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Guan C, Kong L. Mass spectrometry imaging in pulmonary disorders. Clin Chim Acta 2024; 561:119835. [PMID: 38936534 DOI: 10.1016/j.cca.2024.119835] [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: 03/26/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Mass Spectrometry Imaging (MSI) represents a novel and advancing technology that offers unparalleled in situ characterization of tissues. It provides comprehensive insights into the chemical structures, relative abundances, and spatial distributions of a vast array of both identified and unidentified endogenous and exogenous compounds, a capability not paralleled by existing analytical methodologies. Recent scholarly endeavors have increasingly explored the utility of MSI in the adjunct diagnosis and biomarker research of pulmonary disorders, including but not limited to lung cancer. Concurrently, MSI has proven instrumental in elucidating the spatiotemporal dynamics of various pharmacological agents. This review concisely delineates the fundamental principles underpinning MSI, its applications in pulmonary disease diagnosis, biomarker discovery, and drug distribution investigations. Additionally, it presents a forward-looking perspective on the prospective trajectories of MSI technological advancements.
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Affiliation(s)
- Chunliu Guan
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China
| | - Lu Kong
- Key Laboratory of Environment Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China.
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Dannhorn A, Kazanc E, Flint L, Guo F, Carter A, Hall AR, Jones SA, Poulogiannis G, Barry ST, Sansom OJ, Bunch J, Takats Z, Goodwin RJA. Morphological and molecular preservation through universal preparation of fresh-frozen tissue samples for multimodal imaging workflows. Nat Protoc 2024:10.1038/s41596-024-00987-z. [PMID: 38806741 DOI: 10.1038/s41596-024-00987-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 05/30/2024]
Abstract
The landscape of tissue-based imaging modalities is constantly and rapidly evolving. While formalin-fixed, paraffin-embedded material is still useful for histological imaging, the fixation process irreversibly changes the molecular composition of the sample. Therefore, many imaging approaches require fresh-frozen material to get meaningful results. This is particularly true for molecular imaging techniques such as mass spectrometry imaging, which are widely used to probe the spatial arrangement of the tissue metabolome. As high-quality fresh-frozen tissues are limited in their availability, any sample preparation workflow they are subjected to needs to ensure morphological and molecular preservation of the tissues and be compatible with as many of the established and emerging imaging techniques as possible to obtain the maximum possible insights from the tissues. Here we describe a universal sample preparation workflow, from the initial step of freezing the tissues to the cold embedding in a new hydroxypropyl methylcellulose/polyvinylpyrrolidone-enriched hydrogel and the generation of thin tissue sections for analysis. Moreover, we highlight the optimized storage conditions that limit molecular and morphological degradation of the sections. The protocol is compatible with human and plant tissues and can be easily adapted for the preparation of alternative sample formats (e.g., three-dimensional cell cultures). The integrated workflow is universally compatible with histological tissue analysis, mass spectrometry imaging and imaging mass cytometry, as well as spatial proteomic, genomic and transcriptomic tissue analysis. The protocol can be completed within 4 h and requires minimal prior experience in the preparation of tissue samples for multimodal imaging experiments.
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Affiliation(s)
- Andreas Dannhorn
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Emine Kazanc
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Lucy Flint
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Fei Guo
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Alfie Carter
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Andrew R Hall
- Safety Innovations, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Stewart A Jones
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | - Simon T Barry
- Bioscience, Discovery, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington, UK
| | - Zoltan Takats
- Department of Digestion, Metabolism and Reproduction, Sir Alexander Fleming Building, Imperial College London, London, UK
| | - Richard J A Goodwin
- Imaging and Data analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK.
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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Pattaroni C, Begka C, Cardwell B, Jaffar J, Macowan M, Harris NL, Westall GP, Marsland BJ. Multi-omics integration reveals a nonlinear signature that precedes progression of lung fibrosis. Clin Transl Immunology 2024; 13:e1485. [PMID: 38269243 PMCID: PMC10807351 DOI: 10.1002/cti2.1485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
Objectives Idiopathic pulmonary fibrosis (IPF) is a devastating progressive interstitial lung disease with poor outcomes. While decades of research have shed light on pathophysiological mechanisms associated with the disease, our understanding of the early molecular events driving IPF and its progression is limited. With this study, we aimed to model the leading edge of fibrosis using a data-driven approach. Methods Multiple omics modalities (transcriptomics, metabolomics and lipidomics) of healthy and IPF lung explants representing different stages of fibrosis were combined using an unbiased approach. Multi-Omics Factor Analysis of datasets revealed latent factors specifically linked with established fibrotic disease (Factor1) and disease progression (Factor2). Results Features characterising Factor1 comprised well-established hallmarks of fibrotic disease such as defects in surfactant, epithelial-mesenchymal transition, extracellular matrix deposition, mitochondrial dysfunction and purine metabolism. Comparatively, Factor2 identified a signature revealing a nonlinear trajectory towards disease progression. Molecular features characterising Factor2 included genes related to transcriptional regulation of cell differentiation, ciliogenesis and a subset of lipids from the endocannabinoid class. Machine learning models, trained upon the top transcriptomics features of each factor, accurately predicted disease status and progression when tested on two independent datasets. Conclusion This multi-omics integrative approach has revealed a unique signature which may represent the inflection point in disease progression, representing a promising avenue for the identification of therapeutic targets aimed at addressing the progressive nature of the disease.
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Affiliation(s)
- Céline Pattaroni
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Christina Begka
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Bailey Cardwell
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Jade Jaffar
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Matthew Macowan
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Nicola L Harris
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
| | - Glen P Westall
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
- Department of Respiratory MedicineAlfred HospitalMelbourneVICAustralia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational MedicineMonash UniversityMelbourneVICAustralia
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