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Schurman CA, Bons J, Woo JJ, Yee C, Tao N, Alliston T, Angel PM, Schilling B. Mass Spectrometry Imaging of the Subchondral Bone in Osteoarthritis Reveals Tissue Remodeling of Extracellular Matrix Proteins that Precede Cartilage Loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.03.606482. [PMID: 39211075 PMCID: PMC11361078 DOI: 10.1101/2024.08.03.606482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Osteoarthritis (OA) of the knee is a degenerative condition of the skeletal extracellular matrix (ECM) marked by the loss of articular cartilage and subchondral bone homeostasis. Treatments for OA in the knee beyond full joint replacement are lacking primarily due to gaps in molecular knowledge of the biological drivers of disease. Here, Mass Spectrometry Imaging (MSI) enabled molecular spatial mapping of the proteomic landscape of human knee tissues. Histologic sections of human tibial plateaus from OA patients and cadaveric controls were treated with collagenase III to target ECM proteins prior to imaging using a timsTOF fleX mass spectrometer (Bruker) for matrix-assisted laser desorption ionization (MALDI)-MSI of bone and cartilage proteins in human knees. Spatial MSI data of the knee, using sections of the tibial plateau from non-arthritic, cadaveric donors or from knee replacement patients with medial OA were processed and automatically segmented identifying distinct areas of joint damage. ECM peptide markers compared either OA to cadaveric tissues or OA medial to OA lateral. Not only did candidate peptides distinguish OA relative to intact cartilage, but also emphasized a significant spatial difference between OA and intact subchondral bone (AUROC >0.85). Overall, 31 peptide candidates from ECM proteins, including COL1A1, COL3A1, and unanticipated detection of collagens COL6A1 and COL6A3 in adult bone, exhibited significantly elevated abundance in diseased tissue. Highly specific hydroxyproline-containing collagens dominated OA subchondral bone directly under regions of lost cartilage revealing dramatic tissue remodeling providing molecular details on the progression of joint degeneration in OA. The identification of specific spatial markers for the progression of subchondral bone degeneration in OA advances our molecular understanding of coupled deterioration of joint tissues.
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Chadha RS, Guerrero JA, Wei L, Sanchez LM. Seeing is Believing: Developing Multimodal Metabolic Insights at the Molecular Level. ACS CENTRAL SCIENCE 2024; 10:758-774. [PMID: 38680555 PMCID: PMC11046475 DOI: 10.1021/acscentsci.3c01438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 05/01/2024]
Abstract
This outlook explores how two different molecular imaging approaches might be combined to gain insight into dynamic, subcellular metabolic processes. Specifically, we discuss how matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and stimulated Raman scattering (SRS) microscopy, which have significantly pushed the boundaries of imaging metabolic and metabolomic analyses in their own right, could be combined to create comprehensive molecular images. We first briefly summarize the recent advances for each technique. We then explore how one might overcome the inherent limitations of each individual method, by envisioning orthogonal and interchangeable workflows. Additionally, we delve into the potential benefits of adopting a complementary approach that combines both MSI and SRS spectro-microscopy for informing on specific chemical structures through functional-group-specific targets. Ultimately, by integrating the strengths of both imaging modalities, researchers can achieve a more comprehensive understanding of biological and chemical systems, enabling precise metabolic investigations. This synergistic approach holds substantial promise to expand our toolkit for studying metabolites in complex environments.
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Affiliation(s)
- Rahuljeet S Chadha
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 United States
| | - Jason A Guerrero
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064 United States
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 United States
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064 United States
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3
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Bender K, Wang Y, Zhai CY, Saenz Z, Wang A, Neumann EK. Sample Preparation Method for MALDI Mass Spectrometry Imaging of Fresh-Frozen Spines. Anal Chem 2023; 95:17337-17346. [PMID: 37886878 PMCID: PMC10688227 DOI: 10.1021/acs.analchem.3c03672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
Technologies assessing the lipidomics, genomics, epigenomics, transcriptomics, and proteomics of tissue samples at single-cell resolution have deepened our understanding of physiology and pathophysiology at an unprecedented level of detail. However, the study of single-cell spatial metabolomics in undecalcified bones faces several significant challenges, such as the fragility of bone, which often requires decalcification or fixation leading to the degradation or removal of lipids and other molecules. As such, we describe a method for performing mass spectrometry imaging on undecalcified spine that is compatible with other spatial omics measurements. In brief, we use fresh-frozen rat spines and a system of carboxyl methylcellulose embedding, cryofilm, and polytetrafluoroethylene rollers to maintain tissue integrity while avoiding signal loss from variations in laser focus and artifacts from traditional tissue processing. This reveals various tissue types and lipidomic profiles of spinal regions at 10 μm spatial resolutions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We expect this method to be adapted and applied to the analysis of the spinal cord, shedding light on the mechanistic aspects of cellular heterogeneity, development, and disease pathogenesis underlying different bone-related conditions and diseases. This study furthers the methodology for high spatial metabolomics of spines and adds to the collective efforts to achieve a holistic understanding of diseases via single-cell spatial multiomics.
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Affiliation(s)
- Kayle
J. Bender
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Yongheng Wang
- Department
of Biomedical Engineering, University of
California, Davis, Davis, California 95616, United States
| | - Chuo Ying Zhai
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Zoe Saenz
- Department
of Surgery, School of Medicine, University
of California, Davis, Sacramento, California 95817, United States
| | - Aijun Wang
- Center
for Surgical Bioengineering, Department of Surgery, School of Medicine, University of California, Davis, Sacramento, California 95817, United States
- Institute
for Pediatric Regenerative Medicine, Shriners
Hospital for Children Northern California, UC Davis School of Medicine, Sacramento, California 96817, United States
| | - Elizabeth K. Neumann
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
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4
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Bender KJ, Wang Y, Zhai CY, Saenz Z, Wang A, Neumann EK. Spatial lipidomics of fresh-frozen spines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554488. [PMID: 37662353 PMCID: PMC10473750 DOI: 10.1101/2023.08.23.554488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Technologies assessing the lipidomics, genomics, epigenomics, transcriptomics, and proteomics of tissue samples at single-cell resolution have deepened our understanding of physiology and pathophysiology at an unprecedented level of detail. However, the study of single-cell spatial metabolomics in undecalcified bones faces several significant challenges, such as the fragility of bone which often requires decalcification or fixation leading to the degradation or removal of lipids and other molecules and. As such, we describe a method for performing mass spectrometry imaging on undecalcified spine that is compatible with other spatial omics measurements. In brief, we use fresh-freeze rat spines and a system of carboxyl methylcellulose embedding, cryofilm, and polytetrafluoroethylene rollers to maintain tissue integrity, while avoiding signal loss from variations in laser focus and artifacts from traditional tissue processing. This reveals various tissue types and lipidomic profiles of spinal regions at 10 μm spatial resolutions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We expect this method to be adapted and applied to the analysis of spinal cord, shedding light on the mechanistic aspects of cellular heterogeneity, development, and disease pathogenesis underlying different bone-related conditions and diseases. This study furthers the methodology for high spatial metabolomics of spines, as well as adds to the collective efforts to achieve a holistic understanding of diseases via single-cell spatial multi-omics.
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Affiliation(s)
- Kayle J. Bender
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Yongheng Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, United States
| | - Chuo Ying Zhai
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Zoe Saenz
- Department of Surgery, University of California, Davis, School of Medicine, Sacramento, CA 95817, United States
| | - Aijun Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, United States
- Department of Surgery, University of California, Davis, School of Medicine, Sacramento, CA 95817, United States
- Institute for Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, UC Davis School of Medicine, Sacramento, CA 96817, United States
| | - Elizabeth K. Neumann
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
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5
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Lukowski JK, Olson H, Velickovic M, Wang J, Kyle JE, Kim YM, Williams SM, Zhu Y, Huyck HL, McGraw MD, Poole C, Rogers L, Misra R, Alexandrov T, Ansong C, Pryhuber GS, Clair G, Adkins JN, Carson JP, Anderton CR. An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue. Front Mol Biosci 2022; 9:1022775. [PMID: 36465564 PMCID: PMC9709465 DOI: 10.3389/fmolb.2022.1022775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/02/2022] [Indexed: 04/23/2024] Open
Abstract
Human disease states are biomolecularly multifaceted and can span across phenotypic states, therefore it is important to understand diseases on all levels, across cell types, and within and across microanatomical tissue compartments. To obtain an accurate and representative view of the molecular landscape within human lungs, this fragile tissue must be inflated and embedded to maintain spatial fidelity of the location of molecules and minimize molecular degradation for molecular imaging experiments. Here, we evaluated agarose inflation and carboxymethyl cellulose embedding media and determined effective tissue preparation protocols for performing bulk and spatial mass spectrometry-based omics measurements. Mass spectrometry imaging methods were optimized to boost the number of annotatable molecules in agarose inflated lung samples. This optimized protocol permitted the observation of unique lipid distributions within several airway regions in the lung tissue block. Laser capture microdissection of these airway regions followed by high-resolution proteomic analysis allowed us to begin linking the lipidome with the proteome in a spatially resolved manner, where we observed proteins with high abundance specifically localized to the airway regions. We also compared our mass spectrometry results to lung tissue samples preserved using two other inflation/embedding media, but we identified several pitfalls with the sample preparation steps using this preservation method. Overall, we demonstrated the versatility of the inflation method, and we can start to reveal how the metabolome, lipidome, and proteome are connected spatially in human lungs and across disease states through a variety of different experiments.
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Affiliation(s)
| | - Heather Olson
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Marija Velickovic
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Juan Wang
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Jennifer E. Kyle
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Young-Mo Kim
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Sarah M. Williams
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Ying Zhu
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Heidi L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Matthew D. McGraw
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Cory Poole
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Lisa Rogers
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Ravi Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Charles Ansong
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Geremy Clair
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Joshua N. Adkins
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - James P. Carson
- Texas Advanced Computing Center (TACC), University of Texas at Austin, Austin, TX, United States
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7
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Darie-Ion L, Whitham D, Jayathirtha M, Rai Y, Neagu AN, Darie CC, Petre BA. Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research. Molecules 2022; 27:6196. [PMID: 36234736 PMCID: PMC9570737 DOI: 10.3390/molecules27196196] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is one of the most widely used techniques in proteomics to achieve structural identification and characterization of proteins and peptides, including their variety of proteoforms due to post-translational modifications (PTMs) or protein-protein interactions (PPIs). MALDI-MS and MALDI tandem mass spectrometry (MS/MS) have been developed as analytical techniques to study small and large molecules, offering picomole to femtomole sensitivity and enabling the direct analysis of biological samples, such as biofluids, solid tissues, tissue/cell homogenates, and cell culture lysates, with a minimized procedure of sample preparation. In the last decades, structural identification of peptides and proteins achieved by MALDI-MS/MS helped researchers and clinicians to decipher molecular function, biological process, cellular component, and related pathways of the gene products as well as their involvement in pathogenesis of diseases. In this review, we highlight the applications of MALDI ionization source and tandem approaches for MS for analyzing biomedical relevant peptides and proteins. Furthermore, one of the most relevant applications of MALDI-MS/MS is to provide "molecular pictures", which offer in situ information about molecular weight proteins without labeling of potential targets. Histology-directed MALDI-mass spectrometry imaging (MSI) uses MALDI-ToF/ToF or other MALDI tandem mass spectrometers for accurate sequence analysis of peptide biomarkers and biological active compounds directly in tissues, to assure complementary and essential spatial data compared with those obtained by LC-ESI-MS/MS technique.
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Affiliation(s)
- Laura Darie-Ion
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Yashveen Rai
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 22, 700505 Iasi, Romania
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Brînduşa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
- Center for Fundamental Research and Experimental Development in Translation Medicine–TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania
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8
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Cheng CF, Liao HJ, Wu CS. Tissue microenvironment dictates inflammation and disease activity in rheumatoid arthritis. J Formos Med Assoc 2022; 121:1027-1033. [PMID: 35144834 DOI: 10.1016/j.jfma.2022.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/08/2022] [Accepted: 01/23/2022] [Indexed: 12/12/2022]
Abstract
The recent advance in treatments for rheumatoid arthritis (RA) has significantly improved the prognosis of RA patients. However, these novel therapies do not work well for all RA patients. The unmet need suggests that the current understanding about how inflammatory response arises and progresses in RA is limited. Recent accumulating evidence reveals an important role for the tissue microenvironment in the pathogenesis of RA. The synovium, the main tissue where the RA activity occurs, is composed by a unique extracellular matrix (ECM) and residing cells. The ECM molecules provide environmental signals that determine programmed site-specific cell behavior. Improved understanding of the tissue microenvironment, especially how the synovial architecture, ECM molecules, and site-specific cell behavior promote chronic inflammation and tissue destruction, will enhance deciphering the pathogenesis of RA. Moreover, in-depth analysis of tissue microenvironment will allow us to identify potential therapeutic targets. Research is now undertaken to explore potential candidates, both cellular and ECM molecules, to develop novel therapies. This article reviews recent advances in knowledge about how changes in cellular and ECM factors within the tissue microenvironment result in propagation of chronic inflammation in RA.
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Affiliation(s)
- Chiao-Feng Cheng
- Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin County, Taiwan
| | - Hsiu-Jung Liao
- Department of Orthopedic Surgery, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Chien-Sheng Wu
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan.
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9
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Engel KM, Prabutzki P, Leopold J, Nimptsch A, Lemmnitzer K, Vos DRN, Hopf C, Schiller J. A new update of MALDI-TOF mass spectrometry in lipid research. Prog Lipid Res 2022; 86:101145. [PMID: 34995672 DOI: 10.1016/j.plipres.2021.101145] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/06/2021] [Accepted: 12/29/2021] [Indexed: 01/06/2023]
Abstract
Matrix-assisted laser desorption and ionization (MALDI) mass spectrometry (MS) is an indispensable tool in modern lipid research since it is fast, sensitive, tolerates sample impurities and provides spectra without major analyte fragmentation. We will discuss some methodological aspects, the related ion-forming processes and the MALDI MS characteristics of the different lipid classes (with the focus on glycerophospholipids) and the progress, which was achieved during the last ten years. Particular attention will be given to quantitative aspects of MALDI MS since this is widely considered as the most serious drawback of the method. Although the detailed role of the matrix is not yet completely understood, it will be explicitly shown that the careful choice of the matrix is crucial (besides the careful evaluation of the positive and negative ion mass spectra) in order to be able to detect all lipid classes of interest. Two developments will be highlighted: spatially resolved Imaging MS is nowadays well established and the distribution of lipids in tissues merits increasing interest because lipids are readily detectable and represent ubiquitous compounds. It will also be shown that a combination of MALDI MS with thin-layer chromatography (TLC) enables a fast spatially resolved screening of an entire TLC plate which makes the method competitive with LC/MS.
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Affiliation(s)
- Kathrin M Engel
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - Patricia Prabutzki
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - Jenny Leopold
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - Ariane Nimptsch
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - Katharina Lemmnitzer
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany
| | - D R Naomi Vos
- Center for Biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, D-68163 Mannheim, Germany
| | - Carsten Hopf
- Center for Biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, D-68163 Mannheim, Germany
| | - Jürgen Schiller
- Leipzig University, Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstraße 16-18, D-04107, Germany.
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10
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Nauta SP, Poeze M, Heeren RMA, Porta Siegel T. Clinical use of mass spectrometry (imaging) for hard tissue analysis in abnormal fracture healing. Clin Chem Lab Med 2021; 58:897-913. [PMID: 32049645 DOI: 10.1515/cclm-2019-0857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/16/2019] [Indexed: 12/23/2022]
Abstract
Common traumas to the skeletal system are bone fractures and injury-related articular cartilage damage. The healing process can be impaired resulting in non-unions in 5-10% of the bone fractures and in post-traumatic osteoarthritis (PTOA) in up to 75% of the cases of cartilage damage. Despite the amount of research performed in the areas of fracture healing and cartilage repair as well as non-unions and PTOA, still, the outcome of a bone fracture or articular cartilage damage cannot be predicted. Here, we discuss known risk factors and key molecules involved in the repair process, together with the main challenges associated with the prediction of outcome of these injuries. Furthermore, we review and discuss the opportunities for mass spectrometry (MS) - an analytical tool capable of detecting a wide variety of molecules in tissues - to contribute to extending molecular understanding of impaired healing and the discovery of predictive biomarkers. Therefore, the current knowledge and challenges concerning MS imaging of bone and cartilage tissue as well as in vivo MS are discussed. Finally, we explore the possibilities of in situ, real-time MS for the prediction of outcome during surgery of bone fractures and injury-related articular cartilage damage.
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Affiliation(s)
- Sylvia P Nauta
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands.,Department of Orthopedic Surgery and Traumasurgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Martijn Poeze
- Department of Surgery, Division of Traumasurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Ron M A Heeren
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
| | - Tiffany Porta Siegel
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, The Netherlands
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11
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Location, location, location: how the tissue microenvironment affects inflammation in RA. Nat Rev Rheumatol 2021; 17:195-212. [PMID: 33526927 DOI: 10.1038/s41584-020-00570-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Current treatments for rheumatoid arthritis (RA) do not work well for a large proportion of patients, or at all in some individuals, and cannot cure or prevent this disease. One major obstacle to developing better drugs is a lack of complete understanding of how inflammatory joint disease arises and progresses. Emerging evidence indicates an important role for the tissue microenvironment in the pathogenesis of RA. Each tissue is made up of cells surrounded and supported by a unique extracellular matrix (ECM). These complex molecular networks define tissue architecture and provide environmental signals that programme site-specific cell behaviour. In the synovium, a main site of disease activity in RA, positional and disease stage-specific cellular diversity exist. Improved understanding of the architecture of the synovium from gross anatomy to the single-cell level, in parallel with evidence demonstrating how the synovial ECM is vital for synovial homeostasis and how dysregulated signals from the ECM promote chronic inflammation and tissue destruction in the RA joint, has opened up new ways of thinking about the pathogenesis of RA. These new ideas provide novel therapeutic approaches for patients with difficult-to-treat disease and could also be used in disease prevention.
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12
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Lee YR, Briggs MT, Kuliwaba JS, Anderson PH, Condina MR, Hoffmann P. Gelatin-coated indium tin oxide slides improve human cartilage-bone tissue adherence and N-glycan signal intensity for mass spectrometry imaging. Anal Bioanal Chem 2020; 413:2675-2682. [PMID: 33063168 DOI: 10.1007/s00216-020-02986-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/28/2020] [Accepted: 10/02/2020] [Indexed: 12/16/2022]
Abstract
Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) has been successfully used to elucidate the relative abundance and spatial mapping of analytes in situ. Currently, sample preparation workflows for soft formalin-fixed paraffin-embedded (FFPE) tissues, such as brain, liver, kidney, and heart, have been successfully developed. However, hard tissues, such as cartilage-bone, tooth, and whole mouse body, have resulted in the loss of morphology or tissue during the heat-induced epitope retrieval (HIER) step on commercially available conductive indium tin oxide (ITO) slides. Therefore, we have successfully developed a novel and cost-effective sample preparation workflow in which commercial conductive ITO slides are pre-coated with gelatin and chromium potassium sulfate dodecahydrate to improve the adherence of FFPE human osteoarthritic cartilage-bone tissue sections. Gelatin-coated ITO slides also resulted in overall higher N-glycan signal intensity for not only FFPE osteoarthritic cartilage-bone tissue but also for FFPE hard-boiled egg white used as a quality control to assess the quality of sample preparation and MALDI-MSI acquisition. In summary, we present a novel straightforward workflow to improve slide adherence and morphological preservation of FFPE cartilage-bone tissue sections during HIER while improving the signal intensity of N-glycans spatially mapped from the same tissue sections by MALDI-MSI.
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Affiliation(s)
- Yea-Rin Lee
- Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA, 5001, Australia.,Future Industries Institute, Mawson Lakes Campus, University of South Australia, Mawson Lakes, SA, 5095, Australia.,Discipline of Orthopaedics and Trauma, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Matthew T Briggs
- Future Industries Institute, Mawson Lakes Campus, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Julia S Kuliwaba
- Discipline of Orthopaedics and Trauma, Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Paul H Anderson
- Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA, 5001, Australia
| | - Mark R Condina
- Future Industries Institute, Mawson Lakes Campus, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Peter Hoffmann
- Future Industries Institute, Mawson Lakes Campus, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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Sample preparation of formalin-fixed paraffin-embedded tissue sections for MALDI-mass spectrometry imaging. Anal Bioanal Chem 2020; 412:1263-1275. [PMID: 31989198 PMCID: PMC7021751 DOI: 10.1007/s00216-019-02296-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/06/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MALDI MSI) has become a powerful tool with a high potential relevance for the analysis of biomolecules in tissue samples in the context of diseases like cancer and cardiovascular or cardiorenal diseases. In recent years, significant progress has been made in the technology of MALDI MSI. However, a more systematic optimization of sample preparation would likely achieve an increase in the molecular information derived from MALDI MSI. Therefore, we have employed a systematic approach to develop, establish and validate an optimized "standard operating protocol" (SOP) for sample preparation in MALDI MSI of formalin-fixed paraffin-embedded (FFPE) tissue sample analyses within this study. The optimized parameters regarding the impact on the resulting signal-to-noise (S/N) ratio were as follows: (i) trypsin concentration, solvents, deposition method, and incubation time; (ii) tissue washing procedures and drying processes; and (iii) spray flow rate, number of layers of trypsin deposition, and grid size. The protocol was evaluated on interday variability and its applicability for analyzing the mouse kidney, aorta, and heart FFPE tissue samples. In conclusion, an optimized SOP for MALDI MSI of FFPE tissue sections was developed to generate high sensitivity, to enhance spatial resolution and reproducibility, and to increase its applicability for various tissue types. This optimized SOP will further increase the molecular information content and intensify the use of MSI in future basic research and diagnostic applications. Graphical Abstract.
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Neagu AN. Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:55-98. [PMID: 31347042 DOI: 10.1007/978-3-030-15950-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania.
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Leopold J, Popkova Y, Engel KM, Schiller J. Visualizing phosphatidylcholine via mass spectrometry imaging: relevance to human health. Expert Rev Proteomics 2018; 15:791-800. [PMID: 30241449 DOI: 10.1080/14789450.2018.1526679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Mass spectrometry imaging (MSI) techniques are nowadays widely used to obtain spatially resolved metabolite information from biological tissues. Since (phospho)lipids occur in all animal tissues and are very sensitively detectable, they are often in the focus of such studies. This particularly applies for phosphatidylcholines (PC) which are very sensitively detectable as positive ions due to the permanent positive charge of their choline headgroup. Areas covered: After a short introduction of lipid species occurring in biological systems and approaches normally used to obtain spatially resolved mass spectra (with the focus on matrix-assisted laser desorption/ionization coupled to time-of-flight (MALDI-TOF) MSI) a survey will be given which diseases have so far been characterized by changes of the PC composition. Expert commentary: Since PC species are very sensitively detectable by MS, sensitivity is not a major issue. However, spatial resolution is still limited and cellular dimensions can be hardly resolved by MALDI-TOF MSI, which is a critical point of the available approaches. Due to lacks of reproducibility and standardization further development is required.
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Affiliation(s)
- Jenny Leopold
- a Faculty of Medicine, Institute for Medical Physics and Biophysics , Leipzig University , Leipzig , Germany
| | - Yulia Popkova
- a Faculty of Medicine, Institute for Medical Physics and Biophysics , Leipzig University , Leipzig , Germany
| | - Kathrin M Engel
- a Faculty of Medicine, Institute for Medical Physics and Biophysics , Leipzig University , Leipzig , Germany
| | - Jürgen Schiller
- a Faculty of Medicine, Institute for Medical Physics and Biophysics , Leipzig University , Leipzig , Germany
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