- Department of Cell Biology, Blavatnik Institute, Ludwig Center, Harvard Medical School, Boston, MA, United Statees of America
| | - Marcia C. Haigis
- Department of Cell Biology, Blavatnik Institute, Ludwig Center, Harvard Medical School, Boston, MA, United Statees of America
- * E-mail: (MCH); (NYRA)
| | - Nathalie Y. R. Agar
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United Statees of America
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United Statees of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United Statees of America
- * E-mail: (MCH); (NYRA)
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4
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Zahraei A, Guo G, Varnava KG, Demarais NJ, Donaldson PJ, Grey AC. Mapping Glucose Uptake, Transport and Metabolism in the Bovine Lens Cortex. Front Physiol 2022; 13:901407. [PMID: 35711316 PMCID: PMC9194507 DOI: 10.3389/fphys.2022.901407] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: To spatially correlate the pattern of glucose uptake to glucose transporter distributions in cultured lenses and map glucose metabolism in different lens regions. Methods: Ex vivo bovine lenses were incubated in artificial aqueous humour containing normoglycaemic stable isotopically-labelled (SIL) glucose (5 mM) for 5 min-20 h. Following incubations, lenses were frozen for subsequent matrix-assisted laser desorption/ionisation (MALDI) imaging mass spectrometry (IMS) analysis using high resolution mass spectrometry. Manually dissected, SIL-incubated lenses were subjected to gas chromatography-mass spectrometry (GC-MS) to verify the identity of metabolites detected by MALDI-IMS. Normal, unincubated lenses were manually dissected into epithelium flat mounts and fibre cell fractions and then subjected to either gel-based proteomic analysis (Gel-LC/MS) to detect facilitative glucose transporters (GLUTs) by liquid chromatography tandem mass spectrometry (LC-MS/MS). Indirect immunofluorescence and confocal microscopy of axial lens sections from unincubated fixed lenses labelled with primary antibodies specific for GLUT 1 or GLUT 3 were utilised for protein localisation. Results: SIL glucose uptake at 5 min was concentrated in the equatorial region of the lens. At later timepoints, glucose gradually distributed throughout the epithelium and the cortical lens fibres, and eventually the deeper lens nucleus. SIL glucose metabolites found in glycolysis, the sorbitol pathway, the pentose phosphate pathway, and UDP-glucose formation were mapped to specific lens regions, with distinct regional signal changes up to 20 h of incubation. Spatial proteomic analysis of the lens epithelium detected GLUT1 and GLUT3. GLUT3 was in higher abundance than GLUT1 throughout the epithelium, while GLUT1 was more abundant in lens fibre cells. Immunohistochemical mapping localised GLUT1 to epithelial and cortical fibre cell membranes. Conclusion: The major uptake site of glucose in the bovine lens has been mapped to the lens equator. SIL glucose is rapidly metabolised in epithelial and fibre cells to many metabolites, which are most abundant in the metabolically more active cortical fibre cells in comparison to central fibres, with low levels of metabolic activity observed in the nucleus.
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Affiliation(s)
- Ali Zahraei
- Department of Physiology in the School of Medical Sciences, Auckland, New Zealand
| | - George Guo
- Department of Physiology in the School of Medical Sciences, Auckland, New Zealand.,Mass Spectrometry Hub, Auckland, New Zealand
| | - Kyriakos G Varnava
- Department of Physiology in the School of Medical Sciences, Auckland, New Zealand.,Mass Spectrometry Hub, Auckland, New Zealand
| | - Nicholas J Demarais
- Mass Spectrometry Hub, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul J Donaldson
- Department of Physiology in the School of Medical Sciences, Auckland, New Zealand
| | - Angus C Grey
- Department of Physiology in the School of Medical Sciences, Auckland, New Zealand.,Mass Spectrometry Hub, Auckland, New Zealand
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5
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Deininger SO, Bollwein C, Casadonte R, Wandernoth P, Gonçalves JPL, Kriegsmann K, Kriegsmann M, Boskamp T, Kriegsmann J, Weichert W, Schirmacher P, Ly A, Schwamborn K. Multicenter Evaluation of Tissue Classification by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Anal Chem 2022; 94:8194-8201. [PMID: 35658398 DOI: 10.1021/acs.analchem.2c00097] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many studies have demonstrated that tissue phenotyping (tissue typing) based on mass spectrometric imaging data is possible; however, comprehensive studies assessing variation and classifier transferability are largely lacking. This study evaluated the generalization of tissue classification based on Matrix Assisted Laser Desorption/Ionization (MALDI) mass spectrometric imaging (MSI) across measurements performed at different sites. Sections of a tissue microarray (TMA) consisting of different formalin-fixed and paraffin-embedded (FFPE) human tissue samples from different tumor entities (leiomyoma, seminoma, mantle cell lymphoma, melanoma, breast cancer, and squamous cell carcinoma of the lung) were prepared and measured by MALDI-MSI at different sites using a standard protocol (SOP). Technical variation was deliberately introduced on two separate measurements via a different sample preparation protocol and a MALDI Time of Flight mass spectrometer that was not tuned to optimal performance. Using standard data preprocessing, a classification accuracy of 91.4% per pixel was achieved for intrasite classifications. When applying a leave-one-site-out cross-validation strategy, accuracy per pixel over sites was 78.6% for the SOP-compliant data sets and as low as 36.1% for the mistuned instrument data set. Data preprocessing designed to remove technical variation while retaining biological information substantially increased classification accuracy for all data sets with SOP-compliant data sets improved to 94.3%. In particular, classification accuracy of the mistuned instrument data set improved to 81.3% and from 67.0% to 87.8% per pixel for the non-SOP-compliant data set. We demonstrate that MALDI-MSI-based tissue classification is possible across sites when applying histological annotation and an optimized data preprocessing pipeline to improve generalization of classifications over technical variation and increasing overall robustness.
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Affiliation(s)
| | - Christine Bollwein
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstrasse 18, 81675 München, Germany
| | - Rita Casadonte
- Proteopath GmbH, Max-Planck-Strasse 17, 54296 Trier, Germany
| | - Petra Wandernoth
- MVZ für Histologie, Zytologie und molekulare Diagnostik Trier GmbH, Max-Planck-Strasse 5, 54296 Trier, Germany
| | | | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Tobias Boskamp
- Bruker Daltonics GmbH & Co KG, Fahrenheitstrasse 4, 28359 Bremen, Germany.,Center for Industrial Mathematics, University of Bremen, 28359 Bremen, Germany
| | - Jörg Kriegsmann
- MVZ für Histologie, Zytologie und molekulare Diagnostik Trier GmbH, Max-Planck-Strasse 5, 54296 Trier, Germany.,Danube Private University (DPU) Faculty of Medicine/Dentistry, Steiner Landstrasse 124, 3500 Krems-Stein, Austria
| | - Wilko Weichert
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstrasse 18, 81675 München, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Alice Ly
- Bruker Daltonics GmbH & Co KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Kristina Schwamborn
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstrasse 18, 81675 München, Germany
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6
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Capturing the third dimension in drug discovery: Spatially-resolved tools for interrogation of complex 3D cell models. Biotechnol Adv 2021; 55:107883. [PMID: 34875362 DOI: 10.1016/j.biotechadv.2021.107883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
Abstract
Advanced three-dimensional (3D) cell models have proven to be capable of depicting architectural and microenvironmental features of several tissues. By providing data of higher physiological and pathophysiological relevance, 3D cell models have been contributing to a better understanding of human development, pathology onset and progression mechanisms, as well as for 3D cell-based assays for drug discovery. Nonetheless, the characterization and interrogation of these tissue-like structures pose major challenges on the conventional analytical methods, pushing the development of spatially-resolved technologies. Herein, we review recent advances and pioneering technologies suitable for the interrogation of multicellular 3D models, while capable of retaining biological spatial information. We focused on imaging technologies and omics tools, namely transcriptomics, proteomics and metabolomics. The advantages and shortcomings of these novel methodologies are discussed, alongside the opportunities to intertwine data from the different tools.
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7
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Lohse M, Haag R, Lippold E, Vetterlein D, Reemtsma T, Lechtenfeld OJ. Direct Imaging of Plant Metabolites in the Rhizosphere Using Laser Desorption Ionization Ultra-High Resolution Mass Spectrometry. FRONTIERS IN PLANT SCIENCE 2021; 12:753812. [PMID: 34925405 PMCID: PMC8678481 DOI: 10.3389/fpls.2021.753812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
The interplay of rhizosphere components such as root exudates, microbes, and minerals results in small-scale gradients of organic molecules in the soil around roots. The current methods for the direct chemical imaging of plant metabolites in the rhizosphere often lack molecular information or require labeling with fluorescent tags or isotopes. Here, we present a novel workflow using laser desorption ionization (LDI) combined with mass spectrometric imaging (MSI) to directly analyze plant metabolites in a complex soil matrix. Undisturbed samples of the roots and the surrounding soil of Zea mays L. plants from either field- or laboratory-scale experiments were embedded and cryosectioned to 100 μm thin sections. The target metabolites were detected with a spatial resolution of 25 μm in the root and the surrounding soil based on accurate masses using ultra-high mass resolution laser desorption ionization Fourier-transform ion cyclotron resonance mass spectrometry (LDI-FT-ICR-MS). Using this workflow, we could determine the rhizosphere gradients of a dihexose (e.g., sucrose) and other plant metabolites (e.g., coumaric acid, vanillic acid). The molecular gradients for the dihexose showed a high abundance of this metabolite in the root and a strong depletion of the signal intensity within 150 μm from the root surface. Analyzing several sections from the same undisturbed soil sample allowed us to follow molecular gradients along the root axis. Benefiting from the ultra-high mass resolution, isotopologues of the dihexose could be readily resolved to enable the detection of stable isotope labels on the compound level. Overall, the direct molecular imaging via LDI-FT-ICR-MS allows for the first time a non-targeted or targeted analysis of plant metabolites in undisturbed soil samples, paving the way to study the turnover of root-derived organic carbon in the rhizosphere with high chemical and spatial resolution.
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Affiliation(s)
- Martin Lohse
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Rebecca Haag
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Ansbach University of Applied Sciences, Ansbach, Germany
| | - Eva Lippold
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- Soil Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - Oliver J. Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- ProVIS – Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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8
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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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9
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Wolrab D, Jirásko R, Chocholoušková M, Peterka O, Holčapek M. Oncolipidomics: Mass spectrometric quantitation of lipids in cancer research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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10
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Ly A, Ragionieri L, Liessem S, Becker M, Deininger SO, Neupert S, Predel R. Enhanced Coverage of Insect Neuropeptides in Tissue Sections by an Optimized Mass-Spectrometry-Imaging Protocol. Anal Chem 2019; 91:1980-1988. [DOI: 10.1021/acs.analchem.8b04304] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alice Ly
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Lapo Ragionieri
- Department for Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Sander Liessem
- Department for Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Michael Becker
- Bruker Daltonik GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | | | - Susanne Neupert
- Department for Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Reinhard Predel
- Department for Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
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11
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Corinti D, Crestoni ME, Fornarini S, Pieper M, Niehaus K, Giampà M. An integrated approach to study novel properties of a MALDI matrix (4-maleicanhydridoproton sponge) for MS imaging analyses. Anal Bioanal Chem 2018; 411:953-964. [DOI: 10.1007/s00216-018-1531-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 02/02/2023]
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12
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Rzagalinski I, Hainz N, Meier C, Tschernig T, Volmer DA. Spatial and molecular changes of mouse brain metabolism in response to immunomodulatory treatment with teriflunomide as visualized by MALDI-MSI. Anal Bioanal Chem 2018; 411:353-365. [PMID: 30417265 DOI: 10.1007/s00216-018-1444-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/05/2018] [Accepted: 10/22/2018] [Indexed: 12/30/2022]
Abstract
Multiple sclerosis (MS) is an immune-mediated neurodegenerative disease of the central nervous system (CNS). One of the most promising recent medications for MS is teriflunomide. Its primary mechanism of action is linked to effects on the peripheral immune system by inhibiting dihydroorotate dehydrogenase (DHODH)-catalyzed de novo pyrimidine synthesis and reducing the expansion of lymphocytes in the peripheral immune system. Some in vitro studies suggested, however, that it can also have a direct effect on the CNS compartment. This potential alternative mode of action depends on the drug's capacity to traverse the blood-brain barrier (BBB) and to exert an effect on the complex network of brain biochemical pathways. In this paper, we demonstrate the application of high-resolution/high-accuracy matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry for molecular imaging of the mouse brain coronal sections from animals treated with teriflunomide. Specifically, in order to assess the effect of teriflunomide on the mouse CNS compartment, we investigated the feasibility of teriflunomide to traverse the BBB. Secondly, we systematically evaluated the spatial and semi-quantitative brain metabolic profiles of 24 different endogenous compounds after 4-day teriflunomide administration. Even though the drug was not detected in the examined cerebral sections (despite the high detection sensitivity of the developed method), in-depth study of the endogenous metabolic compartment revealed noticeable alterations as a result of teriflunomide administration compared to the control animals. The observed differences, particularly for purine and pyrimidine nucleotides as well as for glutathione and carbohydrate metabolism intermediates, shed some light on the potential impact of teriflunomide on the mouse brain metabolic networks. Graphical Abstract.
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Affiliation(s)
- Ignacy Rzagalinski
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Nadine Hainz
- Institute of Anatomy and Cell Biology, Saarland University, 66421, Homburg, Germany
| | - Carola Meier
- Institute of Anatomy and Cell Biology, Saarland University, 66421, Homburg, Germany
| | - Thomas Tschernig
- Institute of Anatomy and Cell Biology, Saarland University, 66421, Homburg, Germany
| | - Dietrich A Volmer
- Department of Chemistry, Humboldt University of Berlin, 12489, Berlin, Germany.
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13
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González de San Román E, Bidmon HJ, Malisic M, Susnea I, Küppers A, Hübbers R, Wree A, Nischwitz V, Amunts K, Huesgen PF. Molecular composition of the human primary visual cortex profiled by multimodal mass spectrometry imaging. Brain Struct Funct 2018; 223:2767-2783. [PMID: 29633039 PMCID: PMC5995978 DOI: 10.1007/s00429-018-1660-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
The primary visual cortex (area V1) is an extensively studied part of the cerebral cortex with well-characterized connectivity, cellular and molecular architecture and functions (for recent reviews see Amunts and Zilles, Neuron 88:1086-1107, 2015; Casagrande and Xu, Parallel visual pathways: a comparative perspective. The visual neurosciences, MIT Press, Cambridge, pp 494-506, 2004). In humans, V1 is defined by heavily myelinated fibers arriving from the radiatio optica that form the Gennari stripe in cortical layer IV, which is further subdivided into laminae IVa, IVb, IVcα and IVcβ. Due to this unique laminar pattern, V1 represents an excellent region to test whether multimodal mass spectrometric imaging could reveal novel biomolecular markers for a functionally relevant parcellation of the human cerebral cortex. Here we analyzed histological sections of three post-mortem brains with matrix-assisted laser desorption/ionization mass spectrometry imaging and laser ablation inductively coupled plasma mass spectrometry imaging to investigate the distribution of lipids, proteins and metals in human V1. We identified 71 peptides of 13 different proteins by in situ tandem mass spectrometry, of which 5 proteins show a differential laminar distribution pattern revealing the border between V1 and V2. High-accuracy mass measurements identified 123 lipid species, including glycerolipids, glycerophospholipids and sphingolipids, of which at least 20 showed differential distribution within V1 and V2. Specific lipids labeled not only myelinated layer IVb, but also IVa and especially IVc in a layer-specific manner, but also and clearly separated V1 from V2. Elemental imaging further showed a specific accumulation of copper in layer IV. In conclusion, multimodal mass spectrometry imaging identified novel biomolecular and elemental markers with specific laminar and inter-areal differences. We conclude that mass spectrometry imaging provides a promising new approach toward multimodal, molecule-based cortical parcellation.
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Affiliation(s)
- Estibaliz González de San Román
- Central Institute of Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- Cécile and Oskar Vogt Institute of Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hans-Jürgen Bidmon
- Cécile and Oskar Vogt Institute of Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Milena Malisic
- Central Institute of Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- Cécile and Oskar Vogt Institute of Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Iuliana Susnea
- Central Institute of Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Astrid Küppers
- Central Institute of Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Rene Hübbers
- Cécile and Oskar Vogt Institute of Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine, INM-1, Forschungszentrum Jülich, Jülich, Germany
| | - Andreas Wree
- Institute of Anatomy, Rostock University Medical Center, Rostock, Germany
| | - Volker Nischwitz
- Central Institute of Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Katrin Amunts
- Cécile and Oskar Vogt Institute of Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Institute of Neuroscience and Medicine, INM-1, Forschungszentrum Jülich, Jülich, Germany.
| | - Pitter F Huesgen
- Central Institute of Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany.
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14
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Swales JG, Dexter A, Hamm G, Nilsson A, Strittmatter N, Michopoulos F, Hardy C, Morentin-Gutierrez P, Mellor M, Andren PE, Clench MR, Bunch J, Critchlow SE, Goodwin RJA. Quantitation of Endogenous Metabolites in Mouse Tumors Using Mass-Spectrometry Imaging. Anal Chem 2018; 90:6051-6058. [PMID: 29668267 DOI: 10.1021/acs.analchem.7b05239] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Described is a quantitative-mass-spectrometry-imaging (qMSI) methodology for the analysis of lactate and glutamate distributions in order to delineate heterogeneity among mouse tumor models used to support drug-discovery efficacy testing. We evaluate and report on preanalysis-stabilization methods aimed at improving the reproducibility and efficiency of quantitative assessments of endogenous molecules in tissues. Stability experiments demonstrate that optimum stabilization protocols consist of frozen-tissue embedding, post-tissue-sectioning desiccation, and storage at -80 °C of tissue sections sealed in vacuum-tight containers. Optimized stabilization protocols are used in combination with qMSI methodology for the absolute quantitation of lactate and glutamate in tumors, incorporating the use of two different stable-isotope-labeled versions of each analyte and spectral-clustering performed on each tissue section using k-means clustering to allow region-specific, pixel-by-pixel quantitation. Region-specific qMSI was used to screen different tumor models and identify a phenotype that has low lactate heterogeneity, which will enable accurate measurements of lactate modulation in future drug-discovery studies. We conclude that using optimized qMSI protocols, it is possible to quantify endogenous metabolites within tumors, and region-specific quantitation can provide valuable insight into tissue heterogeneity and the tumor microenvironment.
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Affiliation(s)
- John G Swales
- Pathology, Drug Safety & Metabolism, IMED Biotech Unit , AstraZeneca , Darwin Building, Cambridge Science Park, Milton Road , Cambridge , Cambridgeshire CB4 0WG , U.K.,Centre for Mass Spectrometry Imaging, Biomolecular Research Centre , Sheffield Hallam University , Sheffield S1 1WB , U.K
| | - Alex Dexter
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI) , National Physical Laboratory , Teddington TW11 0LW , U.K
| | - Gregory Hamm
- Pathology, Drug Safety & Metabolism, IMED Biotech Unit , AstraZeneca , Darwin Building, Cambridge Science Park, Milton Road , Cambridge , Cambridgeshire CB4 0WG , U.K
| | - Anna Nilsson
- Biomolecular Mass Spectrometry Imaging, National Resource for MSI, Science for Life Laboratory, Department of Pharmaceutical Biosciences , Uppsala University , Uppsala 752 37 , Sweden
| | - Nicole Strittmatter
- Pathology, Drug Safety & Metabolism, IMED Biotech Unit , AstraZeneca , Darwin Building, Cambridge Science Park, Milton Road , Cambridge , Cambridgeshire CB4 0WG , U.K
| | | | - Christopher Hardy
- Pathology, Drug Safety & Metabolism, IMED Biotech Unit , AstraZeneca , Darwin Building, Cambridge Science Park, Milton Road , Cambridge , Cambridgeshire CB4 0WG , U.K
| | | | - Martine Mellor
- Bioscience, Oncology, IMED Biotech Unit , AstraZeneca , Cambridge CB4 0WG , U.K
| | - Per E Andren
- Biomolecular Mass Spectrometry Imaging, National Resource for MSI, Science for Life Laboratory, Department of Pharmaceutical Biosciences , Uppsala University , Uppsala 752 37 , Sweden
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre , Sheffield Hallam University , Sheffield S1 1WB , U.K
| | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI) , National Physical Laboratory , Teddington TW11 0LW , U.K
| | - Susan E Critchlow
- Bioscience, Oncology, IMED Biotech Unit , AstraZeneca , Cambridge CB4 0WG , U.K
| | - Richard J A Goodwin
- Pathology, Drug Safety & Metabolism, IMED Biotech Unit , AstraZeneca , Darwin Building, Cambridge Science Park, Milton Road , Cambridge , Cambridgeshire CB4 0WG , U.K
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15
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Abstract
Mass spectrometry imaging (MSI) is a technique which is gaining increasing interest in biomedical research due to its capacity to visualize molecules in tissues. First applied to the field of clinical proteomics, its potential for metabolite imaging in biomedical studies is now being recognized. Here we describe how to set up experiments for mass spectrometry imaging of metabolites in clinical tissues and how to tackle most of the obstacles in the subsequent analysis of the data.
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Affiliation(s)
- Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, The Netherlands
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16
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Gao D, Cazares LH, Fish EN. CCL5-CCR5 interactions modulate metabolic events during tumor onset to promote tumorigenesis. BMC Cancer 2017; 17:834. [PMID: 29216863 PMCID: PMC5721608 DOI: 10.1186/s12885-017-3817-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/22/2017] [Indexed: 01/16/2023] Open
Abstract
Background In earlier studies we have shown that CCL5 activation of CCR5 induces the proliferation and survival of breast cancer cells in a mechanistic target of rapamycin (mTOR)-dependent manner and that this is in part due to CCR5-mediated increases in glycolytic metabolism. Methods Using the MDA-MB-231 triple negative human breast cancer cell line and mouse mammary tumor virus – polyomavirus middle T-antigen (MMTV-PyMT) mouse primary breast cancer cells, we conducted in vivo tumor transplant experiments to examine the effects of CCL5-CCR5 interactions in the context of regulating tumor metabolism. Additionally, we employed Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry imaging (MALDI-FTICR-MSI) to evaluate tumor utilization of cellular metabolites. Results We provide evidence that, in the absence of CCR5, the early events associated with rapid tumor growth in the MMTV-PyMT mouse model of spontaneous breast cancer development, are diminished, as demonstrated by a delay in tumor onset. In tumor transplant studies into immunocompromised mice we identify a direct correlation between reduced tumor proliferation and decreased metabolic activity, specifically associated with tumor expression of CCR5. The reduction in tumorigenesis is accompanied by decreases in glucose uptake, glucose transporter-1 (GLUT-1) cell surface expression, intracellular ATP and lactate levels, as well as reduced CCL5 production. Using MALDI-FTICR-MS, we show that the rapid early tumor growth of CCR5+/+ triple negative breast cancer cells in vivo is attributable to increased levels of glycolytic intermediates required for anabolic processes, in contrast to the slower growth rate of their corresponding CCR5−/− cells, that exhibit reduced glycolytic metabolism. Conclusions These findings suggest that CCL5-CCR5 interactions in the tumor microenvironment modulate metabolic events during tumor onset to promote tumorigenesis. Electronic supplementary material The online version of this article (10.1186/s12885-017-3817-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Darrin Gao
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada.,Department of Immunology, University of Toronto, Toronto, Canada
| | - Lisa H Cazares
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, USA
| | - Eleanor N Fish
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada. .,Department of Immunology, University of Toronto, Toronto, Canada.
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17
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Armitage EG, Ciborowski M. Applications of Metabolomics in Cancer Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:209-234. [PMID: 28132182 DOI: 10.1007/978-3-319-47656-8_9] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the start of metabolomics as a field of research, the number of studies related to cancer has grown to such an extent that cancer metabolomics now represents its own discipline. In this chapter, the applications of metabolomics in cancer studies are explored. Different approaches and analytical platforms can be employed for the analysis of samples depending on the goal of the study and the aspects of the cancer metabolome being investigated. Analyses have concerned a range of cancers including lung, colorectal, bladder, breast, gastric, oesophageal and thyroid, amongst others. Developments in these strategies and methodologies that have been applied are discussed, in addition to exemplifying the use of cancer metabolomics in the discovery of biomarkers and in the assessment of therapy (both pharmaceutical and nutraceutical). Finally, the application of cancer metabolomics in personalised medicine is presented.
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Affiliation(s)
- Emily Grace Armitage
- Centre for Metabolomics and Bioanalysis (CEMBIO), Faculty of Pharmacy, Universidad CEU San Pablo, Campus Monteprincipe, Madrid, Spain. .,Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, Sir Graeme Davies Building, University of Glasgow, Glasgow, UK. .,Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
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18
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Lou S, Balluff B, Cleven AHG, Bovée JVMG, McDonnell LA. Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:376-383. [PMID: 27873216 PMCID: PMC5227002 DOI: 10.1007/s13361-016-1544-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 05/22/2023]
Abstract
Metabolites can be an important read-out of disease. The identification and validation of biomarkers in the cancer metabolome that can stratify high-risk patients is one of the main current research aspects. Mass spectrometry has become the technique of choice for metabolomics studies, and mass spectrometry imaging (MSI) enables their visualization in patient tissues. In this study, we used MSI to identify prognostic metabolite biomarkers in high grade sarcomas; 33 high grade sarcoma patients, comprising osteosarcoma, leiomyosarcoma, myxofibrosarcoma, and undifferentiated pleomorphic sarcoma were analyzed. Metabolite MSI data were obtained from sections of fresh frozen tissue specimens with matrix-assisted laser/desorption ionization (MALDI) MSI in negative polarity using 9-aminoarcridine as matrix. Subsequent annotation of tumor regions by expert pathologists resulted in tumor-specific metabolite signatures, which were then tested for association with patient survival. Metabolite signals with significant clinical value were further validated and identified by high mass resolution Fourier transform ion cyclotron resonance (FTICR) MSI. Three metabolite signals were found to correlate with overall survival (m/z 180.9436 and 241.0118) and metastasis-free survival (m/z 160.8417). FTICR-MSI identified m/z 241.0118 as inositol cyclic phosphate and m/z 160.8417 as carnitine. Graphical Abstract ᅟ.
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Affiliation(s)
- Sha Lou
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Balluff
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Maastricht MultiModal Molecular Imaging institute (M4I), Maastricht University, Maastricht, The Netherlands
| | - Arjen H G Cleven
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy.
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19
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Abstract
One of the big clinical challenges in the treatment of cancer is the different behavior of cancer patients under guideline therapy. An important determinant for this phenomenon has been identified as inter- and intratumor heterogeneity. While intertumor heterogeneity refers to the differences in cancer characteristics between patients, intratumor heterogeneity refers to the clonal and nongenetic molecular diversity within a patient. The deciphering of intratumor heterogeneity is recognized as key to the development of novel therapeutics or treatment regimens. The investigation of intratumor heterogeneity is challenging since it requires an untargeted molecular analysis technique that accounts for the spatial and temporal dynamics of the tumor. So far, next-generation sequencing has contributed most to the understanding of clonal evolution within a cancer patient. However, it falls short in accounting for the spatial dimension. Mass spectrometry imaging (MSI) is a powerful tool for the untargeted but spatially resolved molecular analysis of biological tissues such as solid tumors. As it provides multidimensional datasets by the parallel acquisition of hundreds of mass channels, multivariate data analysis methods can be applied for the automated annotation of tissues. Moreover, it integrates the histology of the sample, which enables studying the molecular information in a histopathological context. This chapter will illustrate how MSI in combination with statistical methods and histology has been used for the description and discovery of intratumor heterogeneity in different cancers. This will give evidence that MSI constitutes a unique tool for the investigation of intratumor heterogeneity, and could hence become a key technology in cancer research.
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20
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Buck A, Aichler M, Huber K, Walch A. In Situ Metabolomics in Cancer by Mass Spectrometry Imaging. Adv Cancer Res 2016; 134:117-132. [PMID: 28110648 DOI: 10.1016/bs.acr.2016.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metabolomics is a rapidly evolving and a promising research field with the expectation to improve diagnosis, therapeutic treatment prediction, and prognosis of particular diseases. Among all techniques used to assess the metabolome in biological systems, mass spectrometry imaging is the method of choice to qualitatively and quantitatively analyze metabolite distribution in tissues with a high spatial resolution, thus providing molecular data in relation to cancer histopathology. The technique is ideally suited to study tissues molecular content and is able to provide molecular biomarkers or specific mass signatures which can be used in classification or the prognostic evaluation of tumors. Recently, it was shown that FFPE tissue samples are also suitable for metabolic analyses. This progress in methodology allows access to a highly valuable resource of tissues believed to widen and strengthen metabolic discovery-driven studies.
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Affiliation(s)
- A Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - M Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - K Huber
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - A Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
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21
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Ly A, Buck A, Balluff B, Sun N, Gorzolka K, Feuchtinger A, Janssen KP, Kuppen PJK, van de Velde CJH, Weirich G, Erlmeier F, Langer R, Aubele M, Zitzelsberger H, McDonnell L, Aichler M, Walch A. High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue. Nat Protoc 2016; 11:1428-43. [PMID: 27414759 DOI: 10.1038/nprot.2016.081] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue specimens are the gold standard for histological examination, and they provide valuable molecular information in tissue-based research. Metabolite assessment from archived tissue samples has not been extensively conducted because of a lack of appropriate protocols and concerns about changes in metabolite content or chemical state due to tissue processing. We present a protocol for the in situ analysis of metabolite content from FFPE samples using a high-mass-resolution matrix-assisted laser desorption/ionization fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR-MSI) platform. The method involves FFPE tissue sections that undergo deparaffinization and matrix coating by 9-aminoacridine before MALDI-MSI. Using this platform, we previously detected ∼1,500 m/z species in the mass range m/z 50-1,000 in FFPE samples; the overlap compared with fresh frozen samples is 72% of m/z species, indicating that metabolites are largely conserved in FFPE tissue samples. This protocol can be reproducibly performed on FFPE tissues, including small samples such as tissue microarrays and biopsies. The procedure can be completed in a day, depending on the size of the sample measured and raster size used. Advantages of this approach include easy sample handling, reproducibility, high throughput and the ability to demonstrate molecular spatial distributions in situ. The data acquired with this protocol can be used in research and clinical practice.
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Affiliation(s)
- Alice Ly
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Achim Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, the Netherlands
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Karin Gorzolka
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Gregor Weirich
- Institute of Pathology, Technische Universität München, Munich, Germany
| | | | - Rupert Langer
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Michaela Aubele
- Institute of Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Liam McDonnell
- Centre for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, the Netherlands.,Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - Michaela Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
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22
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Giampà M, Lissel MB, Patschkowski T, Fuchser J, Hans VH, Gembruch O, Bednarz H, Niehaus K. Maleic anhydride proton sponge as a novel MALDI matrix for the visualization of small molecules (<250 m/z) in brain tumors by routine MALDI ToF imaging mass spectrometry. Chem Commun (Camb) 2016; 52:9801-4. [DOI: 10.1039/c6cc02387h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel MALDI matrix MAPS, able to visualize deviating metabolism in glioma using a routine MALDI-ToF-MSI procedure, is presented.
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Affiliation(s)
- M. Giampà
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - M. B. Lissel
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - T. Patschkowski
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - J. Fuchser
- Bruker Daltonics GmbH
- BU Pharma
- 28259 Bremen
- Germany
| | - V. H. Hans
- Institut für Pathologie Ruhr-Universität Bochum
- 44789 Bochum
- Germany
- Institut für Neuropathologie
- Universitätsklinikum Essen (AöR)
| | - O. Gembruch
- Klinik für Neurochirurgie
- Universitätsklinikum Essen (AöR)
- 45147 Essen
- Germany
| | - H. Bednarz
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - K. Niehaus
- Center for Biotechnology and Department for Proteome and Metabolome Research
- Faculty of Biology
- Bielefeld University
- 33615 Bielefeld
- Germany
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23
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Martin-Lorenzo M, Balluff B, Maroto AS, Carreira RJ, van Zeijl RJ, Gonzalez-Calero L, de la Cuesta F, Barderas MG, Lopez-Almodovar LF, Padial LR, McDonnell LA, Vivanco F, Alvarez-Llamas G. Lipid and protein maps defining arterial layers in atherosclerotic aorta. Data Brief 2015; 4:328-31. [PMID: 26217810 PMCID: PMC4510571 DOI: 10.1016/j.dib.2015.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 11/24/2022] Open
Abstract
Subclinical atherosclerosis cannot be predicted and novel therapeutic targets are needed. The molecular anatomy of healthy and atherosclerotic tissue is pursued to identify ongoing molecular changes in atherosclerosis development. Mass Spectrometry Imaging (MSI) accounts with the unique advantage of analyzing proteins and metabolites (lipids) while preserving their original localization; thus two dimensional maps can be obtained. Main molecular alterations were investigated in a rabbit model in response to early development of atherosclerosis. Aortic arterial layers (intima and media) and calcified regions were investigated in detail by MALDI-MSI and proteins and lipids specifically defining those areas of interest were identified. These data further complement main findings previously published in J Proteomics (M. Martin-Lorenzo et al., J. Proteomics. (In press); M. Martin-Lorenzo et al., J. Proteomics 108 (2014) 465-468.) [1,2].
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Affiliation(s)
- Marta Martin-Lorenzo
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Madrid, Spain
| | - Benjamin Balluff
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aroa S. Maroto
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Madrid, Spain
| | - Ricardo J. Carreira
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rene J.M. van Zeijl
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Fernando de la Cuesta
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | - Maria G Barderas
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | | | - Luis R Padial
- Department of Cardiology, Hospital Virgen de la Salud, SESCAM, Toledo, Spain
| | - Liam A. McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Fernando Vivanco
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Madrid, Spain
- Department of Biochemistry and Molecular Biology I, Universidad Complutense, Madrid, Spain
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24
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Martin-Lorenzo M, Balluff B, Maroto AS, Carreira RJ, van Zeijl RJM, Gonzalez-Calero L, de la Cuesta F, Barderas MG, Lopez-Almodovar LF, Padial LR, McDonnell LA, Vivanco F, Alvarez-Llamas G. Molecular anatomy of ascending aorta in atherosclerosis by MS Imaging: Specific lipid and protein patterns reflect pathology. J Proteomics 2015; 126:245-51. [PMID: 26079611 DOI: 10.1016/j.jprot.2015.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 12/22/2022]
Abstract
The molecular anatomy of healthy and atherosclerotic tissue is pursued here to identify ongoing molecular changes in atherosclerosis development. Subclinical atherosclerosis cannot be predicted and novel therapeutic targets are needed. Mass spectrometry imaging (MSI) is a novel unexplored ex vivo imaging approach in CVD able to provide in-tissue molecular maps. A rabbit model of early atherosclerosis was developed and high-spatial-resolution MALDI-MSI was applied to comparatively analyze histologically-based arterial regions of interest from control and early atherosclerotic aortas. Specific protocols were applied to identify lipids and proteins significantly altered in response to atherosclerosis. Observed protein alterations were confirmed by immunohistochemistry in rabbit tissue, and additionally in human aortas. Molecular features specifically defining different arterial regions were identified. Localized in the intima, increased expression of SFA and lysolipids and intimal spatial organization showing accumulation of PI, PG and SM point to endothelial dysfunction and triggered inflammatory response. TG, PA, SM and PE-Cer were identified specifically located in calcified regions. Thymosin β4 (TMSB4X) protein was upregulated in intima versus media layer and also in response to atherosclerosis. This overexpression and localization was confirmed in human aortas. In conclusion, molecular histology by MS Imaging identifies spatial organization of arterial tissue in response to atherosclerosis.
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Affiliation(s)
- Marta Martin-Lorenzo
- Department of Immunology, IIS-Fundación Jiménez Díaz, UAM, REDinREN, Madrid, Spain
| | - Benjamin Balluff
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aroa S Maroto
- Department of Immunology, IIS-Fundación Jiménez Díaz, UAM, REDinREN, Madrid, Spain
| | - Ricardo J Carreira
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rene J M van Zeijl
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Fernando de la Cuesta
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | - Maria G Barderas
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
| | | | - Luis R Padial
- Department of Cardiology, Hospital Virgen de la Salud, SESCAM, Toledo, Spain
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Fernando Vivanco
- Department of Immunology, IIS-Fundación Jiménez Díaz, UAM, REDinREN, Madrid, Spain; Department of Biochemistry and Molecular Biology I, Universidad Complutense, Madrid, Spain
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25
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Crecelius AC, Schubert US, von Eggeling F. MALDI mass spectrometric imaging meets “omics”: recent advances in the fruitful marriage. Analyst 2015; 140:5806-20. [DOI: 10.1039/c5an00990a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI MSI) is a method that allows the investigation of the molecular content of surfaces, in particular, tissues, within its morphological context.
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Affiliation(s)
- A. C. Crecelius
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - U. S. Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - F. von Eggeling
- Jena Center for Soft Matter (JCSM)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Institute of Physical Chemistry
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26
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Affiliation(s)
- Bernhard Spengler
- Justus Liebig University Giessen, Institute of Inorganic and Analytical
Chemistry, Schubertstrasse
60, Building 16, 35392 Giessen, Germany
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