1
|
Chardin D, Jing L, Chazal-Ngo-Mai M, Guigonis JM, Rigau V, Goze C, Duffau H, Virolle T, Pourcher T, Burel-Vandenbos F. Identification of Metabolomic Markers in Frozen or Formalin-Fixed and Paraffin-Embedded Samples of Diffuse Glioma from Adults. Int J Mol Sci 2023; 24:16697. [PMID: 38069019 PMCID: PMC10705927 DOI: 10.3390/ijms242316697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The aim of this study was to identify metabolomic signatures associated with the gliomagenesis pathway (IDH-mutant or IDH-wt) and tumor grade of diffuse gliomas (DGs) according to the 2021 WHO classification on frozen samples and to evaluate the diagnostic performances of these signatures in tumor samples that are formalin-fixed and paraffin-embedded (FFPE). An untargeted metabolomic study was performed using liquid chromatography/mass spectrometry on a cohort of 213 DG samples. Logistic regression with LASSO penalization was used on the frozen samples to build classification models in order to identify IDH-mutant vs. IDH-wildtype DG and high-grade vs low-grade DG samples. 2-Hydroxyglutarate (2HG) was a metabolite of interest to predict IDH mutational status and aminoadipic acid (AAA) and guanidinoacetic acid (GAA) were significantly associated with grade. The diagnostic performances of the models were 82.6% AUC, 70.6% sensitivity and 80.4% specificity for 2HG to predict IDH status and 84.7% AUC, 78.1% sensitivity and 73.4% specificity for AAA and GAA to predict grade from FFPE samples. Thus, this study showed that AAA and GAA are two novel metabolites of interest in DG and that metabolomic data can be useful in the classification of DG, both in frozen and FFPE samples.
Collapse
Affiliation(s)
- David Chardin
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Cote d’Azur (UCA), 06000 Nice, France; (D.C.); (L.J.); (J.-M.G.); (T.P.)
- Service de Médecine Nucléaire, Centre Antoine Lacassagne, Université Cote d’Azur, 06000 Nice, France
| | - Lun Jing
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Cote d’Azur (UCA), 06000 Nice, France; (D.C.); (L.J.); (J.-M.G.); (T.P.)
| | | | - Jean-Marie Guigonis
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Cote d’Azur (UCA), 06000 Nice, France; (D.C.); (L.J.); (J.-M.G.); (T.P.)
| | - Valérie Rigau
- Department of Pathology and Oncobiology, Institute for Neurosciences of Montpellier, INSERM U1051, University Hospital of Montpellier, 34000 Montpellier, France;
| | - Catherine Goze
- Laboratory of Solid Tumors Biology, Institute for Neurosciences of Montpellier, INSERM U1051, University Hospital of Montpellier, 34000 Montpellier, France;
| | - Hugues Duffau
- Neurosurgery Department, Institute for Neurosciences of Montpellier, INSERM U1051, University Hospital of Montpellier, 34000 Montpellier, France;
| | - Thierry Virolle
- Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-Tumor Heterogeneity”, Institut de Biologie Valrose, Université Côte D’Azur, CNRS, INSERM, 06000 Nice, France;
| | - Thierry Pourcher
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des Sciences du Vivant Frederic Joliot, Commissariat a l’Energie Atomique et aux Energies Alternatives (CEA), Université Cote d’Azur (UCA), 06000 Nice, France; (D.C.); (L.J.); (J.-M.G.); (T.P.)
| | - Fanny Burel-Vandenbos
- Department of Pathology, University Hospital of Nice, 06000 Nice, France;
- Laboratory “Cancer Stem Cell Plasticity and Functional Intra-Tumor Heterogeneity”, UMR CNRS 7277-UMR INSERM 1091, Institute of Biology Valrose, University Côte d’Azur, 06000 Nice, France
| |
Collapse
|
2
|
Maciel LÍL, Bernardo RA, Martins RO, Batista Junior AC, Oliveira JVA, Chaves AR, Vaz BG. Desorption electrospray ionization and matrix-assisted laser desorption/ionization as imaging approaches for biological samples analysis. Anal Bioanal Chem 2023:10.1007/s00216-023-04783-8. [PMID: 37329466 DOI: 10.1007/s00216-023-04783-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/19/2023]
Abstract
The imaging of biological tissues can offer valuable information about the sample composition, which improves the understanding of analyte distribution in such complex samples. Different approaches using mass spectrometry imaging (MSI), also known as imaging mass spectrometry (IMS), enabled the visualization of the distribution of numerous metabolites, drugs, lipids, and glycans in biological samples. The high sensitivity and multiple analyte evaluation/visualization in a single sample provided by MSI methods lead to various advantages and overcome drawbacks of classical microscopy techniques. In this context, the application of MSI methods, such as desorption electrospray ionization-MSI (DESI-MSI) and matrix-assisted laser desorption/ionization-MSI (MALDI-MSI), has significantly contributed to this field. This review discusses the evaluation of exogenous and endogenous molecules in biological samples using DESI and MALDI imaging. It offers rare technical insights not commonly found in the literature (scanning speed and geometric parameters), making it a comprehensive guide for applying these techniques step-by-step. Furthermore, we provide an in-depth discussion of recent research findings on using these methods to study biological tissues.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Boniek Gontijo Vaz
- Instituto de Química, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil.
| |
Collapse
|
3
|
Giampà M, Andersen MK, Krossa S, Denti V, Smith A, Moestue SA. Visualization of Small Intact Proteins in Breast Cancer FFPE Tissue. Methods Mol Biol 2023; 2688:161-172. [PMID: 37410292 DOI: 10.1007/978-1-0716-3319-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Molecular visualization of metabolites, lipids, and proteins by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is becoming an in-demand analytical approach to aid the histopathological analysis of breast cancer. Particularly, proteins seem to play a role in cancer progression, and specific proteins are currently used in the clinic for staging. Formalin-fixed paraffin-embedded (FFPE) tissues are ideal for correlating the molecular markers with clinical outcomes due to their long-term storage. So far, to obtain proteomic information by MSI from this kind of tissue, antigen retrieval and tryptic digestion steps are required. In this chapter, we present a protocol to spatially detect small proteins in tumor and necrotic regions of patient-derived breast cancer xenograft FFPE tissues without employing any on-tissue digestion. This protocol can be used for other kinds of FFPE tissue following specific optimization of the sample preparation phases.
Collapse
Affiliation(s)
- Marco Giampà
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.
| | - Maria K Andersen
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Sebastian Krossa
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Vanna Denti
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, Vedano al Lambro, Italy
| | - Andrew Smith
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, Vedano al Lambro, Italy
| | - Siver Andreas Moestue
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Pharmacy, Nord University, Bodø, Norway
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Isberg OG, Giunchiglia V, McKenzie JS, Takats Z, Jonasson JG, Bodvarsdottir SK, Thorsteinsdottir M, Xiang Y. Automated Cancer Diagnostics via Analysis of Optical and Chemical Images by Deep and Shallow Learning. Metabolites 2022; 12:455. [PMID: 35629959 PMCID: PMC9143055 DOI: 10.3390/metabo12050455] [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: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Optical microscopy has long been the gold standard to analyse tissue samples for the diagnostics of various diseases, such as cancer. The current diagnostic workflow is time-consuming and labour-intensive, and manual annotation by a qualified pathologist is needed. With the ever-increasing number of tissue blocks and the complexity of molecular diagnostics, new approaches have been developed as complimentary or alternative solutions for the current workflow, such as digital pathology and mass spectrometry imaging (MSI). This study compares the performance of a digital pathology workflow using deep learning for tissue recognition and an MSI approach utilising shallow learning to annotate formalin-fixed and paraffin-embedded (FFPE) breast cancer tissue microarrays (TMAs). Results show that both deep learning algorithms based on conventional optical images and MSI-based shallow learning can provide automated diagnostics with F1-scores higher than 90%, with the latter intrinsically built on biochemical information that can be used for further analysis.
Collapse
Affiliation(s)
- Olof Gerdur Isberg
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, 107 Reykjavik, Iceland
- Biomedical Center, School of Health Sciences, University of Iceland, 101 Reykjavik, Iceland;
| | - Valentina Giunchiglia
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
| | - James S. McKenzie
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
| | - Jon Gunnlaugur Jonasson
- Department of Pathology, Landspitali the National University Hospital, Hringbraut, 101 Reykjavik, Iceland;
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | | | - Margret Thorsteinsdottir
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, 107 Reykjavik, Iceland
- Biomedical Center, School of Health Sciences, University of Iceland, 101 Reykjavik, Iceland;
| | - Yuchen Xiang
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (O.G.I.); (V.G.); (J.S.M.); (Z.T.)
| |
Collapse
|
6
|
Cintron-Diaz YL, Gomez-Hernandez ME, Verhaert MMHA, Verhaert PDEM, Fernandez-Lima F. Spatially Resolved Neuropeptide Characterization from Neuropathological Formalin-Fixed, Paraffin-Embedded Tissue Sections by a Combination of Imaging MALDI FT-ICR Mass Spectrometry Histochemistry and Liquid Extraction Surface Analysis-Trapped Ion Mobility Spectrometry-Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:681-687. [PMID: 35258288 PMCID: PMC9390806 DOI: 10.1021/jasms.1c00376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
To make the vast collections of well-documented human clinical samples archived in biobanks accessible for mass spectrometry imaging (MSI), recent developments have focused on the label-free top-down MS analysis of neuropeptides in sections of formalin-fixed, paraffin-embedded (FFPE) tissues. In analogy to immunohistochemistry (IHC), this variant of MSI has been designated MSHC (mass spectrometry histochemistry). Besides the detection and localization of neuropeptide and other biomolecular MS signals in these FFPE samples, there is great interest in their molecular identification and full characterization. We here used matrix assisted laser desorption ionization (MALDI) MSI employing ultrahigh-resolution FT-ICR MS on 2,5-dihydroxybenzoic acid (DHB) coated five-micron sections of human FFPE pituitary to demonstrate clear isotope patterns and elemental composition assignment of neuropeptides (with ∼1 ppm mass accuracy). Besides tandem MS fragmentation pattern analysis to deduce or confirm amino acid sequence information (Arg-vasopressin for the case presented here), there is a need for orthogonal primary structure characterization of the peptide-like MS signals of biomolecules desorbed directly off FFPE tissue sections. In the present work, we performed liquid extraction surface analysis (LESA) extractions on consecutive (uncoated) tissue slices. This enables the successful characterization by ion mobility MS of vasopressin present in FFPE material. Differences in sequence coverage are discussed on the basis of the mobility selected collision induced dissociation (CID), electron capture dissociation (ECD), and UV photodissociation (UVPD) MS/MS. Using Arg-vasopressin as model case (a peptide with a disulfide bridged ring structure), we illustrate the use of LESA in combination with a reduction agent for effective sequencing using mobility selected CID, ECD, and UVPD MS/MS.
Collapse
Affiliation(s)
- Yarixa L Cintron-Diaz
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
| | - Mario E Gomez-Hernandez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
| | - Marthe M H A Verhaert
- ProteoFormiX, JLABS@BE, Janssen Pharmaceutica Campus, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Peter D E M Verhaert
- ProteoFormiX, JLABS@BE, Janssen Pharmaceutica Campus, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
- Biomolecular Science Institute, Florida International University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
| |
Collapse
|
7
|
Ogrinc N, Attencourt C, Colin E, Boudahi A, Tebbakha R, Salzet M, Testelin S, Dakpé S, Fournier I. Mass Spectrometry-Based Differentiation of Oral Tongue Squamous Cell Carcinoma and Nontumor Regions With the SpiderMass Technology. FRONTIERS IN ORAL HEALTH 2022; 3:827360. [PMID: 35309279 PMCID: PMC8929397 DOI: 10.3389/froh.2022.827360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/26/2022] [Indexed: 12/14/2022] Open
Abstract
Oral cavity cancers are the 15th most common cancer with more than 350,000 new cases and ~178,000 deaths each year. Among them, squamous cell carcinoma (SCC) accounts for more than 90% of tumors located in the oral cavity and on oropharynx. For the oral cavity SCC, the surgical resection remains the primary course of treatment. Generally, surgical margins are defined intraoperatively using visual and tactile elements. However, in 15–30% of cases, positive margins are found after histopathological examination several days postsurgery. Technologies based on mass spectrometry (MS) were recently developed to help guide surgical resection. The SpiderMass technology is designed for in-vivo real-time analysis under minimally invasive conditions. This instrument achieves tissue microsampling and real-time molecular analysis with the combination of a laser microprobe and a mass spectrometer. It ultimately acts as a tool to support histopathological decision-making and diagnosis. This pilot study included 14 patients treated for tongue SCC (T1 to T4) with the surgical resection as the first line of treatment. Samples were first analyzed by a pathologist to macroscopically delineate the tumor, dysplasia, and peritumoral areas. The retrospective and prospective samples were sectioned into three consecutive sections and thaw-mounted on slides for H&E staining (7 μm), SpiderMass analysis (20 μm), and matrix-assisted laser desorption ionization (MALDI) MS imaging (12 μm). The SpiderMass microprobe collected lipidometabolic profiles of the dysplasia, tumor, and peritumoral regions annotated by the pathologist. The MS spectra were then subjected to the multivariate statistical analysis. The preliminary data demonstrate that the lipidometabolic molecular profiles collected with the SpiderMass are significantly different between the tumor and peritumoral regions enabling molecular classification to be established by linear discriminant analysis (LDA). MALDI images of the different samples were submitted to segmentation for cross instrument validation and revealed additional molecular discrimination within the tumor and nontumor regions. These very promising preliminary results show the applicability of the SpiderMass to SCC of the tongue and demonstrate its interest in the surgical treatment of head and neck cancers.
Collapse
Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse – PRISM, Lille, France
- *Correspondence: Nina Ogrinc
| | - Christophe Attencourt
- Department of Pathology, CHU Amiens-Picardie, Amiens, France
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
| | - Emilien Colin
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
| | - Ahmed Boudahi
- Department of Pathology, CHU Amiens-Picardie, Amiens, France
| | - Riad Tebbakha
- Tumorothèque de Picardie, CHU Amiens-Picardie, Amiens, 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
| | - Sylvie Testelin
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
| | - Stéphanie Dakpé
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
- Stéphanie Dakpé
| | - 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
- Isabelle Fournier
| |
Collapse
|