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Parmar D, Rosado-Rosa JM, Shrout JD, Sweedler JV. Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms. Methods 2024; 224:21-34. [PMID: 38295894 PMCID: PMC11149699 DOI: 10.1016/j.ymeth.2024.01.014] [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: 07/20/2023] [Revised: 12/17/2023] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.
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Affiliation(s)
- Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joenisse M Rosado-Rosa
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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Saigusa D, Saito R, Kawamoto K, Uruno A, Kano K, Shimma S, Aoki J, Yamamoto M, Kawamoto T. Improving the Signal Intensity of Cryosections Using a Conductive Adhesive Film in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Mass Spectrom (Tokyo) 2023; 12:A0137. [PMID: 38107656 PMCID: PMC10721960 DOI: 10.5702/massspectrometry.a0137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/27/2023] [Indexed: 12/19/2023] Open
Abstract
The matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) technique was used to obtain the molecular images of cryosections without labeling. Although MALDI-MSI has been widely used to detect small molecules from biological tissues, issues remain due to the technical process of cryosectioning and limited mass spectrometry parameters. The use of a conductive adhesive film is a unique method to obtain high-quality sections from cutting tissue, such as bone, muscle, adipose tissue, and whole body of mice or fish, and we have reported the utilization of the film for MALDI-MSI in previous. However, some signal of the small molecules using the conductive adhesive films was still lower than on the indium tin oxide (ITO) glass slide. Here, the sample preparation and analytical conditions for MALDI-MSI using an advanced conductive adhesive film were optimized to obtain strong signals from whole mice heads. The effects of tissue thickness and laser ionization power on signal intensity were verified using MALDI-MSI. The phospholipid signal intensity was measured for samples with three tissue thicknesses (5, 10, and 20 μm); compared to the signals from the samples on the ITO glass slides, the signals with conductive adhesive films exhibited significantly higher intensities when a laser with a higher range of power was used to ionize the small molecules. Thus, the technique using the advanced conductive adhesive film showed an improvement in MALDI-MSI analysis.
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Affiliation(s)
- Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, 2–11–1 Kaga, Itabashi-ku, Tokyo 173–8605, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8573, Japan
| | - Ritsumi Saito
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Komei Kawamoto
- School of Dental Medicine, Tsurumi University, 2–1–3 Tsurumi, Tsurumi-ku, Yokohama, Kanagawa 230–8501, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8573, Japan
- Medical Biochemistry, Tohoku University School of Medicine, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8575, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113–0033, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamada-oka, Suita, Osaka 565–0871, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113–0033, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8573, Japan
- Medical Biochemistry, Tohoku University School of Medicine, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8575, Japan
| | - Tadafumi Kawamoto
- School of Dental Medicine, Tsurumi University, 2–1–3 Tsurumi, Tsurumi-ku, Yokohama, Kanagawa 230–8501, Japan
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Chen Y, Liu Y, Li X, He Y, Li W, Peng Y, Zheng J. Recent Advances in Mass Spectrometry-Based Spatially Resolved Molecular Imaging of Drug Disposition and Metabolomics. Drug Metab Dispos 2023; 51:1273-1283. [PMID: 37295949 DOI: 10.1124/dmd.122.001069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/04/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Mass spectrometric imaging is a nontargeted, tag-free, high-throughput, and highly responsive analytical approach. The highly accurate molecular visualization detection technology enables qualitative and quantitative analyses of biologic tissues or cells scanned by mass spectrometry in situ, extracting known and unknown multiple compounds, and simultaneously assessing relative contents of targeting molecules by monitoring their molecular ions and pinpointing the spatial locations of those molecules distributed. Five mass spectrometric imaging techniques and their characteristics are introduced in the review, including matrix-assisted laser desorption ionization mass spectrometry, secondary ion mass spectrometry, desorption electrospray ionization mass spectrometry, laser ablation electrospray ionization mass spectrometry, and laser ablation inductively coupled plasma mass spectrometry. The mass spectrometry-based techniques provide the possibility for spatial metabolomics with the capability of high throughput and precision detection. The approaches have been widely employed to spatially image not only metabolome of endogenous amino acids, peptides, proteins, neurotransmitters, and lipids but also the disposition of exogenous chemicals, such as pharmaceutical agents, environmental pollutants, toxicants, natural products, and heavy metals. The techniques also provide us with spatial distribution imaging of analytes in single cells, tissue microregions, organs, and whole animals. SIGNIFICANCE STATEMENT: The review article includes an overview of five commonly used mass spectrometers for spatial imaging and describes the advantages and disadvantages of each. Examples of the technology applications cover drug disposition, diseases, and omics. Technical aspects of relative and absolute quantification by mass spectrometric imaging and challenges for future new applications are discussed as well. The reviewed knowledge may benefit the development of new drugs and provide a better understanding of biochemical processes related to physiology and diseases.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ximei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Yan He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Peng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
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Chen X, Shu W, Zhao L, Wan J. Advanced mass spectrometric and spectroscopic methods coupled with machine learning for in vitro diagnosis. VIEW 2022. [DOI: 10.1002/viw.20220038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Xiaonan Chen
- School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Weikang Shu
- School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Liang Zhao
- School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Jingjing Wan
- School of Chemistry and Molecular Engineering East China Normal University Shanghai China
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Wang Y, Wei X, Liu JH, Wu CX, Zhang X, Chen ML, Wang JH. Cryogenic Laser Ablation in a Rapid Cooling Chamber Ensures Excellent Elemental Imaging in Fresh Biological Tissues. Anal Chem 2022; 94:8547-8553. [PMID: 35653437 DOI: 10.1021/acs.analchem.2c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Laser ablation inductively coupled plasma mass spectrometry imaging of biologically significant targets largely relies on maintaining the original structures of samples. The temperature regulation capability of the ablation cell is crucial. Herein, a rapid cooling cryogenic sample cell (RCCSC) was developed. In the RCCSC chamber, the temperature reduces to -20 °C in 4 min with a minimum 10 h variation of ±0.1 °C at -26 °C. Improvements on the precision were achieved for the elements of interest in NIST 612 and spiked agarose gel under cryogenic conditions. The limits of detection improved by up to 1.57, 1.70, 3.26, and 1.33 fold for 63Cu, 66Zn, 57Fe, and 140Ce in agarose gel, respectively, were obtained under cryogenic conditions compared with those at room temperature. In a time period of testing (10 h), the cryogenic ablation maintains the native state of biological tissues with a high water content to ensure better elemental imaging by reducing thermal effects in ablation and suppressing evaporation of water. The rapid cooling cryogenic ablation significantly improves elemental imaging, as demonstrated by the imaging of various elements in coriander leaves. The present study may provide further insights into elemental distributions in fresh biological samples.
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Affiliation(s)
- Yu Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Xing Wei
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Jin-Hui Liu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Cheng-Xin Wu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Xuan Zhang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Ming-Li Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
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6
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Pytskii IS, Kuznetsova ES, Buryak AK. Mass Spectrometric Imaging of Surfaces: Effect of the Way of Applying a Marker Substance on the Quality of Obtained Data. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422050259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Good CJ, Neumann EK, Butrico CE, Cassat JE, Caprioli RM, Spraggins JM. High Spatial Resolution MALDI Imaging Mass Spectrometry of Fresh-Frozen Bone. Anal Chem 2022; 94:3165-3172. [PMID: 35138834 PMCID: PMC9741954 DOI: 10.1021/acs.analchem.1c04604] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bone and bone marrow are vital to mammalian structure, movement, and immunity. These tissues are also commonly subjected to molecular alterations giving rise to debilitating diseases like rheumatoid arthritis and osteomyelitis. Technologies such as matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) facilitate the discovery of spatially resolved chemical information in biological tissue samples to help elucidate the complex molecular processes underlying pathology. Traditionally, preparation of osseous tissue for MALDI IMS has been difficult due to its mineralized composition and heterogeneous morphology, and compensation for these challenges with decalcification and fixation protocols can remove or delocalize molecular species. Here, sample preparation methods were advanced to enable multimodal MALDI IMS of undecalcified, fresh-frozen murine femurs, allowing the distribution of endogenous lipids to be linked to tissue structures and cell types. Adhesive-bound bone sections were mounted onto conductive glass slides with microscopy-compatible glue and freeze-dried to minimize artificial bone marrow damage. High spatial resolution (10 μm) MALDI IMS was employed to characterize lipid distributions, and use of complementary microscopy modalities aided tissue and cell assignments. For example, various phosphatidylcholines localize to the bone marrow, adipose tissue, marrow adipose tissue, and muscle. Further, sphingomyelin(42:1) was abundant in megakaryocytes, whereas sphingomyelin(42:2) was diminished in this cell type. These data reflect the vast molecular and cellular heterogeneity indicative of the bone marrow and the soft tissue surrounding the femur. Multimodal MALDI IMS has the potential to advance bone-related biomedical research by offering deep molecular coverage with spatial relevance in a preserved native bone microenvironment.
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Affiliation(s)
- Christopher J Good
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Casey E Butrico
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - James E Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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Zhu X, Xu T, Peng C, Wu S. Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues. Front Chem 2022; 9:782432. [PMID: 35186891 PMCID: PMC8850921 DOI: 10.3389/fchem.2021.782432] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Compared with conventional optical microscopy techniques, mass spectrometry imaging (MSI) or imaging mass spectrometry (IMS) is a powerful, label-free analytical technique, which can sensitively and simultaneously detect, quantify, and map hundreds of biomolecules, such as peptides, proteins, lipid, and other organic compounds in cells and tissues. So far, although several soft ionization techniques, such as desorption electrospray ionization (DESI) and secondary ion mass spectrometry (SIMS) have been used for imaging biomolecules, matrix-assisted laser desorption/ionization (MALDI) is still the most widespread MSI scanning method. Here, we aim to provide a comprehensive review of MALDI-MSI with an emphasis on its advances of the instrumentation, methods, application, and future directions in single cell and biological tissues.
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Affiliation(s)
- Xiaoping Zhu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tianyi Xu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Shihua Wu, ; Shihua Wu,
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9
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Mass spectrometry imaging in drug distribution and drug metabolism studies – Principles, applications and perspectives. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2021.116482] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Pathmasiri KC, Nguyen TTA, Khamidova N, Cologna SM. Mass spectrometry-based lipid analysis and imaging. CURRENT TOPICS IN MEMBRANES 2021; 88:315-357. [PMID: 34862030 DOI: 10.1016/bs.ctm.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool for in situ mapping of analytes across a sample. With growing interest in lipid biochemistry, the ability to perform such mapping without antibodies has opened many opportunities for MSI and lipid analysis. Herein, we discuss the basics of MSI with particular emphasis on MALDI mass spectrometry and lipid analysis. A discussion of critical advancements as well as protocol details are provided to the reader. In addition, strategies for improving the detection of lipids, as well as applications in biomedical research, are presented.
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Affiliation(s)
- Koralege C Pathmasiri
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Thu T A Nguyen
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Nigina Khamidova
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States; Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, United States.
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Kawamoto K, Suzuki T, Nagano T, Kawamoto T, Gomi K. A Study of Bone Formation around Titanium Implants Using Frozen Sections. J HARD TISSUE BIOL 2021. [DOI: 10.2485/jhtb.30.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Komei Kawamoto
- Department of Periodontology, School of Dental Medicine, Tsurumi University
| | - Takuma Suzuki
- Department of Periodontology, School of Dental Medicine, Tsurumi University
| | - Takatoshi Nagano
- Department of Periodontology, School of Dental Medicine, Tsurumi University
| | | | - Kazuhiro Gomi
- Department of Periodontology, School of Dental Medicine, Tsurumi University
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12
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Preparation of Thin Frozen Sections from Nonfixed and Undecalcified Hard Tissues Using Kawamoto's Film Method (2020). Methods Mol Biol 2021; 2230:259-281. [PMID: 33197019 DOI: 10.1007/978-1-0716-1028-2_15] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A method for preparing frozen sections with an adhesive film is described. In order to observe fine structures and weak fluorescence of samples, new types of adhesive films [Cryofilm type 3C(16UF) and 4D(16UF)] are used. The adhesive film is made with very clear and very low autofluorescence. For gene analysis, a very thin adhesive film (LMD film) is used to cut by means of the laser microdissection (LMD). For MALDI mass spectrometry imaging (MALDI-MSI), a conductive adhesive film (Cryofilm type MS) is used to avoid electric charge of the sample. A biological sample is frozen quickly and freeze-embedded. The frozen sample is cut with a very sharp disposable blade made from fine tungsten carbide. The combination of the adhesive films and the blade can generate 3 micrometer thick sections from samples including bone, while it is also possible to generate 1 μm thick sections. The morphology of bone and soft tissues are preserved using this method. Cells such as osteoblasts, fibroblasts, and osteoclasts are clearly observed with an oil immersion lens at high magnification. Sections generated using the Cryofilm type 3C(16UF) shows weak fluorescent signals more clearly than sections generated with the previously reported adhesive films [Cryofilm type 2C(9) and 2C(10)]. Furthermore fluorescence of the fine structures in cells is clearly shown using a super-high-resolution microscope. Several staining and experimental methods such as histology, histochemistry, enzyme histochemistry, immunohistochemistry, and in situ hybridization can be performed on these sections. This method is also useful for preparing frozen sections of large sample such as a whole-body mouse and rat. In gene analysis, gene quality of sample collected from the section made with the LMD film is superior to that of sample made by a conventional method. The Cryofilm type MS makes almost complete section from tissues including hard tissues and large samples. The satisfactory signals are detected from the section with MALDI-MSI.
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Saigusa D, Matsukawa N, Hishinuma E, Koshiba S. Identification of biomarkers to diagnose diseases and find adverse drug reactions by metabolomics. Drug Metab Pharmacokinet 2020; 37:100373. [PMID: 33631535 DOI: 10.1016/j.dmpk.2020.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Abstract
Metabolomics has been widely used for investigating the biological functions of disease expression and has the potential to discover biomarkers in circulating biofluids or tissue extracts that reflect in phenotypic changes. Metabolic profiling has advantages because of the use of unbiased techniques, including multivariate analysis, and has been applied in pharmacological studies to predict therapeutic and adverse reactions of drugs, which is called pharmacometabolomics (PMx). Nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics has contributed to the discovery of recent disease biomarkers; however, the optimal strategy for the study purpose must be selected from many established protocols, methodologies and analytical platforms. Additionally, information on molecular localization in tissue is essential for further functional analyses related to therapeutic and adverse effects of drugs in the process of drug development. MS imaging (MSI) is a promising technology that can visualize molecules on tissue surfaces without labeling and thus provide localized information. This review summarizes recent uses of MS-based global and wide-targeted metabolomics technologies and the advantages of the MSI approach for PMx and highlights the PMx technique for the biomarker discovery of adverse drug effects.
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Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Eiji Hishinuma
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
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14
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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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15
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Boughton BA, Thomas ORB, Demarais NJ, Trede D, Swearer SE, Grey AC. Detection of small molecule concentration gradients in ocular tissues and humours. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4460. [PMID: 31654531 DOI: 10.1002/jms.4460] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/02/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
The eye is an elegant organ consisting of a number of tissues and fluids with specialised functions that together allow it to effectively transmit and transduce light input to the brain for visual perception. One key determinant of this integrated function is the spatial relationship of ocular tissues. Biomolecular distributions within the main ocular tissues cornea, lens, and retina have been studied extensively in isolation, yet the potential for metabolic communication between ocular tissues via the ocular humours has been difficult to visualise. To address this limitation, the current study presents a method to map spatial distributions of metabolites and small molecules in whole eyes, including ocular humours. Using a tape-transfer system and freeze-drying, the spatial distribution of ocular small molecules was investigated in mouse, rat, fish (black bream), and rabbit eyes using negative ion mode MALDI imaging mass spectrometry. Full-scan imaging was used for discovery experiments, while MS/MS imaging for identification and localisation was also demonstrated. In all eyes, metabolites such as glutathione and phospholipids were localised in the main ocular tissues. In addition, in rodent eyes, major metabolites were distributed relatively uniformly in ocular humours. In contrast, both uniform and spatially defined ocular metabolite distributions were observed in the black bream eye. Tissue and ocular humour distributions were reproducible, as demonstrated by the three-dimensional analysis of a mouse eye, and able to be captured with high spatial resolution analysis. The presented method could be used to further investigate the role of inter-tissue metabolism in ocular health, and to support the development of therapeutics to treat major ocular diseases.
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Affiliation(s)
- Berin A Boughton
- Metabolomics Australia, University of Melbourne, Melbourne, Australia
| | - Oliver R B Thomas
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Nicholas J Demarais
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Stephen E Swearer
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Angus C Grey
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
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16
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Uranbileg B, Ito N, Kurano M, Saigusa D, Saito R, Uruno A, Kano K, Ikeda H, Yamada Y, Sumitani M, Sekiguchi M, Aoki J, Yatomi Y. Alteration of the lysophosphatidic acid and its precursor lysophosphatidylcholine levels in spinal cord stenosis: A study using a rat cauda equina compression model. Sci Rep 2019; 9:16578. [PMID: 31719574 PMCID: PMC6851136 DOI: 10.1038/s41598-019-52999-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/22/2019] [Indexed: 12/13/2022] Open
Abstract
Cauda equina compression (CEC) is a major cause of neurogenic claudication and progresses to neuropathic pain (NP). A lipid mediator, lysophosphatidic acid (LPA), is known to induce NP via the LPA1 receptor. To know a possible mechanism of LPA production in neurogenic claudication, we determined the levels of LPA, lysophosphatidylcholine (LPC) and LPA-producing enzyme autotaxin (ATX), in the cerebrospinal fluid (CSF) and spinal cord (SC) using a CEC as a possible model of neurogenic claudication. Using silicon blocks within the lumbar epidural space, we developed a CEC model in rats with motor dysfunction. LPC and LPA levels in the CSF were significantly increased from day 1. Importantly, specific LPA species (16:0, 18:2, 20:4) were upregulated, which have been shown to produce by ATX detected in the CSF, without changes on its level. In SC, the LPC and LPA levels did not change, but mass spectrometry imaging analysis revealed that LPC was present in a region where the silicon blocks were inserted. These results propose a model for LPA production in SC and CSF upon neurogenic claudication that LPC produced locally by tissue damages is converted to LPA by ATX, which then leak out into the CSF.
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Affiliation(s)
- Baasanjav Uranbileg
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuko Ito
- Department of Anesthesiology and Pain Relief Center, The University of Tokyo, Tokyo, Japan.
| | - Makoto Kurano
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Miyagi, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Ritsumi Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Miyagi, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Miyagi, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Kuniyuki Kano
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Miyagi, Japan
| | - Hitoshi Ikeda
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshitsugu Yamada
- Department of Anesthesiology and Pain Relief Center, The University of Tokyo, Tokyo, Japan
| | - Masahiko Sumitani
- Department of Pain and Palliative Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Miho Sekiguchi
- Department of Orthopaedic Surgery, Fukushima Medical University, School of Medicine, Fukushima, Japan
| | - Junken Aoki
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Miyagi, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo, Japan
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