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Bindi G, Pagani L, Ceku J, de Oliveira GS, Porto NS, Monza N, Denti V, Mescia F, Chinello C, Fraggetta F, Magni F, Pagni F, Alberici F, L'Imperio V, Smith A. Feasibility of MALDI-MSI-Based Proteomics Using Bouin-Fixed Pathology Samples: Untapping the Goldmine of Nephropathology Archives. J Proteome Res 2024; 23:2542-2551. [PMID: 38869849 DOI: 10.1021/acs.jproteome.4c00198] [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] [Indexed: 06/14/2024]
Abstract
The application of innovative spatial proteomics techniques, such as those based upon matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) technology, has the potential to impact research in the field of nephropathology. Notwithstanding, the possibility to apply this technology in more routine diagnostic contexts remains limited by the alternative fixatives employed by this ultraspecialized diagnostic field, where most nephropathology laboratories worldwide use bouin-fixed paraffin-embedded (BFPE) samples. Here, the feasibility of performing MALDI-MSI on BFPE renal tissue is explored, evaluating variability within the trypsin-digested proteome as a result of different preanalytical conditions and comparing them with the more standardized formalin-fixed paraffin-embedded (FFPE) counterparts. A large proportion of the features (270, 68.9%) was detected in both BFPE and FFPE renal samples, demonstrating only limited variability in signal intensity (10.22-10.06%). Samples processed with either fixative were able to discriminate the principal parenchyma regions along with diverse renal substructures, such as glomeruli, tubules, and vessels. This was observed when performing an additional "stress test", showing comparable results in both BFPE and FFPE samples when the distribution of several amyloid fingerprint proteins was mapped. These results suggest the utility of BFPE tissue specimens in MSI-based nephropathology research, further widening their application in this field.
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Affiliation(s)
- Greta Bindi
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
| | - Lisa Pagani
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
| | - Joranda Ceku
- Department of Medicine and Surgery, Pathology, IRCCS Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza 20900, MB, Italy
| | - Glenda Santos de Oliveira
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
| | - Natalia Shelly Porto
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
| | - Nicole Monza
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
| | - Vanna Denti
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
| | - Federica Mescia
- Nephrology Unit, Spedali Civili Hospital, ASST Spedali Civili di Brescia, Brescia 25123, BS, Italy
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia 25123, BS, Italy
| | - Clizia Chinello
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
| | - Filippo Fraggetta
- Pathology Unit, Gravina Hospital Caltagirone, ASP Catania, Caltagirone 95041, CT, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, IRCCS Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza 20900, MB, Italy
| | - Federico Alberici
- Nephrology Unit, Spedali Civili Hospital, ASST Spedali Civili di Brescia, Brescia 25123, BS, Italy
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia 25123, BS, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, IRCCS Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza 20900, MB, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro 20854, MB, Italy
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Bindi G, Smith A, Oliveira G, Eccher A, Vatrano S, Alberici F, Cazzaniga G, Galimberti S, Capitoli G, Magni F, Pagni F, L'Imperio V. Spatial resolution of renal amyloid deposits through MALDI-MSI: a combined digital and molecular approach to monoclonal gammopathies. J Clin Pathol 2024; 77:402-410. [PMID: 36813560 DOI: 10.1136/jcp-2023-208790] [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: 01/17/2023] [Accepted: 02/10/2023] [Indexed: 02/24/2023]
Abstract
AIMS Identification and characterisation of monoclonal gammopathies of renal significance (MGRS) is critical for therapeutic purposes. Amyloidosis represents one of the most common forms of MGRS, and renal biopsy remains the gold standard for their classification, although mass spectrometry has shown greater sensitivity in this area. METHODS In the present study, a new in situ proteomic technique, matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI), is investigated as an alternative to conventional laser capture microdissection MS for the characterisation of amyloids. MALDI-MSI was performed on 16 cases (3 lambda light chain amyloidosis (AL), 3 AL kappa, 3 serum amyloid A amyloidosis (SAA), 2 lambda light chain deposition disease (LCDD), 2 challenging amyloid cases and 3 controls). Analysis began with regions of interest labelled by the pathologist, and then automatic segmentation was performed. RESULTS MALDI-MSI correctly identified and typed cases with known amyloid type (AL kappa, AL lambda and SAA). A 'restricted fingerprint' for amyloid detection composed of apolipoprotein E, serum amyloid protein and apolipoprotein A1 showed the best automatic segmentation performance (area under the curve >0.7). CONCLUSIONS MALDI-MSI correctly assigned minimal/challenging cases of amyloidosis to the correct type (AL lambda) and identified lambda light chains in LCDD cases, highlighting the promising role of MALDI-MSI for amyloid typing.
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Affiliation(s)
- Greta Bindi
- Department of Medicine and Surgery, Proteomics and Metabolomics Units, University of Milano-Bicocca, Monza, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Units, University of Milano-Bicocca, Monza, Italy
| | - Glenda Oliveira
- Department of Medicine and Surgery, Proteomics and Metabolomics Units, University of Milano-Bicocca, Monza, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Simona Vatrano
- Pathology Unit, ASP Catania, "Gravina" Hospital, Caltagirone, Italy
| | - Federico Alberici
- Nephrology Unit, Spedali Civili Hospital, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Giorgio Cazzaniga
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy
| | - Stefania Galimberti
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Giulia Capitoli
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Proteomics and Metabolomics Units, University of Milano-Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy
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Dabija LG, Yousefi-Taemeh M, Duli E, Lemaire M, Ifa DR. Assessment of MALDI matrices for the detection and visualization of phosphatidylinositols and phosphoinositides in mouse kidneys through matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). Anal Bioanal Chem 2024; 416:1857-1865. [PMID: 38319357 DOI: 10.1007/s00216-024-05184-1] [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: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
Phosphatidylinositols and their phosphorylated derivatives, known as phosphoinositides, are crucial in cellular processes, with their abnormalities linked to various diseases. Thus, identifying and measuring phosphoinositide levels in tissues are crucial for understanding their contributions to cellular processes and disease development. One powerful technique for mapping the spatial distribution of molecules in biological samples is matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). This technique allows for the simultaneous detection and analysis of multiple lipid classes in situ, making it invaluable for unbiased lipidomic studies. However, detecting phosphoinositides with MALDI-MSI is challenging due to their relatively low abundance in tissues and complex matrix effects. Addressing this, our study focused on optimizing matrix selection and thickness for better detection of phosphatidylinositols and their phosphorylated forms in mouse kidney tissues. Various matrices were assessed, including 9AA, DAN, CMBT, and DHA, adjusting their coating to improve ionization efficiency. Our results demonstrate that DAN, DHA, and CMBT matrices produced high-intensity chemical images of phosphatidylinositol distributions within kidney sections. These matrices, particularly DAN, DHA, and CMBT, allowed the identification of even low-abundance phosphoinositides, through tentative identifications. Notably, DAN and DHA served as optimal candidates due to their prominent detection and ability to map a majority of phosphatidylinositol species, while CMBT showed potential detection capability for phosphatidylinositol triphosphate compounds. These findings not only provide valuable insights for future research on the involvement of phosphoinositides in kidney pathophysiology, but also propose the use of the identified optimal matrices, particularly DAN and DHA, as the preferred choices for enhanced detection and mapping of these lipid species in future studies.
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Affiliation(s)
- Laurentiu G Dabija
- Department of Chemistry, Faculty of Science, York University, Toronto, ON, Canada
| | | | - Ergi Duli
- Cell Biology Program, Division of Nephrology, Department of Pediatrics, SickKids Research Institute, The Hospital for Sick Children, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mathieu Lemaire
- Cell Biology Program, Division of Nephrology, Department of Pediatrics, SickKids Research Institute, The Hospital for Sick Children, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Demian R Ifa
- Department of Chemistry, Faculty of Science, York University, Toronto, ON, Canada.
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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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L'Imperio V, Casati G, Cazzaniga G, Tarabini A, Bolognesi MM, Gibilisco F, Fraggetta F, Pagni F. Improvements in digital pathology equipment for renal biopsies: updating the standard model. J Nephrol 2024; 37:221-229. [PMID: 36786977 DOI: 10.1007/s40620-023-01568-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/01/2023] [Indexed: 02/15/2023]
Abstract
INTRODUCTION Digital pathology can improve the technical and interpretative workflows in nephropathology by creating hub-spoke networks and virtuous collaboration projects among centers in different geographical regions. New high-resolution fast-scanning instruments combined with currently existing equipment were tested in a nephropathology hub to evaluate possible upgrading in the routine processing phases. METHODS The scanning performance of two different instruments (Aperio vs hybrid MIDI II) was evaluated and a comparative quality control check was performed on obtained whole slide images. RESULTS Both with default and custom settings for light microscopy, MIDI II proved to be faster, with only slightly more time required to prepare the scan and larger final file size as compared to Aperio (p < 0.001). No differences were noted in the number of out-of-focus slides per case (p = 0.75). Regarding immunofluorescence, the new scanner required longer preparation time (p = 0.001) with comparable scanning times and final file size (p = 0.169 and p = 0.177, respectively). Quality control showed differences in 3 quality features related to white background and blurriness (p < 0.001). No major discordances in the final diagnosis were recorded after comparing the report obtained with slides scanned using the two instruments, with only one case (4%) showing minor disagreement. CONCLUSION The present report describes the experience of a hub nephropathology center adopting next generation digital pathology tools for the routine assessment of renal biopsies, highlighting the need for a complementary approach towards a philosophy of interoperability.
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Affiliation(s)
- Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy
| | - Gabriele Casati
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy
| | - Giorgio Cazzaniga
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy
| | - Andrea Tarabini
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy
| | - Maddalena Maria Bolognesi
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy
| | - Fabio Gibilisco
- Pathology Unit, ASP Catania, "Gravina" Hospital, Caltagirone, Italy
| | | | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University of Milano-Bicocca, IRCCS Fondazione San Gerardo dei Tintori, Monza, Italy.
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Cazzaniga G, Bolognesi MM, Stefania MD, Mascadri F, Eccher A, Alberici F, Mescia F, Smith A, Fraggetta F, Rossi M, Gambaro G, Pagni F, L'Imperio V. Congo Red Staining in Digital Pathology: The Streamlined Pipeline for Amyloid Detection Through Congo Red Fluorescence Digital Analysis. J Transl Med 2023; 103:100243. [PMID: 37634845 DOI: 10.1016/j.labinv.2023.100243] [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] [Received: 07/20/2023] [Revised: 08/04/2023] [Accepted: 08/21/2023] [Indexed: 08/29/2023] Open
Abstract
Renal amyloidosis is a rare condition caused by the progressive accumulation of misfolded proteins within glomeruli, vessels, and interstitium, causing functional decline and requiring prompt treatment due to its significant morbidity and mortality. Congo red (CR) stain on renal biopsy samples is the gold standard for diagnosis, but the need for polarized light is limiting the digitization of this nephropathology field. This study explores the feasibility and reliability of CR fluorescence on virtual slides (CRFvs) in evaluating the diagnostic accuracy and proposing an automated digital pipeline for its assessment. Whole-slide images from 154 renal biopsies with CR were scanned through a Texas red fluorescence filter (NanoZoomer S60, Hamamatsu) at the digital Nephropathology Center of the Istituto di Ricovero e Cura a Carattere Scientifico San Gerardo, Monza, Italy, and evaluated double-blinded for the detection and quantification through the amyloid score and a custom ImageJ pipeline was built to automatically detect amyloid-containing regions. Interobserver agreement for CRFvs was optimal (k = 0.90; 95% CI, 0.81-0.98), with even better concordance when consensus-based CRFvs evaluation was compared to the standard CR birefringence (BR) (k = 0.98; 95% CI, 0.93-1). Excellent performance was achieved in the assessment of amyloid score overall by CRFvs (weighted k = 0.70; 95% CI, 0.08-1), especially within the interstitium (weighted k = 0.60; 95% CI, 0.35-0.84), overcoming the misinterpretation of interstitial and capsular collagen BR. The application of an automated digital pathology pipeline (Streamlined Pipeline for Amyloid detection through CR fluorescence Digital Analysis, SPADA) further increased the performance of pathologists, leading to a complete concordance with the standard BR. This study represents an initial step in the validation of CRFvs, demonstrating its general reliability in a digital nephropathology center. The computational method used in this study has the potential to facilitate the integration of spatial omics and artificial intelligence tools for the diagnosis of amyloidosis, streamlining its detection process.
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Affiliation(s)
- Giorgio Cazzaniga
- Department of Medicine and Surgery, Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza, Italy
| | - Maddalena Maria Bolognesi
- Department of Medicine and Surgery, Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza, Italy
| | - Matteo Davide Stefania
- Department of Medicine and Surgery, Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza, Italy
| | - Francesco Mascadri
- Department of Medicine and Surgery, Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy; Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Federico Alberici
- Nephrology Unit, Spedali Civili Hospital, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili di Brescia, Brescia, Italy; Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Federica Mescia
- Nephrology Unit, Spedali Civili Hospital, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili di Brescia, Brescia, Italy; Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Monza, Italy
| | - Filippo Fraggetta
- Pathology Unit, Azienda Sanitaria Provinciale (ASP) Catania, "Gravina" Hospital, Caltagirone, Italy
| | - Mattia Rossi
- Division of Nephrology, Department of Medicine, University of Verona, Verona, Italy
| | - Giovanni Gambaro
- Division of Nephrology, Department of Medicine, University of Verona, Verona, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione San Gerardo dei Tintori, University of Milano-Bicocca, Monza, Italy.
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Piga I, L'Imperio V, Capitoli G, Denti V, Smith A, Magni F, Pagni F. Paving the path toward multi-omics approaches in the diagnostic challenges faced in thyroid pathology. Expert Rev Proteomics 2023; 20:419-437. [PMID: 38000782 DOI: 10.1080/14789450.2023.2288222] [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: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 11/26/2023]
Abstract
INTRODUCTION Despite advancements in diagnostic methods, the classification of indeterminate thyroid nodules still poses diagnostic challenges not only in pre-surgical evaluation but even after histological evaluation of surgical specimens. Proteomics, aided by mass spectrometry and integrated with artificial intelligence and machine learning algorithms, shows great promise in identifying diagnostic markers for thyroid lesions. AREAS COVERED This review provides in-depth exploration of how proteomics has contributed to the understanding of thyroid pathology. It discusses the technical advancements related to immunohistochemistry, genetic and proteomic techniques, such as mass spectrometry, which have greatly improved sensitivity and spatial resolution up to single-cell level. These improvements allowed the identification of specific protein signatures associated with different types of thyroid lesions. EXPERT COMMENTARY Among all the proteomics approaches, spatial proteomics stands out due to its unique ability to capture the spatial context of proteins in both cytological and tissue thyroid samples. The integration of multi-layers of molecular information combining spatial proteomics, genomics, immunohistochemistry or metabolomics and the implementation of artificial intelligence and machine learning approaches, represent hugely promising steps forward toward the possibility to uncover intricate relationships and interactions among various molecular components, providing a complete picture of the biological landscape whilst fostering thyroid nodule diagnosis.
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Affiliation(s)
- Isabella Piga
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milan-Bicocca, Monza, Italy
| | - Giulia Capitoli
- Department of Medicine and Surgery, Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, University of Milan - Bicocca (UNIMIB), Monza, Italy
| | - Vanna Denti
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milan-Bicocca, Monza, Italy
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Denti V, Capitoli G, Piga I, Clerici F, Pagani L, Criscuolo L, Bindi G, Principi L, Chinello C, Paglia G, Magni F, Smith A. Spatial Multiomics of Lipids, N-Glycans, and Tryptic Peptides on a Single FFPE Tissue Section. J Proteome Res 2022; 21:2798-2809. [PMID: 36259755 PMCID: PMC9639202 DOI: 10.1021/acs.jproteome.2c00601] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Mass spectrometry
imaging (MSI) is an emerging technology
that
is capable of mapping various biomolecules within their native spatial
context, and performing spatial multiomics on formalin-fixed paraffin-embedded
(FFPE) tissues may further increase the molecular characterization
of pathological states. Here we present a novel workflow which enables
the sequential MSI of lipids, N-glycans, and tryptic peptides on a
single FFPE tissue section and highlight the enhanced molecular characterization
that is offered by combining the multiple spatial omics data sets.
In murine brain and clear cell renal cell carcinoma (ccRCC) tissue,
the three molecular levels provided complementary information and
characterized different histological regions. Moreover, when the spatial
omics data was integrated, the different histopathological regions
of the ccRCC tissue could be better discriminated with respect to
the imaging data set of any single omics class. Taken together, these
promising findings demonstrate the capability to more comprehensively
map the molecular complexity within pathological tissue.
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Affiliation(s)
- Vanna Denti
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Giulia Capitoli
- Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Isabella Piga
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Francesca Clerici
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Lisa Pagani
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Lucrezia Criscuolo
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Greta Bindi
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Lucrezia Principi
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Clizia Chinello
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Giuseppe Paglia
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
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Paglia G, Smith AJ, Astarita G. Ion mobility mass spectrometry in the omics era: Challenges and opportunities for metabolomics and lipidomics. MASS SPECTROMETRY REVIEWS 2022; 41:722-765. [PMID: 33522625 DOI: 10.1002/mas.21686] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.
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Affiliation(s)
- Giuseppe Paglia
- School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Andrew J Smith
- School of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Giuseppe Astarita
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
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10
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The evolving landscape of Anatomic Pathology. Crit Rev Oncol Hematol 2022; 178:103776. [DOI: 10.1016/j.critrevonc.2022.103776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/11/2022] Open
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11
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He MJ, Pu W, Wang X, Zhang W, Tang D, Dai Y. Comparing DESI-MSI and MALDI-MSI Mediated Spatial Metabolomics and Their Applications in Cancer Studies. Front Oncol 2022; 12:891018. [PMID: 35924152 PMCID: PMC9340374 DOI: 10.3389/fonc.2022.891018] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/20/2022] [Indexed: 12/12/2022] Open
Abstract
Metabolic heterogeneity of cancer contributes significantly to its poor treatment outcomes and prognosis. As a result, studies continue to focus on identifying new biomarkers and metabolic vulnerabilities, both of which depend on the understanding of altered metabolism in cancer. In the recent decades, the rise of mass spectrometry imaging (MSI) enables the in situ detection of large numbers of small molecules in tissues. Therefore, researchers look to using MSI-mediated spatial metabolomics to further study the altered metabolites in cancer patients. In this review, we examined the two most commonly used spatial metabolomics techniques, MALDI-MSI and DESI-MSI, and some recent highlights of their applications in cancer studies. We also described AFADESI-MSI as a recent variation from the DESI-MSI and compare it with the two major techniques. Specifically, we discussed spatial metabolomics results in four types of heterogeneous malignancies, including breast cancer, esophageal cancer, glioblastoma and lung cancer. Multiple studies have effectively classified cancer tissue subtypes using altered metabolites information. In addition, distribution trends of key metabolites such as fatty acids, high-energy phosphate compounds, and antioxidants were identified. Therefore, while the visualization of finer distribution details requires further improvement of MSI techniques, past studies have suggested spatial metabolomics to be a promising direction to study the complexity of cancer pathophysiology.
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Affiliation(s)
- Michelle Junyi He
- Department of Biology, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Wenjun Pu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Xi Wang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Wei Zhang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin, 924st Hospital, Guilin, China
- *Correspondence: Yong Dai,
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12
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Ajith A, Milnes PJ, Johnson GN, Lockyer NP. Mass Spectrometry Imaging for Spatial Chemical Profiling of Vegetative Parts of Plants. PLANTS 2022; 11:plants11091234. [PMID: 35567235 PMCID: PMC9102225 DOI: 10.3390/plants11091234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 11/23/2022]
Abstract
The detection of chemical species and understanding their respective localisations in tissues have important implications in plant science. The conventional methods for imaging spatial localisation of chemical species are often restricted by the number of species that can be identified and is mostly done in a targeted manner. Mass spectrometry imaging combines the ability of traditional mass spectrometry to detect numerous chemical species in a sample with their spatial localisation information by analysing the specimen in a 2D manner. This article details the popular mass spectrometry imaging methodologies which are widely pursued along with their respective sample preparation and the data analysis methods that are commonly used. We also review the advancements through the years in the usage of the technique for the spatial profiling of endogenous metabolites, detection of xenobiotic agrochemicals and disease detection in plants. As an actively pursued area of research, we also address the hurdles in the analysis of plant tissues, the future scopes and an integrated approach to analyse samples combining different mass spectrometry imaging methods to obtain the most information from a sample of interest.
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Affiliation(s)
- Akhila Ajith
- Department of Chemistry, Photon Science Institute, University of Manchester, Manchester M13 9PL, UK;
| | - Phillip J. Milnes
- Syngenta, Jeolott’s Hill International Research Centre, Bracknell RG42 6EY, UK;
| | - Giles N. Johnson
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PY, UK;
| | - Nicholas P. Lockyer
- Department of Chemistry, Photon Science Institute, University of Manchester, Manchester M13 9PL, UK;
- Correspondence:
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13
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Smoluch M, Sobczyk J, Szewczyk I, Karaszkiewicz P, Silberring J. Mass spectrometry in art conservation-With focus on paintings. MASS SPECTROMETRY REVIEWS 2021:e21767. [PMID: 34870867 DOI: 10.1002/mas.21767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/02/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Conservation of historic artifacts has been a multidisciplinary field from its very beginning. Traditionally, it has been and still is associated with the history of art. It applies knowledge from technical and basic sciences, adapting their solutions to its goals. At present, however, a new tendency is clearly emerging-scientific research is starting to play an increasingly important role not only as a service, but also by proposing new solutions both in the traditional conservation areas and in new areas of conservation activities. The above trend opens up new perspectives for the field of preservation of our heritage but may also create new threats. Therefore, the conservators' caution in introducing new technologies should always be justified; after all, they are responsible for the effects of any activities on the historic objects. This, quite selective review, discusses application of mass spectrometry techniques for the detection of various components that are important to the conservators of our heritage with particular focus on paintings. The text also contains some basic knowledge of technical details to introduce the methodology to a broader group of professionals.
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Affiliation(s)
- Marek Smoluch
- AGH University of Science and Technology, Mickiewicza, Poland
| | - Joanna Sobczyk
- Department of Museum Prevention, Krakow Division, National Museum, Kraków, Poland
| | - Ireneusz Szewczyk
- Department of Museum Prevention, Krakow Division, National Museum, Kraków, Poland
| | - Pawel Karaszkiewicz
- Department of Museum Prevention, Krakow Division, National Museum, Kraków, Poland
| | - Jerzy Silberring
- AGH University of Science and Technology, Mickiewicza, Poland
- Department of Museum Prevention, Krakow Division, National Museum, Kraków, Poland
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14
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Klinkhammer BM, Lammers T, Mottaghy FM, Kiessling F, Floege J, Boor P. Non-invasive molecular imaging of kidney diseases. Nat Rev Nephrol 2021; 17:688-703. [PMID: 34188207 PMCID: PMC7612034 DOI: 10.1038/s41581-021-00440-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
In nephrology, differential diagnosis or assessment of disease activity largely relies on the analysis of glomerular filtration rate, urinary sediment, proteinuria and tissue obtained through invasive kidney biopsies. However, currently available non-invasive functional parameters, and most serum and urine biomarkers, cannot capture intrarenal molecular disease processes specifically. Moreover, although histopathological analyses of kidney biopsy samples enable the visualization of pathological morphological and molecular alterations, they only provide information about a small part of the kidney and do not allow longitudinal monitoring. These limitations not only hinder understanding of the dynamics of specific disease processes in the kidney, but also limit the targeting of treatments to active phases of disease and the development of novel targeted therapies. Molecular imaging enables non-invasive and quantitative assessment of physiological or pathological processes by combining imaging technologies with specific molecular probes. Here, we discuss current preclinical and clinical molecular imaging approaches in nephrology. Non-invasive visualization of the kidneys through molecular imaging can be used to detect and longitudinally monitor disease activity and can therefore provide companion diagnostics to guide clinical trials, as well as the safe and effective use of drugs.
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Affiliation(s)
| | - Twan Lammers
- Institute for Experimental Molecular Imaging, RWTH Aachen University Hospital, Aachen, Germany
- Department of Pharmaceutics, Utrecht University, Utrecht, Netherlands
- Department of Targeted Therapeutics, University of Twente, Enschede, Netherlands
| | - Felix M Mottaghy
- Department of Nuclear Medicine, University Hospital RWTH, Aachen, Germany
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, Netherlands
| | - Fabian Kiessling
- Institute for Experimental Molecular Imaging, RWTH Aachen University Hospital, Aachen, Germany
- Fraunhofer Institute for Digital Medicine MEVIS, Bremen, Germany
| | - Jürgen Floege
- Department of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Peter Boor
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany.
- Department of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, Germany.
- Electron Microscopy Facility, RWTH Aachen University Hospital, Aachen, Germany.
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15
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Israr MZ, Bernieh D, Salzano A, Cassambai S, Yazaki Y, Suzuki T. Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS): basics and clinical applications. Clin Chem Lab Med 2021; 58:883-896. [PMID: 32229653 DOI: 10.1515/cclm-2019-0868] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 02/21/2020] [Indexed: 01/23/2023]
Abstract
Background Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS) has been used for more than 30 years. Compared with other analytical techniques, it offers ease of use, high throughput, robustness, cost-effectiveness, rapid analysis and sensitivity. As advantages, current clinical techniques (e.g. immunoassays) are unable to directly measure the biomarker; rather, they measure secondary signals. MALDI-MS has been extensively researched for clinical applications, and it is set for a breakthrough as a routine tool for clinical diagnostics. Content This review reports on the principles of MALDI-MS and discusses current clinical applications and the future clinical prospects for MALDI-MS. Furthermore, the review assesses the limitations currently experienced in clinical assays, the advantages and the impact of MALDI-MS to transform clinical laboratories. Summary MALDI-MS is widely used in clinical microbiology for the screening of microbial isolates; however, there is scope to apply MALDI-MS in the diagnosis, prognosis, therapeutic drug monitoring and biopsy imaging in many diseases. Outlook There is considerable potential for MALDI-MS in clinic as a tool for screening, profiling and imaging because of its high sensitivity and specificity over alternative techniques.
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Affiliation(s)
- Muhammad Zubair Israr
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Dennis Bernieh
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Andrea Salzano
- IRCCS SDN, Diagnostic and Nuclear Research Institute, Naples, Italy
| | - Shabana Cassambai
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Yoshiyuki Yazaki
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Toru Suzuki
- Department of Cardiovascular Sciences and NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
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16
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Re F, Sartore L, Borsani E, Ferroni M, Baratto C, Mahajneh A, Smith A, Dey K, Almici C, Guizzi P, Bernardi S, Faglia G, Magni F, Russo D. Mineralization of 3D Osteogenic Model Based on Gelatin-Dextran Hybrid Hydrogel Scaffold Bioengineered with Mesenchymal Stromal Cells: A Multiparametric Evaluation. MATERIALS 2021; 14:ma14143852. [PMID: 34300769 PMCID: PMC8306641 DOI: 10.3390/ma14143852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/17/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Gelatin–dextran hydrogel scaffolds (G-PEG-Dx) were evaluated for their ability to activate the bone marrow human mesenchymal stromal cells (BM-hMSCs) towards mineralization. G-PEG-Dx1 and G-PEG-Dx2, with identical composition but different architecture, were seeded with BM-hMSCs in presence of fetal bovine serum or human platelet lysate (hPL) with or without osteogenic medium. G-PEG-Dx1, characterized by a lower degree of crosslinking and larger pores, was able to induce a better cell colonization than G-PEG-Dx2. At day 28, G-PEG-Dx2, with hPL and osteogenic factors, was more efficient than G-PEG-Dx1 in inducing mineralization. Scanning electron microscopy (SEM) and Raman spectroscopy showed that extracellular matrix produced by BM-hMSCs and calcium-positive mineralization were present along the backbone of the G-PEG-Dx2, even though it was colonized to a lesser degree by hMSCs than G-PEG-Dx1. These findings were confirmed by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), detecting distinct lipidomic signatures that were associated with the different degree of scaffold mineralization. Our data show that the architecture and morphology of G-PEG-Dx2 is determinant and better than that of G-PEG-Dx1 in promoting a faster mineralization, suggesting a more favorable and active role for improving bone repair.
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Affiliation(s)
- Federica Re
- Bone Marrow Transplant Unit, Department of Clinical and Experimental Sciences, University of Brescia, ASST Spedali Civili, Piazzale Spedali Civili 1, 25123 Brescia, Italy; (F.R.); (S.B.)
- Centro di Ricerca Emato-Oncologica AIL (CREA), ASST Spedali Civili, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Luciana Sartore
- Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze 38, 25123 Brescia, Italy; (L.S.); (K.D.)
| | - Elisa Borsani
- Division of Anatomy and Physiopathology, Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa 11, 25123 Brescia, Italy;
| | - Matteo Ferroni
- Department of Civil, Environmental, Architectural Engineering and Mathematics (DICATAM), University of Brescia, Via Valotti 9, 25123 Brescia, Italy;
- CNR-IMM Bologna, Via Gobetti 101, 40129 Bologna, Italy
| | | | - Allia Mahajneh
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Via Raoul Follereau 3, 20854 Vedano al Lambro, Italy; (A.M.); (A.S.); (F.M.)
| | - Andrew Smith
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Via Raoul Follereau 3, 20854 Vedano al Lambro, Italy; (A.M.); (A.S.); (F.M.)
| | - Kamol Dey
- Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze 38, 25123 Brescia, Italy; (L.S.); (K.D.)
- Department of Applied Chemistry and Chemical Engineering, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Camillo Almici
- Laboratory for Stem Cell Manipulation and Cryopreservation, Department of Transfusion Medicine, ASST Spedali Civili, Piazzale Spedali Civili 1, 25123 Brescia, Italy;
| | - Pierangelo Guizzi
- Orthopedics and Traumatology Unit, ASST Spedali Civili, Via Papa Giovanni XXIII 4, 25063 Gardone Val Trompia, 25123 Brescia, Italy;
| | - Simona Bernardi
- Bone Marrow Transplant Unit, Department of Clinical and Experimental Sciences, University of Brescia, ASST Spedali Civili, Piazzale Spedali Civili 1, 25123 Brescia, Italy; (F.R.); (S.B.)
- Centro di Ricerca Emato-Oncologica AIL (CREA), ASST Spedali Civili, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Guido Faglia
- PRISM Lab, CNR-INO, 25123 Brescia, Italy; (C.B.); (G.F.)
- Department of Information Engineering (DII), University of Brescia, Via Branze 38, 25123 Brescia, Italy
| | - Fulvio Magni
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Via Raoul Follereau 3, 20854 Vedano al Lambro, Italy; (A.M.); (A.S.); (F.M.)
| | - Domenico Russo
- Bone Marrow Transplant Unit, Department of Clinical and Experimental Sciences, University of Brescia, ASST Spedali Civili, Piazzale Spedali Civili 1, 25123 Brescia, Italy; (F.R.); (S.B.)
- Correspondence:
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Wu H, Liu X, Gao ZY, Lin M, Zhao X, Sun Y, Pu XP. Icaritin Provides Neuroprotection in Parkinson's Disease by Attenuating Neuroinflammation, Oxidative Stress, and Energy Deficiency. Antioxidants (Basel) 2021; 10:antiox10040529. [PMID: 33805302 PMCID: PMC8066334 DOI: 10.3390/antiox10040529] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/17/2022] Open
Abstract
Neuroinflammation, oxidative stress, and mitochondrial dysfunction are all important pathogenic mechanisms underlying motor dysfunction and dopaminergic neuronal damage observed in patients with Parkinson’s disease (PD). However, despite extensive efforts, targeting inflammation and oxidative stress using various approaches has not led to meaningful clinical outcomes, and mitochondrial enhancers have also failed to convincingly achieve disease-modifying effects. We tested our hypothesis that treatment approaches in PD should simultaneously reduce neuroinflammation, oxidative stress, and improve alterations in neuronal energy metabolism using the flavonoid icaritin in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. Using matrix-assisted laser desorption/ionization–mass spectrometry imaging (MALDI-MSI), coupled with biochemical analyses and behavioral tests, we demonstrate that icaritin improves PD by attenuating the the NOD-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome activity and stabilizing mitochondrial function, based on our extensive analyses showing the inhibition of NLRP3 inflammasome, reduction of NLRP3-mediated IL-1β secretion, and improvements in the levels of antioxidant molecules. Our data also indicated that icaritin stabilized the levels of proteins related to mitochondrial function, such as voltage-dependent anion channel (VDAC) and ATP synthase subunit beta (ATP5B), as well as those of molecules related to energy metabolism, such as ATP and ADP, ultimately improving mitochondrial dysfunction. By employing molecular docking, we also discovered that icaritin can interact with NLRP3, VDAC, ATP5B, and several blood–brain barrier (BBB)-related proteins. These data provide insights into the promising therapeutic potential of icaritin in PD.
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Affiliation(s)
- Hao Wu
- National Key Research Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; (H.W.); (X.L.); (Z.-Y.G.); (M.L.); (X.Z.); (Y.S.)
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xi Liu
- National Key Research Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; (H.W.); (X.L.); (Z.-Y.G.); (M.L.); (X.Z.); (Y.S.)
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ze-Yu Gao
- National Key Research Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; (H.W.); (X.L.); (Z.-Y.G.); (M.L.); (X.Z.); (Y.S.)
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ming Lin
- National Key Research Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; (H.W.); (X.L.); (Z.-Y.G.); (M.L.); (X.Z.); (Y.S.)
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xin Zhao
- National Key Research Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; (H.W.); (X.L.); (Z.-Y.G.); (M.L.); (X.Z.); (Y.S.)
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yi Sun
- National Key Research Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; (H.W.); (X.L.); (Z.-Y.G.); (M.L.); (X.Z.); (Y.S.)
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiao-Ping Pu
- National Key Research Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; (H.W.); (X.L.); (Z.-Y.G.); (M.L.); (X.Z.); (Y.S.)
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: ; Tel.: +86-10-8280-2431
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Abstract
![]()
Previously, we have
demonstrated native mass spectrometry imaging
(native MSI) in which the spatial distribution of proteins maintained
in their native-like, folded conformations was determined using liquid
extraction surface analysis (LESA). While providing an excellent testbed
for proof of principle, the spatial resolution of LESA is currently
limited for imaging primarily by the physical size of the sampling
pipette tip. Here, we report the adoption of nanospray-desorption
electrospray ionization (nano-DESI) for native MSI, delivering substantial
improvements in resolution versus native LESA MSI. In addition, native
nano-DESI may be used for location-targeted top–down proteomics
analysis directly from tissue. Proteins, including a homodimeric complex
not previously detected by native MSI, were identified through a combination
of collisional activation, high-resolution MS and proton transfer
charge reduction.
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Affiliation(s)
- Oliver J Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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Rossi F, L'Imperio V, Marti HP, Svarstad E, Smith A, Bolognesi MM, Magni F, Pagni F, Pieruzzi F. Proteomics for the study of new biomarkers in Fabry disease: State of the art. Mol Genet Metab 2021; 132:86-93. [PMID: 33077353 DOI: 10.1016/j.ymgme.2020.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 12/25/2022]
Abstract
Nephropathy represents a major complication of Fabry Disease and its accurate characterization is of paramount importance in predicting the disease progression and assessing the therapeutic responses. The diagnostic process still relies on performing renal biopsy, nevertheless many efforts have been made to discover early reliable biomarkers allowing us to avoid invasive procedures. In this field, proteomics offers a sensitive and fast method leading to an accurate detection of specific pathological proteins and the discovery of diagnostic and prognostic biomarkers that reflect disease progression and facilitate the evaluation of therapeutic responses. Here, we report a review of selected literature focusing on the investigation of several proteomic techniques highlighting their advantages, limitations and future perspectives in their application in the routine study of Fabry Nephropathy.
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Affiliation(s)
- Federica Rossi
- Department of Medicine and Surgery, University of Milano-Bicocca, Nephrology and Dialysis Unit, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy.
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy.
| | - Hans-Peter Marti
- Department of Medicine, Haukeland University Hospital, Jonas Lies Vei 65, Bergen, Norway; Department of Clinical Medicine, University of Bergen, Jonas Lies Vei 87, Bergen, Norway
| | - Einar Svarstad
- Department of Clinical Medicine, University of Bergen, Jonas Lies Vei 87, Bergen, Norway
| | - Andrew Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Via Raoul Follereau 3, Vedano al Lambro, Italy
| | - Maddalena Maria Bolognesi
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Via Raoul Follereau 3, Vedano al Lambro, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, University of Milano-Bicocca, Pathology, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
| | - Federico Pieruzzi
- Department of Medicine and Surgery, University of Milano-Bicocca, Nephrology and Dialysis Unit, San Gerardo Hospital, Via G.B. Pergolesi 33, Monza, Italy
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Smith A, Piga I, Denti V, Chinello C, Magni F. Elaboration Pipeline for the Management of MALDI-MS Imaging Datasets. Methods Mol Biol 2021; 2361:129-142. [PMID: 34236659 DOI: 10.1007/978-1-0716-1641-3_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF)-mass spectrometry imaging (MSI) enables the spatial localization of proteins to be mapped directly on tissue sections, simultaneously detecting hundreds in a single analysis. However, the large data size, as well as the complexity of MALDI-MSI proteomics datasets, requires the appropriate tools and statistical approaches in order to reduce the complexity and mine the dataset in a successful manner. Here, a pipeline for the management of MALDI-MSI data is described, starting with preprocessing of the raw data, followed by statistical analysis using both supervised and unsupervised statistical approaches and, finally, annotation of those discriminatory protein signals highlighted by the data mining procedure.
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Affiliation(s)
- Andrew Smith
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Milan, Italy.
| | - Isabella Piga
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Milan, Italy
| | - Vanna Denti
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Milan, Italy
| | - Clizia Chinello
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Milan, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, Milan, Italy
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21
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Abstract
Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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Kriegsmann M, Casadonte R, Maurer N, Stoehr C, Erlmeier F, Moch H, Junker K, Zgorzelski C, Weichert W, Schwamborn K, Deininger SO, Gaida M, Mechtersheimer G, Stenzinger A, Schirmacher P, Hartmann A, Kriegsmann J, Kriegsmann K. Mass Spectrometry Imaging Differentiates Chromophobe Renal Cell Carcinoma and Renal Oncocytoma with High Accuracy. J Cancer 2020; 11:6081-6089. [PMID: 32922548 PMCID: PMC7477404 DOI: 10.7150/jca.47698] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022] Open
Abstract
Background: While subtyping of the majority of malignant chromophobe renal cell carcinoma (cRCC) and benign renal oncocytoma (rO) is possible on morphology alone, additional histochemical, immunohistochemical or molecular investigations are required in a subset of cases. As currently used histochemical and immunohistological stains as well as genetic aberrations show considerable overlap in both tumors, additional techniques are required for differential diagnostics. Mass spectrometry imaging (MSI) combining the detection of multiple peptides with information about their localization in tissue may be a suitable technology to overcome this diagnostic challenge. Patients and Methods: Formalin-fixed paraffin embedded (FFPE) tissue specimens from cRCC (n=71) and rO (n=64) were analyzed by MSI. Data were classified by linear discriminant analysis (LDA), classification and regression trees (CART), k-nearest neighbors (KNN), support vector machine (SVM), and random forest (RF) algorithm with internal cross validation and visualized by t-distributed stochastic neighbor embedding (t-SNE). Most important variables for classification were identified and the classification algorithm was optimized. Results: Applying different machine learning algorithms on all m/z peaks, classification accuracy between cRCC and rO was 85%, 82%, 84%, 77% and 64% for RF, SVM, KNN, CART and LDA. Under the assumption that a reduction of m/z peaks would lead to improved classification accuracy, m/z peaks were ranked based on their variable importance. Reduction to six most important m/z peaks resulted in improved accuracy of 89%, 85%, 85% and 85% for RF, SVM, KNN, and LDA and remained at the level of 77% for CART. t-SNE showed clear separation of cRCC and rO after algorithm improvement. Conclusion: In summary, we acquired MSI data on FFPE tissue specimens of cRCC and rO, performed classification and detected most relevant biomarkers for the differential diagnosis of both diseases. MSI data might be a useful adjunct method in the differential diagnosis of cRCC and rO.
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Affiliation(s)
- Mark Kriegsmann
- Institute of Pathology, Heidelberg University, Heidelberg, Germany
| | | | - Nadine Maurer
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Erlangen, Germany
| | - Christine Stoehr
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Erlangen, Germany
| | - Franziska Erlmeier
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Erlangen, Germany
| | - Holger Moch
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Switzerland
| | - Klaus Junker
- Department of Urology and Pediatric Urology, University of Saarland, Homburg/Saar, Germany
| | | | | | | | | | | | | | | | | | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen-Nürnberg, Erlangen, Germany
| | - Joerg Kriegsmann
- Proteopath Trier, Trier, Germany.,Centre for Histology, Cytology and molecular Diagnostics Trier, Trier, Germany.,Danube Private University, Krems, Austria
| | - Katharina Kriegsmann
- Department Hematology, Oncology and Rheumatology, Heidelberg University, Heidelberg, Germany
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Denti V, Piga I, Guarnerio S, Clerici F, Ivanova M, Chinello C, Paglia G, Magni F, Smith A. Antigen Retrieval and Its Effect on the MALDI-MSI of Lipids in Formalin-Fixed Paraffin-Embedded Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1619-1624. [PMID: 32678590 PMCID: PMC8009503 DOI: 10.1021/jasms.0c00208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue represents the primary source of clinical tissue and is routinely used in MALDI-MSI studies. However, it is not particularly suitable for lipidomics imaging given that many species are depleted during tissue processing. Irrespective, a number of solvent-resistant lipids remain, but their extraction may be hindered by the cross-link between proteins. Therefore, an antigen retrieval step could enable the extraction of a greater number of lipids and may provide information that is complementary to that which can be obtained from other biomolecules, such as proteins. In this short communication, we aim to address the effect of performing antigen retrieval prior to MALDI-MSI of lipids in FFPE tissue. As a result, an increased number of lipid signals could be detected and may have derived from lipid species that are known to be implicated in the lipid-protein cross-linking that is formed as a result of formalin fixation. Human renal cancer tissue was used as a proof of concept to determine whether using these detected lipid signals were also able to highlight the histopathological regions that were present. These preliminary findings may highlight the potential to enhance the clinical relevance of the lipidomic information obtained from FFPE tissue.
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Affiliation(s)
- Vanna Denti
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Isabella Piga
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Sonia Guarnerio
- Biomolecular
Sciences Research Centre, Sheffield-Hallam
University, City Campus, Howard Street, Sheffield S1 1WB, United Kingdom
| | - Francesca Clerici
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Mariia Ivanova
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Clizia Chinello
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Giuseppe Paglia
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Fulvio Magni
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
| | - Andrew Smith
- Clinical
Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, Vedano al Lambro 20854, Italy
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Smith A, Iablokov V, Mazza M, Guarnerio S, Denti V, Ivanova M, Stella M, Piga I, Chinello C, Heijs B, van Veelen PA, Benediktsson H, Muruve DA, Magni F. Detecting Proteomic Indicators to Distinguish Diabetic Nephropathy from Hypertensive Nephrosclerosis by Integrating Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging with High-Mass Accuracy Mass Spectrometry. Kidney Blood Press Res 2020; 45:233-248. [PMID: 32062660 DOI: 10.1159/000505187] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/02/2019] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Diabetic nephropathy (DN) and hypertensive nephrosclerosis (HN) represent the most common causes of chronic kidney disease (CKD) and many patients progress to -end-stage renal disease. Patients are treated primarily through the management of cardiovas-cular risk factors and hypertension; however patients with HN have a more favorable outcome. A noninvasive clinical approach to separate these two entities, especially in hypertensive patients who also have diabetes, would allow for targeted treatment and more appropriate resource allocation to those patients at the highest risk of CKD progression. Meth-ods: In this preliminary study, high-spatial-resolution matrix-assisted laser desorption/ion-ization (MALDI) mass spectrometry imaging (MSI) was integrated with high-mass accuracy MALDI-FTICR-MS and nLC-ESI-MS/MS analysis in order to detect tissue proteins within kidney biopsies to discriminate cases of DN (n = 9) from cases of HN (n = 9). RESULTS Differences in the tryptic peptide profiles of the 2 groups could clearly be detected, with these becoming even more evident in the more severe histological classes, even if this was not evident with routine histology. In particular, 4 putative proteins were detected and had a higher signal intensity within regions of DN tissue with extensive sclerosis or fibrosis. Among these, 2 proteins (PGRMC1 and CO3) had a signal intensity that increased at the latter stages of the disease and may be associated with progression. DISCUSSION/CONCLUSION This preliminary study represents a valuable starting point for a future study employing a larger cohort of patients to develop sensitive and specific protein biomarkers that could reliably differentiate between diabetic and hypertensive causes of CKD to allow for improved diagnosis, fewer biopsy procedures, and refined treatment approaches for clinicians.
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Affiliation(s)
- Andrew Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Vadim Iablokov
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mariafrancesca Mazza
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Sonia Guarnerio
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Vanna Denti
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Mariia Ivanova
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Martina Stella
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Isabella Piga
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Clizia Chinello
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy
| | - Bram Heijs
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hallgrimur Benediktsson
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Daniel A Muruve
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano-Bicocca, Vedano al Lambro, Italy,
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Imaging and quantifying drug delivery in skin - Part 1: Autoradiography and mass spectrometry imaging. Adv Drug Deliv Rev 2020; 153:137-146. [PMID: 31778729 DOI: 10.1016/j.addr.2019.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/21/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022]
Abstract
In this two-part review we present an up-to-date description of different imaging methods available to map the localization of drugs on skin as a complement of established ex-vivo absorption studies. This first part deals with invasive methods which are grouped in two classes according to their underlying principles: i) methods using radioactivity such as autoradiography and ii) mass spectrometry methods such as MALDI and SIMS. For each method, a description of the principle is given along with example applications of imaging and quantifying drug delivery in human skin. Thanks to these techniques a better assessment of the fate of drugs is obtained: its localization on a particular skin structure, its potential accumulation, etc. A critical comparison in terms of capabilities, sensitivity and practical applicability is included that will help the reader to select the most appropriate technique depending on the particular problem to be solved.
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Taherkhani A, Farrokhi Yekta R, Mohseni M, Saidijam M, Arefi Oskouie A. Chronic kidney disease: a review of proteomic and metabolomic approaches to membranous glomerulonephritis, focal segmental glomerulosclerosis, and IgA nephropathy biomarkers. Proteome Sci 2019; 17:7. [PMID: 31889913 PMCID: PMC6925425 DOI: 10.1186/s12953-019-0155-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
Chronic Kidney Disease (CKD) is a global health problem annually affecting millions of people around the world. It is a comprehensive syndrome, and various factors may contribute to its occurrence. In this study, it was attempted to provide an accurate definition of chronic kidney disease; followed by focusing and discussing on molecular pathogenesis, novel diagnosis approaches based on biomarkers, recent effective antigens and new therapeutic procedures related to high-risk chronic kidney disease such as membranous glomerulonephritis, focal segmental glomerulosclerosis, and IgA nephropathy, which may lead to end-stage renal diseases. Additionally, a considerable number of metabolites and proteins that have previously been discovered and recommended as potential biomarkers of various CKDs using ‘-omics-’ technologies, proteomics, and metabolomics were reviewed.
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Affiliation(s)
- Amir Taherkhani
- 1Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Maede Mohseni
- 3Urology and Nephrology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Massoud Saidijam
- 1Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Afsaneh Arefi Oskouie
- 4Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Anti-Myocardial Infarction Effects of Radix Aconiti Lateralis Preparata Extracts and Their Influence on Small Molecules in the Heart Using Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging. Int J Mol Sci 2019; 20:ijms20194837. [PMID: 31569464 PMCID: PMC6801437 DOI: 10.3390/ijms20194837] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/13/2019] [Accepted: 09/27/2019] [Indexed: 12/29/2022] Open
Abstract
Radix Aconiti Lateralis Preparata (fuzi) is the processed product of Aconitum carmichaelii Debeaux tuber, and has great potential anti-myocardial infarction effects, including improving myocardial damage and energy metabolism in rats. However, the effects of Radix Aconiti Lateralis Preparata extracts in a rat model of myocardial infarction have not yet been fully illustrated. Herein, Radix Aconiti Lateral Preparata was used to prepare Radix Aconiti Lateralis Preparata extract (RAE), fuzi polysaccharides (FPS), and fuzi total alkaloid (FTA). Then, we aimed to compare the effects of RAE, FPS, and FTA in MI rats and further explore their influence on small molecules in the heart. We reported that Radix Aconiti Lateralis Preparata extract (RAE) and fuzi total alkaloid (FTA) significantly improved left ventricular function and structure, and reduced myocardial damage and infarct size in rats with myocardial infarction by the left anterior descending artery ligation. In contrast, fuzi polysaccharides (FPS) was less effective than RAE and FTA, indicating that alkaloids might play a major role in the treatment of myocardial infarction. Moreover, via matrix-assisted laser desorption/ionization–mass spectrometry imaging (MALDI–MSI), we further showed that RAE and FTA containing alkaloids as the main common components regulated myocardial energy metabolism-related molecules and phospholipids levels and distribution patterns against myocardial infarction. In particular, it was FTA, not RAE, that could also regulate potassium ions and glutamine to play a cardioprotective role in myocardial infarction, which revealed that an appropriate dose of alkaloids generated more obvious cardiotonic effects. These findings together suggested that Radix Aconiti Lateralis Preparata extracts containing an appropriate dose of alkaloids as its main pharmacological active components exerted protective effects against myocardial infarction by improving myocardial energy metabolism abnormalities and changing phospholipids levels and distribution patterns to stabilize the cardiomyocyte membrane structure. Thus, RAE and FTA extracted from Radix Aconiti Lateralis Preparata are potential candidates for the treatment of myocardial infarction.
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Capitoli G, Piga I, Galimberti S, Leni D, Pincelli AI, Garancini M, Clerici F, Mahajneh A, Brambilla V, Smith A, Magni F, Pagni F. MALDI-MSI as a Complementary Diagnostic Tool in Cytopathology: A Pilot Study for the Characterization of Thyroid Nodules. Cancers (Basel) 2019; 11:cancers11091377. [PMID: 31527543 PMCID: PMC6769566 DOI: 10.3390/cancers11091377] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
The present study applies for the first time as Matrix-Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry Imaging (MSI) on real thyroid Fine Needle Aspirations (FNAs) to test its possible complementary role in routine cytology in the diagnosis of thyroid nodules. The primary aim is to evaluate the potential employment of MALDI-MSI in cytopathology, using challenging samples such as needle washes. Firstly, we designed a statistical model based on the analysis of Regions of Interest (ROIs), according to the morphological triage performed by the pathologist. Successively, the capability of the model to predict the classification of the FNAs was validated in a different group of patients on ROI and pixel-by-pixel approach. Results are very promising and highlight the possibility to introduce MALDI-MSI as a complementary tool for the diagnostic characterization of thyroid nodules.
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Affiliation(s)
- Giulia Capitoli
- Center of Biostatistics for Clinical Epidemiology, Department of Medicine and Surgery, University of Milano - Bicocca, 20900 Vedano al Lambro, Italy.
| | - Isabella Piga
- Proteomics and Metabolomics platform, Department of Medicine and Surgery, University of Milano - Bicocca, 20900 Vedano al Lambro, Italy.
| | - Stefania Galimberti
- Center of Biostatistics for Clinical Epidemiology, Department of Medicine and Surgery, University of Milano - Bicocca, 20900 Vedano al Lambro, Italy.
| | - Davide Leni
- Department of radiology, San Gerardo Hospital, 20900 ASST Monza, Italy.
| | | | - Mattia Garancini
- Department of Surgery, San Gerardo Hospital, 20900 ASST Monza, Italy.
| | - Francesca Clerici
- Proteomics and Metabolomics platform, Department of Medicine and Surgery, University of Milano - Bicocca, 20900 Vedano al Lambro, Italy.
| | - Allia Mahajneh
- Proteomics and Metabolomics platform, Department of Medicine and Surgery, University of Milano - Bicocca, 20900 Vedano al Lambro, Italy.
| | - Virginia Brambilla
- Pathology, Department of Medicine and Surgery, University of Milano - Bicocca, San Gerardo Hospital, 20900 ASST Monza, Italy.
| | - Andrew Smith
- Proteomics and Metabolomics platform, Department of Medicine and Surgery, University of Milano - Bicocca, 20900 Vedano al Lambro, Italy.
| | - Fulvio Magni
- Proteomics and Metabolomics platform, Department of Medicine and Surgery, University of Milano - Bicocca, 20900 Vedano al Lambro, Italy.
| | - Fabio Pagni
- Pathology, Department of Medicine and Surgery, University of Milano - Bicocca, San Gerardo Hospital, 20900 ASST Monza, Italy.
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Ahmed M, Broeckx G, Baggerman G, Schildermans K, Pauwels P, Van Craenenbroeck AH, Dendooven A. Next-generation protein analysis in the pathology department. J Clin Pathol 2019; 73:1-6. [DOI: 10.1136/jclinpath-2019-205864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/12/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023]
Abstract
Traditionally, immunohistochemistry (IHC) is used by pathologists to localise specific proteins or peptides in tissue slides. In the era of personalised medicine, however, molecular tissue analysis becomes indispensable for correct diagnosis, prognosis and therapeutic decision, not only on the DNA or mRNA level but also on the protein level. Combining molecular information with imaging presents many advantages. Therefore, matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) is a promising technique to be added to the armamentarium of the pathologist. Here, we focus on the workflow, advantages and drawbacks of both MALDI IMS and IHC. We also briefly discuss a few other protein imaging modalities and give examples of applications.
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30
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Longuespée R, Casadonte R, Schwamborn K, Kriegsmann M. Proteomics in Pathology: The Special Issue. Proteomics Clin Appl 2019; 13:e1800167. [PMID: 30730117 DOI: 10.1002/prca.201800167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Rémi Longuespée
- Institute of Pathology, University of Heidelberg, 69120, Heidelberg, Germany
| | | | - Kristina Schwamborn
- Institute of Pathology, Technical University of Munich, 81675, Munich, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, 69120, Heidelberg, Germany
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