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Sarkar S, Zheng X, Clair GC, Kwon YM, You Y, Swensen AC, Webb-Robertson BJM, Nakayasu ES, Qian WJ, Metz TO. Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements. Trends Mol Med 2024:S1471-4914(24)00195-3. [PMID: 39152082 DOI: 10.1016/j.molmed.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Type 1 diabetes (T1D) is a devastating autoimmune disease for which advanced mass spectrometry (MS) methods are increasingly used to identify new biomarkers and better understand underlying mechanisms. For example, integration of MS analysis and machine learning has identified multimolecular biomarker panels. In mechanistic studies, MS has contributed to the discovery of neoepitopes, and pathways involved in disease development and identifying therapeutic targets. However, challenges remain in understanding the role of tissue microenvironments, spatial heterogeneity, and environmental factors in disease pathogenesis. Recent advancements in MS, such as ultra-fast ion-mobility separations, and single-cell and spatial omics, can play a central role in addressing these challenges. Here, we review recent advancements in MS-based molecular measurements and their role in understanding T1D.
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Affiliation(s)
- Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yu Mi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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2
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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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3
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Djambazova KV, van Ardenne JM, Spraggins JM. Advances in Imaging Mass Spectrometry for Biomedical and Clinical Research. Trends Analyt Chem 2023; 169:117344. [PMID: 38045023 PMCID: PMC10688507 DOI: 10.1016/j.trac.2023.117344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Imaging mass spectrometry (IMS) allows for the untargeted mapping of biomolecules directly from tissue sections. This technology is increasingly integrated into biomedical and clinical research environments to supplement traditional microscopy and provide molecular context for tissue imaging. IMS has widespread clinical applicability in the fields of oncology, dermatology, microbiology, and others. This review summarizes the two most widely employed IMS technologies, matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI), and covers technological advancements, including efforts to increase spatial resolution, specificity, and throughput. We also highlight recent biomedical applications of IMS, primarily focusing on disease diagnosis, classification, and subtyping.
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Affiliation(s)
- Katerina V. Djambazova
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jacqueline M. van Ardenne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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4
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Long ZG, Le JV, Katz BB, Lopez BG, Tenenbaum ED, Semmling B, Schmidt RJ, Grün F, Butts CT, Martin RW. Spatially resolved detection of small molecules from press-dried plant tissue using MALDI imaging. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11539. [PMID: 37915436 PMCID: PMC10617318 DOI: 10.1002/aps3.11539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 11/03/2023]
Abstract
Premise Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a chemical imaging method that can visualize spatial distributions of particular molecules. Plant tissue imaging has so far mostly used cryosectioning, which can be impractical for the preparation of large-area imaging samples, such as full flower petals. Imaging unsectioned plant tissue presents its own difficulties in extracting metabolites to the surface due to the waxy cuticle. Methods We address this by using established delipidation techniques combined with a solvent vapor extraction prior to applying the matrix with many low-concentration sprays. Results Using this procedure, we imaged tissue from three different plant species (two flowers and one carnivorous plant leaf). Material factorization analysis of the resulting data reveals a wide range of plant-specific small molecules with varying degrees of localization to specific portions of the tissue samples, while facilitating detection and removal of signal from background sources. Conclusions This work demonstrates applicability of MALDI-MSI to press-dried plant samples without freezing or cryosectioning, setting the stage for spatially resolved molecule identification. Increased mass resolution and inclusion of tandem mass spectrometry are necessary next steps to allow more specific and reliable compound identification.
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Affiliation(s)
- Zane G. Long
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
| | - Jonathan V. Le
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCalifornia92697‐3900USA
| | - Benjamin B. Katz
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
| | - Belen G. Lopez
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
| | | | - Bonnie Semmling
- The Chrysler Herbarium and Mycological Collection, School of Environmental and Biological SciencesRutgers UniversityNew BrunswickNew Jersey08901USA
| | - Ryan J. Schmidt
- Department of Ecology, Evolution, and Natural ResourcesRutgers UniversityNew BrunswickNew Jersey08901USA
| | - Felix Grün
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
| | - Carter T. Butts
- Departments of Sociology, Statistics, Computer Science, and Electrical Engineering and Computer ScienceUniversity of CaliforniaIrvineCalifornia92697USA
| | - Rachel W. Martin
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCalifornia92697‐3900USA
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5
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Ramalhete L, Vigia E, Araújo R, Marques HP. Proteomics-Driven Biomarkers in Pancreatic Cancer. Proteomes 2023; 11:24. [PMID: 37606420 PMCID: PMC10443269 DOI: 10.3390/proteomes11030024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. Currently, the sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets. This review aims to offer a comprehensive survey of proteomics' current status in pancreatic cancer research, specifically accentuating its applications and its potential to drastically enhance screening, diagnosis, and treatment response. With respect to screening and diagnostic precision, proteomics carries the capacity to augment the sensitivity and specificity of extant screening and diagnostic methodologies. Nonetheless, more research is imperative for validating potential biomarkers and establishing standard procedures for sample preparation and data analysis. Furthermore, proteomics presents opportunities for unveiling new biomarkers and therapeutic targets, as well as fostering the development of personalized treatment strategies based on protein expression patterns associated with treatment response. In conclusion, proteomics holds great promise for advancing our understanding of pancreatic cancer biology and improving patient outcomes. It is essential to maintain momentum in investment and innovation in this arena to unearth more groundbreaking discoveries and transmute them into practical diagnostic and therapeutic strategies in the clinical context.
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Affiliation(s)
- Luís Ramalhete
- Blood and Transplantation Center of Lisbon—Instituto Português do Sangue e da Transplantação, Alameda das Linhas de Torres, n° 117, 1769-001 Lisbon, Portugal
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- iNOVA4Health—Advancing Precision Medicine, RG11: Reno-Vascular Diseases Group, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
| | - Emanuel Vigia
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
| | - Rúben Araújo
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- CHRC—Comprehensive Health Research Centre, NOVA Medical School, 1150-199 Lisbon, Portugal
| | - Hugo Pinto Marques
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
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6
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Gonçalves JPL, Bollwein C, Noske A, Jacob A, Jank P, Loibl S, Nekljudova V, Fasching PA, Karn T, Marmé F, Müller V, Schem C, Sinn BV, Stickeler E, van Mackelenbergh M, Schmitt WD, Denkert C, Weichert W, Schwamborn K. Characterization of Hormone Receptor and HER2 Status in Breast Cancer Using Mass Spectrometry Imaging. Int J Mol Sci 2023; 24:ijms24032860. [PMID: 36769215 PMCID: PMC9918176 DOI: 10.3390/ijms24032860] [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: 12/10/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Immunohistochemical evaluation of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2 status stratify the different subtypes of breast cancer and define the treatment course. Triple-negative breast cancer (TNBC), which does not register receptor overexpression, is often associated with worse patient prognosis. Mass spectrometry imaging transcribes the molecular content of tissue specimens without requiring additional tags or preliminary analysis of the samples, being therefore an excellent methodology for an unbiased determination of tissue constituents, in particular tumor markers. In this study, the proteomic content of 1191 human breast cancer samples was characterized by mass spectrometry imaging and the epithelial regions were employed to train and test machine-learning models to characterize the individual receptor status and to classify TNBC. The classification models presented yielded high accuracies for estrogen and progesterone receptors and over 95% accuracy for classification of TNBC. Analysis of the molecular features revealed that vimentin overexpression is associated with TNBC, supported by immunohistochemistry validation, revealing a new potential target for diagnosis and treatment.
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Affiliation(s)
- Juliana Pereira Lopes Gonçalves
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstraße 18, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 80336 Munich, Germany
| | - Christine Bollwein
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstraße 18, 81675 Munich, Germany
| | - Aurelia Noske
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstraße 18, 81675 Munich, Germany
| | - Anne Jacob
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstraße 18, 81675 Munich, Germany
| | - Paul Jank
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg (UKGM), 35043 Marburg, Germany
| | - Sibylle Loibl
- German Breast Group (GBG), 63263 Neu-Isenburg, Germany
| | | | - Peter A. Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054 Erlangen, Germany
| | - Thomas Karn
- Department of Gynecology and Obstetrics, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Frederik Marmé
- Department of Obstetrics and Gynecology, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Volkmar Müller
- Department of Gynecology, Universitätsklinikum Hamburg-Eppendorf, 20251 Hamburg, Germany
| | | | | | - Elmar Stickeler
- Department of Obstetrics and Gynecology, University Hospital Aachen, 52074 Aachen, Germany
| | - Marion van Mackelenbergh
- Klinik für Gynäkologie und Geburtshilfe, Universitätsklinikum Schleswig-Holstein, 24105 Kiel, Germany
| | | | - Carsten Denkert
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg (UKGM), 35043 Marburg, Germany
| | - Wilko Weichert
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstraße 18, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 80336 Munich, Germany
| | - Kristina Schwamborn
- Institute of Pathology, School of Medicine, Technical University of Munich, Trogerstraße 18, 81675 Munich, Germany
- Correspondence:
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7
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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