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Stillger MN, Li MJ, Hönscheid P, von Neubeck C, Föll MC. Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma. Proteomics 2024; 24:e2300001. [PMID: 38402423 DOI: 10.1002/pmic.202300001] [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: 06/08/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
MALDI mass spectrometry imaging (MALDI imaging) uniquely advances cancer research, by measuring spatial distribution of endogenous and exogenous molecules directly from tissue sections. These molecular maps provide valuable insights into basic and translational cancer research, including tumor biology, tumor microenvironment, biomarker identification, drug treatment, and patient stratification. Despite its advantages, MALDI imaging is underutilized in studying rare cancers. Sarcomas, a group of malignant mesenchymal tumors, pose unique challenges in medical research due to their complex heterogeneity and low incidence, resulting in understudied subtypes with suboptimal management and outcomes. In this review, we explore the applicability of MALDI imaging in sarcoma research, showcasing its value in understanding this highly heterogeneous and challenging rare cancer. We summarize all MALDI imaging studies in sarcoma to date, highlight their impact on key research fields, including molecular signatures, cancer heterogeneity, and drug studies. We address specific challenges encountered when employing MALDI imaging for sarcomas, and propose solutions, such as using formalin-fixed paraffin-embedded tissues, and multiplexed experiments, and considerations for multi-site studies and digital data sharing practices. Through this review, we aim to spark collaboration between MALDI imaging researchers and clinical colleagues, to deploy the unique capabilities of MALDI imaging in the context of sarcoma.
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Affiliation(s)
- Maren Nicole Stillger
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center, Freiburg, Germany
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Mujia Jenny Li
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center, Freiburg, Germany
- Institute for Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Pia Hönscheid
- Institute of Pathology, Faculty of Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases, Partner Site Dresden, German Cancer Research Center Heidelberg, Dresden, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cläre von Neubeck
- Department of Particle Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Melanie Christine Föll
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
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2
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Abstract
Imaging mass spectrometry is a well-established technology that can easily and succinctly communicate the spatial localization of molecules within samples. This review communicates the recent advances in the field, with a specific focus on matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) applied on tissues. The general sample preparation strategies for different analyte classes are explored, including special considerations for sample types (fresh frozen or formalin-fixed,) strategies for various analytes (lipids, metabolites, proteins, peptides, and glycans) and how multimodal imaging strategies can leverage the strengths of each approach is mentioned. This work explores appropriate experimental design approaches and standardization of processes needed for successful studies, as well as the various data analysis platforms available to analyze data and their strengths. The review concludes with applications of imaging mass spectrometry in various fields, with a focus on medical research, and some examples from plant biology and microbe metabolism are mentioned, to illustrate the breadth and depth of MALDI IMS.
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Affiliation(s)
- Jessica L Moore
- Department of Proteomics, Discovery Life Sciences, Huntsville, Alabama 35806, United States
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, Connecticut 06520, United States
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3
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Liu JTC, Glaser AK, Bera K, True LD, Reder NP, Eliceiri KW, Madabhushi A. Harnessing non-destructive 3D pathology. Nat Biomed Eng 2021; 5:203-218. [PMID: 33589781 PMCID: PMC8118147 DOI: 10.1038/s41551-020-00681-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/17/2020] [Indexed: 02/08/2023]
Abstract
High-throughput methods for slide-free three-dimensional (3D) pathological analyses of whole biopsies and surgical specimens offer the promise of modernizing traditional histology workflows and delivering improvements in diagnostic performance. Advanced optical methods now enable the interrogation of orders of magnitude more tissue than previously possible, where volumetric imaging allows for enhanced quantitative analyses of cell distributions and tissue structures that are prognostic and predictive. Non-destructive imaging processes can simplify laboratory workflows, potentially reducing costs, and can ensure that samples are available for subsequent molecular assays. However, the large size of the feature-rich datasets that they generate poses challenges for data management and computer-aided analysis. In this Perspective, we provide an overview of the imaging technologies that enable 3D pathology, and the computational tools-machine learning, in particular-for image processing and interpretation. We also discuss the integration of various other diagnostic modalities with 3D pathology, along with the challenges and opportunities for clinical adoption and regulatory approval.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Kaustav Bera
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nicholas P Reder
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kevin W Eliceiri
- Department of Medical Physics, University of Wisconsin, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH, USA.
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4
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Kelley AR, Colley M, Dyer S, Bach SBH, Zhu X, Perry G. Ethanol-Fixed, Paraffin-Embedded Tissue Imaging: Implications for Alzheimer's Disease Research. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2416-2420. [PMID: 32803969 DOI: 10.1021/jasms.0c00195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mass spectrometry imaging (MSI) is rapidly becoming a crucial tool in disease research. Fresh-frozen tissue is ideal for MSI because the protein and lipid structures are undisturbed by chemical fixatives; however, that means long-term preservation is limited. Formalin-fixed paraffin-embedded tissue has a virtually infinite shelf life, but whole proteins are difficult or impossible to image directly. To bridge this gap, we examine the use of ethanol-fixed, paraffin-embedded (EFPE) tissue for the localization of intact proteins and lipids and comment on implications in Alzheimer's disease (AD) research. The new sample preparation methods for EFPE tissues have allowed us to greatly broaden the information we can extract from MSI experiments. Our methods involve a xylene-free deparaffination for lipid analysis and an intact protein method for visualizing amyloid-beta plaques from human AD brain tissue. This unique combination streamlines the MSI sample preparation process while allowing for the most biologically and pathologically relevant information to be extracted from a single tissue source.
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Affiliation(s)
| | | | | | | | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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5
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Blutke A, Sun N, Xu Z, Buck A, Harrison L, Schriever SC, Pfluger PT, Wiles D, Kunzke T, Huber K, Schlegel J, Aichler M, Feuchtinger A, Matiasek K, Hauck SM, Walch A. Light sheet fluorescence microscopy guided MALDI-imaging mass spectrometry of cleared tissue samples. Sci Rep 2020; 10:14461. [PMID: 32879402 PMCID: PMC7468256 DOI: 10.1038/s41598-020-71465-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 08/10/2020] [Indexed: 02/08/2023] Open
Abstract
Light sheet fluorescence microscopy (LSFM) of optically cleared biological samples represents a powerful tool to analyze the 3-dimensional morphology of tissues and organs. Multimodal combinations of LSFM with additional analyses of the identical sample help to limit the consumption of restricted specimen and reduce inter-sample variation. Here, we demonstrate the proof-of-concept that LSFM of cleared brain tissue samples can be combined with Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI) for detection and quantification of proteins. Samples of freshly dissected murine brain and of archived formalin-fixed paraffin-embedded (FFPE) human brain tissue were cleared (3DISCO). Tissue regions of interest were defined by LSFM and excised, (re)-embedded in paraffin, and sectioned. Mouse sections were coated with sinapinic acid matrix. Human brain sections were pre-digested with trypsin and coated with α-cyano-4-hydroxycinnamic acid matrix. Subsequently, sections were subjected to MALDI-time-of-flight (TOF)-MSI in mass ranges between 0.8 to 4 kDa (human tissue sections), or 2.5–25 kDa (mouse tissue sections) with a lateral resolution of 50 µm. Protein- and peptide-identities corresponding to acquired MALDI-MSI spectra were confirmed by parallel liquid chromatography tandem mass spectrometry (LC–MS/MS) analysis. The spatial abundance- and intensity-patterns of established marker proteins detected by MALDI-MSI were also confirmed by immunohistochemistry.
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Affiliation(s)
- Andreas Blutke
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Zhihao Xu
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Achim Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Luke Harrison
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.,Division of Metabolic Diseases, Technische Universität München, 80333, Munich, Germany
| | - Sonja C Schriever
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Paul T Pfluger
- Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Institute for Diabetes and Obesity, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | | | - Thomas Kunzke
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Katharina Huber
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Jürgen Schlegel
- Institute for Pathology, Department of Neuropathology, Technische Universität München, 80333, Munich, Germany
| | - Michaela Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany.
| | - Kaspar Matiasek
- Institute for Veterinary Pathology at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Stefanie M Hauck
- Research Unit for Protein Science, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, 8576, Neuherberg, Germany
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6
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Ščupáková K, Balluff B, Tressler C, Adelaja T, Heeren RM, Glunde K, Ertaylan G. Cellular resolution in clinical MALDI mass spectrometry imaging: the latest advancements and current challenges. Clin Chem Lab Med 2020; 58:914-929. [PMID: 31665113 PMCID: PMC9867918 DOI: 10.1515/cclm-2019-0858] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Mass spectrometry (MS) is the workhorse of metabolomics, proteomics and lipidomics. Mass spectrometry imaging (MSI), its extension to spatially resolved analysis of tissues, is a powerful tool for visualizing molecular information within the histological context of tissue. This review summarizes recent developments in MSI and highlights current challenges that remain to achieve molecular imaging at the cellular level of clinical specimens. We focus on matrix-assisted laser desorption/ionization (MALDI)-MSI. We discuss the current status of each of the analysis steps and remaining challenges to reach the desired level of cellular imaging. Currently, analyte delocalization and degradation, matrix crystal size, laser focus restrictions and detector sensitivity are factors that are limiting spatial resolution. New sample preparation devices and laser optic systems are being developed to push the boundaries of these limitations. Furthermore, we review the processing of cellular MSI data and images, and the systematic integration of these data in the light of available algorithms and databases. We discuss roadblocks in the data analysis pipeline and show how technology from other fields can be used to overcome these. Finally, we conclude with curative and community efforts that are needed to enable contextualization of the information obtained.
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Affiliation(s)
- Klára Ščupáková
- Maastricht MultiModal Molecular Imaging Institute (M4I), University of Maastricht, Maastricht, The Netherlands
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I), University of Maastricht, Maastricht, The Netherlands
| | - Caitlin Tressler
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tobi Adelaja
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ron M.A. Heeren
- Corresponding author: Ron M.A. Heeren, Maastricht MultiModal Molecular Imaging Institute (M4I), University of Maastricht, Maastricht, The Netherlands,
| | - Kristine Glunde
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; and The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gökhan Ertaylan
- Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
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7
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New method for rapid identification and quantification of fungal biomass using ergosterol autofluorescence. Talanta 2020; 219:121238. [PMID: 32887129 DOI: 10.1016/j.talanta.2020.121238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 01/06/2023]
Abstract
This research reports on the development of a method to identify and quantify fungal biomass based on ergosterol autofluorescence using excitation-emission matrix (EEM) measurements. In the first stage of this work, several ergosterol extraction methods were evaluated by APCI-MS, where the ultrasound-assisted procedure showed the best results. Following an experimental design, various quantities of the dried mycelium of the fungus Schizophyllum commune were mixed with the starchy solid residue (BBR) from the babassu (Orbignya sp.) oil industry, and these samples were subjected to several ergosterol extraction methods. The EEM spectral data of the samples were subjected to Principal Component Analysis (PCA), which showed the possibility to qualitatively evaluate the presence of ergosterol in the samples by ergosterol autofluorescence without the addition of any reagent. In order to assess the feasibility of quantifying fungal biomass using ergosterol autofluorescence, the EEM spectral data and known amounts of fungal biomass were modeled using partial least squares (PLS) regression and a procedure of backward selection of predictors (AutoPLS) was applied to select the Excitation-Emission wavelength pairs that provide the lowest prediction error. The results revealed that the amount of fungal biomass in samples containing interfering substances (BBR) can be accurately predicted with R2CV = 0.939, R2P = 0.936, RPDcv = 4.07, RPDp = 4.06, RMSECV = 0.0731 and RMSEP = 0.0797. In order to obtain an easy-to-understand equation that expresses the relationship between fungal biomass and fluorescence intensity, multiple linear regression (MLR) was applied to the VIP variables selected by the AutoPLS method. The MLR model selected only 2 variables and showed a very good performance, with R2CV = 0.862, R2P = 0.809, RPDcv = 2.18, RPDp = 2.35, RMSECV = 0.137 and RMSEP = 0.138. This study demonstrated that ergosterol autofluorescence can be successfully used to quantify fungal biomass even when mixed with agroindustrial residues, in this case BBR.
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8
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The impact of crosslinking and non-crosslinking fixatives on antigen retrieval and immunohistochemistry. N Biotechnol 2019; 52:69-83. [PMID: 31082574 DOI: 10.1016/j.nbt.2019.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/29/2022]
Abstract
Pre-analytical factors can greatly influence the outcome of molecular analyses in medical diagnostics and research. This also applies to in situ staining techniques such as immunohistochemistry (IHC), where different types of tissue fixation methods lead to different modifications of proteins and thus can affect differently the detection by antibodies. For formalin-fixed paraffin-embedded (FFPE) tissue, antigen retrieval is applied in order to reverse the negative effects of formalin and re-establish immunoreactivity. Most antibodies and protocols used in IHC are optimized for FFPE tissue, but not for paraffin-embedded tissue treated with other fixatives such as non-crosslinking fixatives. We report results from systematic studies on distinct pre-analytical conditions in IHC, immunofluorescence and electron microscopy. Parameters investigated are the impact of crosslinking and non-crosslinking fixatives (comparing formalin and PAXgene Tissue fixation) on whole tissue, subcellular structures and organelles, as well as on ultrastructure. The results generated show that minor changes in antigen retrieval conditions may have a major impact on IHC results and that protocols optimized for crosslinking fixatives may not be used for other fixatives without re-validation. Key antigen retrieval parameters such as buffers with different pH and duration of microwave treatment must be tested systematically for each antibody and fixation protocol.
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9
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Michno W, Wehrli PM, Blennow K, Zetterberg H, Hanrieder J. Molecular imaging mass spectrometry for probing protein dynamics in neurodegenerative disease pathology. J Neurochem 2018; 151:488-506. [PMID: 30040875 DOI: 10.1111/jnc.14559] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022]
Abstract
Recent advances in the understanding of basic pathological mechanisms in various neurological diseases depend directly on the development of novel bioanalytical technologies that allow sensitive and specific chemical imaging at high resolution in cells and tissues. Mass spectrometry-based molecular imaging (IMS) has gained increasing popularity in biomedical research for mapping the spatial distribution of molecular species in situ. The technology allows for comprehensive, untargeted delineation of in situ distribution profiles of metabolites, lipids, peptides and proteins. A major advantage of IMS over conventional histochemical techniques is its superior molecular specificity. Imaging mass spectrometry has therefore great potential for probing molecular regulations in CNS-derived tissues and cells for understanding neurodegenerative disease mechanism. The goal of this review is to familiarize the reader with the experimental workflow, instrumental developments and methodological challenges as well as to give a concise overview of the major advances and recent developments and applications of IMS-based protein and peptide profiling with particular focus on neurodegenerative diseases. This article is part of the Special Issue "Proteomics".
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Affiliation(s)
- Wojciech Michno
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Patrick M Wehrli
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, UK.,Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
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10
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Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues. PLoS One 2018; 13:e0203608. [PMID: 30192857 PMCID: PMC6128582 DOI: 10.1371/journal.pone.0203608] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/23/2018] [Indexed: 01/02/2023] Open
Abstract
RNA and DNA analyses from paraffin-embedded tissues (PET) are an important diagnostic tool for characterization of a disease, exploring biomarkers and treatment options. Since nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissue are of limited use for molecular analyses due to chemical modifications of biomolecules alternate, formalin-free fixation reagents such as the PAXgene Tissue system are of evolving interest. Furthermore, biomedical research and biomarker development critically relies on using long-term stored PET from medical archives or biobanks to correlate molecular features with long-term disease outcomes. We therefore performed a comparative study to evaluate the effect of long term storage of FFPE and PAXgene Tissue-fixed and paraffin-embedded (PFPE) tissue at different temperatures on nucleic acid stability and usability in PCR. Matched FFPE and PFPE human tissues from routine clinical setting or rat tissues from a highly controlled animal model were stored at room temperature and 4°C, as well as in case of animal tissues frozen at -20°C and -80°C. RNA and DNA were extracted in intervals for up to nine years, and examined for integrity, and usability in quantitative RT-PCR (RT-qPCR) or PCR (qPCR) assays. PET storage at room temperature led to a degradation of nucleic acids which was slowed down by storage at 4°C and prevented by storage at -20°C or -80°C. Degradation was associated with an amplicon length depending decrease of RT-qPCR and qPCR efficiency. Storage at 4°C improved amplifiability in RT-qPCR and qPCR profoundly. Chemically unmodified nucleic acids from PFPE tissue performed superior compared to FFPE tissue, regardless of storage time and temperature in both human and rat tissues. In conclusion molecular analyses from PET can be greatly improved by using a non-crosslinking fixative and storage at lower temperatures such as 4°C, which should be considered in prospective clinical studies.
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11
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Huber K, Khamehgir-Silz P, Schramm T, Gorshkov V, Spengler B, Römpp A. Approaching cellular resolution and reliable identification in mass spectrometry imaging of tryptic peptides. Anal Bioanal Chem 2018; 410:5825-5837. [PMID: 30066193 PMCID: PMC6096711 DOI: 10.1007/s00216-018-1199-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/24/2018] [Accepted: 06/13/2018] [Indexed: 01/19/2023]
Abstract
On-tissue digestion has become the preferred method to identify proteins in mass spectrometry (MS) imaging. In this study, we report advances in data acquisition and protein identification for MS imaging after on-tissue digestion. Tryptic peptides in a coronal mouse brain section were measured at 50 μm pixel size and revealed detailed histological structures, e.g., the ependyma (consisting of one to two cell layers), which was confirmed by H&E staining. This demonstrates that MS imaging of tryptic peptides at or close to cellular resolution is within reach. We also describe a detailed identification workflow which resulted in the identification of 99 proteins (with 435 corresponding peptides), based on comparison with LC-MS/MS data and in silico digest. These results were obtained with stringent parameters, including high mass accuracy in imaging mode (RSME < 3 ppm) and at least two unique peptides per protein showing consistent spatial distribution. We identified almost 50% of proteins with at least four corresponding peptides. As there is no agreed approach for identification of proteins after on-tissue digestion yet, we discuss our workflow in detail and make the corresponding mass spectral data available as “open data” via ProteomeXchange (identifier PXD003172). With this, we would like to contribute to a more effective discussion and the development of new approaches for tryptic peptide identification in MS imaging. From an experimental point of view, we demonstrate the improvement due to the combination of high spatial resolution and high mass resolution/mass accuracy on a measurement at 25 μm pixel size in mouse cerebellum tissue. A whole body section of a mouse pub imaged at 50 μm pixel size (40 GB, 230,000 spectra) demonstrates the stability of our protocol. For this data set, we developed a workflow that is based on conversion to the common data format imzML and sequential application of freely available software tools. In combination, the presented results for spatial resolution, protein identification, and data processing constitute significant improvements for the field of on-tissue digestion. MS imaging of coronal mouse brain cerebellum with a pixel size of 25 μm: A Optical image, B myelin staining, C H&E staining, and D MS image overlay (RGB) of tryptic peptides m/z = 726.4045 ± 0.005, HGFLPR + H+ (red), m/z = 536.3173 ± 0.005, AKPAK + Na+ (green), and m/z = 994.5436 ± 0.005, WRQLIEK + Na+ (blue) ![]()
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Affiliation(s)
- Katharina Huber
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Pegah Khamehgir-Silz
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Thorsten Schramm
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Vladimir Gorshkov
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Andreas Römpp
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany. .,Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitaetsstrasse 30, 95440, Bayreuth, Germany.
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12
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Sanchez I, Betsou F, Culot B, Frasquilho S, McKay SC, Pericleous S, Smith C, Thomas G, Mathieson W. RNA and microRNA Stability in PAXgene-Fixed Paraffin-Embedded Tissue Blocks After Seven Years' Storage. Am J Clin Pathol 2018; 149:536-547. [PMID: 29659661 DOI: 10.1093/ajcp/aqy026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To evaluate the stability of RNA and microRNA (miRNA) in PAXgene-fixed paraffin-embedded tissue blocks after 7 years' storage. METHODS RNA and miRNA were extracted from PAXgene-fixed paraffin-embedded (PFPE) blocks in 2009 then stored at -80°C. Seven years later, RNA and miRNA were again extracted from the same blocks. RNA and miRNA integrity in the 2009 and 2016 extractions were compared using RNA integrity number (RIN), paraffin-embedded RNA metric (PERM), reverse transcription polymerase chain reaction (RT-PCR) for different amplicon lengths, and quantitative RT-PCR (qRT-PCR) for three mRNA and three miRNA targets. RESULTS In PFPE blocks, mRNA was poorer in 2016 extractions compared to the 2009 extractions in all blocks and all assays applied, with transcripts degrading at different rates in the same blocks. For miRNA, qRT-PCR showed no statistically significant differences between 2009 and 2016 extractions. CONCLUSIONS mRNA in PFPE tissue blocks degrades at room temperature storage over 7 years.
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Affiliation(s)
| | - Fay Betsou
- Integrated Biobank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Siobhan C McKay
- Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | - Gerry Thomas
- Department of Surgery and Cancer, Imperial College London, London, UK
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