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Piga I, Magni F, Smith A. The journey towards clinical adoption of MALDI-MS-based imaging proteomics: from current challenges to future expectations. FEBS Lett 2024; 598:621-634. [PMID: 38140823 DOI: 10.1002/1873-3468.14795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
Abstract
Among the spatial omics techniques available, mass spectrometry imaging (MSI) represents one of the most promising owing to its capability to map the distribution of hundreds of peptides and proteins, as well as other classes of biomolecules, within a complex sample background in a multiplexed and relatively high-throughput manner. In particular, matrix-assisted laser desorption/ionisation (MALDI-MSI) has come to the fore and established itself as the most widely used technique in clinical research. However, the march of this technique towards clinical utility has been hindered by issues related to method reproducibility, appropriate biocomputational tools, and data storage. Notwithstanding these challenges, significant progress has been achieved in recent years regarding multiple facets of the technology and has rendered it more suitable for a possible clinical role. As such, there is now more robust and extensive evidence to suggest that the technology has the potential to support clinical decision-making processes under appropriate circumstances. In this review, we will discuss some of the recent developments that have facilitated this progress and outline some of the more promising clinical proteomics applications which have been developed with a clear goal towards implementation in mind.
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Affiliation(s)
- Isabella Piga
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
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2
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Moore JL, Patterson NH, Norris JL, Caprioli RM. Prospective on Imaging Mass Spectrometry in Clinical Diagnostics. Mol Cell Proteomics 2023; 22:100576. [PMID: 37209813 PMCID: PMC10545939 DOI: 10.1016/j.mcpro.2023.100576] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Imaging mass spectrometry (IMS) is a molecular technology utilized for spatially driven research, providing molecular maps from tissue sections. This article reviews matrix-assisted laser desorption ionization (MALDI) IMS and its progress as a primary tool in the clinical laboratory. MALDI mass spectrometry has been used to classify bacteria and perform other bulk analyses for plate-based assays for many years. However, the clinical application of spatial data within a tissue biopsy for diagnoses and prognoses is still an emerging opportunity in molecular diagnostics. This work considers spatially driven mass spectrometry approaches for clinical diagnostics and addresses aspects of new imaging-based assays that include analyte selection, quality control/assurance metrics, data reproducibility, data classification, and data scoring. It is necessary to implement these tasks for the rigorous translation of IMS to the clinical laboratory; however, this requires detailed standardized protocols for introducing IMS into the clinical laboratory to deliver reliable and reproducible results that inform and guide patient care.
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Affiliation(s)
| | - Nathan Heath Patterson
- Frontier Diagnostics, Nashville, Tennessee, USA; Vanderbilt University Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jeremy L Norris
- Frontier Diagnostics, Nashville, Tennessee, USA; Vanderbilt University Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard M Caprioli
- Frontier Diagnostics, Nashville, Tennessee, USA; Vanderbilt University Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA; Departments of Biochemistry, Pharmacology, Chemistry, and Medicine, Vanderbilt University, Nashville, Tennessee, USA.
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3
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Liu L, Wang Z, Zhang Q, Mei Y, Li L, Liu H, Wang Z, Yang L. Ion Mobility Mass Spectrometry for the Separation and Characterization of Small Molecules. Anal Chem 2023; 95:134-151. [PMID: 36625109 DOI: 10.1021/acs.analchem.2c02866] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Longchan Liu
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Ziying Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Qian Zhang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Yuqi Mei
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Linnan Li
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Zhengtao Wang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
| | - Li Yang
- The MOE Key Laboratory of Standardization of Chinese Medicines, The SATCM Key Laboratory of New Resources and Quality Evaluation of Chinese Medicines, The Shanghai Key Laboratory for Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China.,Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, China
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Riefolo M, Conti M, Longhi S, Fabbrizio B, Leone O. Amyloidosis: What does pathology offer? The evolving field of tissue biopsy. Front Cardiovasc Med 2022; 9:1081098. [PMID: 36545023 PMCID: PMC9760761 DOI: 10.3389/fcvm.2022.1081098] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Since the mid-nineteenth century pathology has followed the convoluted story of amyloidosis, recognized its morphology in tissues and made identification possible using specific staining. Since then, pathology studies have made a significant contribution and advanced knowledge of the disease, so providing valuable information on the pathophysiology of amyloid aggregation and opening the way to clinical studies and non-invasive diagnostic techniques. As amyloidosis is a heterogeneous disease with various organ and tissue deposition patterns, histology evaluation, far from offering a simple yes/no indication of amyloid presence, can provide a wide spectrum of qualitative and quantitative information related to and changing with the etiology of the disease, the comorbidities and the clinical characteristics of patients. With the exception of cardiac transthyretin related amyloidosis cases, which today can be diagnosed using non-biopsy algorithms when stringent clinical criteria are met, tissue biopsy is still an essential tool for a definitive diagnosis in doubtful cases and also to define etiology by typing amyloid fibrils. This review describes the histologic approach to amyloidosis today and the current role of tissue screening biopsy or targeted organ biopsy protocols in the light of present diagnostic algorithms and various clinical situations, with particular focus on endomyocardial and renal biopsies. Special attention is given to techniques for typing amyloid fibril proteins, necessary for the new therapies available today for cardiac transthyretin related amyloidosis and to avoid patients receiving inappropriate chemotherapy in presence of plasma cell dyscrasia unrelated to amyloidosis. As the disease is still burdened with high mortality, the role of tissue biopsy in early diagnosis to assure prompt treatment is also mentioned.
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Affiliation(s)
- Mattia Riefolo
- Cardiovascular and Cardiac Transplant Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy,Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Matteo Conti
- Pharmacology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy,Public Health Department, AUSL Imola, Bologna, Italy
| | - Simone Longhi
- Department of Cardiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Benedetta Fabbrizio
- Department of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Ornella Leone
- Cardiovascular and Cardiac Transplant Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy,*Correspondence: Ornella Leone,
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Shintani-Domoto Y, Sugiura Y, Ogawa M, Sugiyama E, Abe H, Sakatani T, Ohashi R, Ushiku T, Fukayama M. N-terminal peptide fragment constitutes core of amyloid deposition of serum amyloid A: An imaging mass spectrometry study. PLoS One 2022; 17:e0275993. [PMID: 36240260 PMCID: PMC9565386 DOI: 10.1371/journal.pone.0275993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Serum amyloid A (SAA) is an acute phase protein, which undergoes structural changes and deposits in the extracellular matrix, causing organ damage. Systemic AA amyloidosis is a relatively common amyloid subtype among the more than 30 amyloid subtypes, but the mechanism of amyloid fibril formation remains unclear. In this study, we investigated the tissue distribution of SAA derived peptides in formalin-fixed paraffin embedded (FFPE) specimens of human myocardium with amyloidosis using matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS). In the whole SAA protein, four trypsin-digested peptides in the range of SAA2-67 were visualized and the N-terminal peptide; SAA2-15, was selectively localized in the Congo red-positive region. The C-terminal peptides; SAA47-62, SAA48-62, and SAA63-67 were detected not only in the Congo red-positive region but also in the surrounding negative region. Our results demonstrate that the N-terminal SAA2-15 plays a critical role in the formation of AA amyloid fibril, as previously reported. Roles of the C-terminal peptides require further investigation.
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Affiliation(s)
- Yukako Shintani-Domoto
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Diagnostic Pathology, Nippon Medical School Hospital, Tokyo, Japan
- * E-mail:
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo, Japan
| | - Makiko Ogawa
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Eiji Sugiyama
- Department of Biochemistry, Keio University School of Medicine, Tokyo, Japan
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Sakatani
- Department of Diagnostic Pathology, Nippon Medical School Hospital, Tokyo, Japan
| | - Ryuji Ohashi
- Department of Diagnostic Pathology, Nippon Medical School Hospital, Tokyo, Japan
- Department of Integrated Diagnostic Pathology, Nippon Medical School, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Asahi Tele Pathology Center, Asahi General Hospital, Asahi-City, Chiba, Japan
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Rognoni P, Mazzini G, Caminito S, Palladini G, Lavatelli F. Dissecting the Molecular Features of Systemic Light Chain (AL) Amyloidosis: Contributions from Proteomics. ACTA ACUST UNITED AC 2021; 57:medicina57090916. [PMID: 34577839 PMCID: PMC8471912 DOI: 10.3390/medicina57090916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/23/2021] [Accepted: 08/29/2021] [Indexed: 02/08/2023]
Abstract
Amyloidoses are characterized by aggregation of proteins into highly ordered amyloid fibrils, which deposit in the extracellular space of tissues, leading to organ dysfunction. In AL (amyloid light chain) amyloidosis, the most common form in Western countries, the amyloidogenic precursor is a misfolding-prone immunoglobulin light chain (LC), which, in the systemic form, is produced in excess by a plasma cell clone and transported to target organs though blood. Due to the primary role that proteins play in the pathogenesis of amyloidoses, mass spectrometry (MS)-based proteomic studies have gained an established position in the clinical management and research of these diseases. In AL amyloidosis, in particular, proteomics has provided important contributions for characterizing the precursor light chain, the composition of the amyloid deposits and the mechanisms of proteotoxicity in target organ cells and experimental models of disease. This review will provide an overview of the major achievements of proteomic studies in AL amyloidosis, with a presentation of the most recent acquisitions and a critical discussion of open issues and ongoing trends.
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Affiliation(s)
- Paola Rognoni
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, V.le Golgi 19, 27100 Pavia, Italy; (G.M.); (S.C.); (G.P.)
- Correspondence: (P.R.); (F.L.); Tel.: +39-0382502984 (P.R.); +39-0382502994 (F.L.)
| | - Giulia Mazzini
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, V.le Golgi 19, 27100 Pavia, Italy; (G.M.); (S.C.); (G.P.)
| | - Serena Caminito
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, V.le Golgi 19, 27100 Pavia, Italy; (G.M.); (S.C.); (G.P.)
- Department of Molecular Medicine, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy
| | - Giovanni Palladini
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, V.le Golgi 19, 27100 Pavia, Italy; (G.M.); (S.C.); (G.P.)
- Department of Molecular Medicine, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy
| | - Francesca Lavatelli
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, V.le Golgi 19, 27100 Pavia, Italy; (G.M.); (S.C.); (G.P.)
- Department of Molecular Medicine, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy
- Correspondence: (P.R.); (F.L.); Tel.: +39-0382502984 (P.R.); +39-0382502994 (F.L.)
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