1
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Arendowski A. Lipidomic approach to identify Escherichia coli and Shigella spp. by matrix-assisted laser desorption/ionization mass spectrometry. Adv Med Sci 2024; 69:238-247. [PMID: 38670227 DOI: 10.1016/j.advms.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/08/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
PURPOSE Escherichia coli (E. coli) and Shigella species, being highly similar, present a challenge for differentiation using classical methods such as phenotyping, 16S rRNA sequencing, or protein profiling using matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The paper proposes a method for identifying E. coli, S. flexneri, S. sonnei, and S. boydii by augmenting the Bruker Biotyper database with reference spectra of lipid profiles obtained using MALDI MS in the positive mode. MATERIALS/METHODS Lipid extracts were made from cultured E. coli, S. flexneri, S. sonnei and S. boydii using the Bligh & Dyer protocol. MALDI MS spectra in positive ion mode were performed for the extracts. Reference spectra were created from 30 spectra for each bacterium and added to the Bruker Biotyper database. RESULTS Identification of bacteria based on lipid profiles in the Biotyper database gave correct results with scores above 2.49. Statistical analysis of the results by Partial Least Squares-Discriminant Analysis (PLS-DA) showed that it is possible to correctly differentiate the microorganisms studied using the lipidomic approach. A panel of six m/z values was proposed for which the value of the area under the ROC curve is 1, thus enabling the identification of E. coli and S. flexneri with 100 % accuracy. CONCLUSIONS Identification of bacteria from lipid fingerprints obtained by the MALDI MS technique is possible and may become a useful tool in the future, especially for microorganisms that are difficult to distinguish by other methods.
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Affiliation(s)
- Adrian Arendowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wileńska 4 Str, Toruń, 87-100, Poland.
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2
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Jha D, Blennow K, Zetterberg H, Savas JN, Hanrieder J. Spatial neurolipidomics-MALDI mass spectrometry imaging of lipids in brain pathologies. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5008. [PMID: 38445816 DOI: 10.1002/jms.5008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/03/2024] [Accepted: 01/25/2024] [Indexed: 03/07/2024]
Abstract
Given the complexity of nervous tissues, understanding neurochemical pathophysiology puts high demands on bioanalytical techniques with respect to specificity and sensitivity. Mass spectrometry imaging (MSI) has evolved to become an important, biochemical imaging technology for spatial biology in biological and translational research. The technique facilitates comprehensive, sensitive elucidation of the spatial distribution patterns of drugs, lipids, peptides, and small proteins in situ. Matrix-assisted laser desorption ionization (MALDI)-based MSI is the dominating modality due to its broad applicability and fair compromise of selectivity, sensitivity price, throughput, and ease of use. This is particularly relevant for the analysis of spatial lipid patterns, where no other comparable spatial profiling tools are available. Understanding spatial lipid biology in nervous tissue is therefore a key and emerging application area of MSI research. The aim of this review is to give a concise guide through the MSI workflow for lipid imaging in central nervous system (CNS) tissues and essential parameters to consider while developing and optimizing MSI assays. Further, this review provides a broad overview of key developments and applications of MALDI MSI-based spatial neurolipidomics to map lipid dynamics in neuronal structures, ultimately contributing to a better understanding of neurodegenerative disease pathology.
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Affiliation(s)
- Durga Jha
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, Mölndal, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, Mölndal, Sweden
- Clinical Neurochemistry Lab, Sahlgrenska University Hospital, Mölndal, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine, Department of Neurology, Institute on Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, China
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, Mölndal, Sweden
- Clinical Neurochemistry Lab, Sahlgrenska University Hospital, Mölndal, Sweden
- UK Dementia Research Institute at UCL, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, Mölndal, Sweden
- Clinical Neurochemistry Lab, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
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3
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Holbrook JH, Kemper GE, Hummon AB. Quantitative mass spectrometry imaging: therapeutics & biomolecules. Chem Commun (Camb) 2024; 60:2137-2151. [PMID: 38284765 PMCID: PMC10878071 DOI: 10.1039/d3cc05988j] [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: 12/08/2023] [Accepted: 01/22/2024] [Indexed: 01/30/2024]
Abstract
Mass spectrometry imaging (MSI) has become increasingly utilized in the analysis of biological molecules. MSI grants the ability to spatially map thousands of molecules within one experimental run in a label-free manner. While MSI is considered by most to be a qualitative method, recent advancements in instrumentation, sample preparation, and development of standards has made quantitative MSI (qMSI) more common. In this feature article, we present a tailored review of recent advancements in qMSI of therapeutics and biomolecules such as lipids and peptides/proteins. We also provide detailed experimental considerations for conducting qMSI studies on biological samples, aiming to advance the methodology.
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Affiliation(s)
- Joseph H Holbrook
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Gabrielle E Kemper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amanda B Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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4
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Griffiths WJ, Yutuc E, Wang Y. Mass Spectrometry Imaging of Cholesterol and Oxysterols. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1440:73-87. [PMID: 38036876 DOI: 10.1007/978-3-031-43883-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Mass spectrometry imaging (MSI) is a new technique in the toolbox of the analytical biochemist. It allows the generation of a compound-specific image from a tissue slice where a measure of compound abundance is given pixel by pixel, usually displayed on a color scale. As mass spectra are recorded at each pixel, the data can be interrogated to generate images of multiple different compounds all in the same experiment. Mass spectrometry (MS) requires the ionization of analytes, but cholesterol and other neutral sterols tend to be poorly ionized by the techniques employed in most MSI experiments, so despite their high abundance in mammalian tissues, cholesterol is poorly represented in the MSI literature. In this chapter, we discuss some of the MSI studies where cholesterol has been imaged and introduce newer methods for its analysis by MSI. Disturbed cholesterol metabolism is linked to many disorders, and the potential of MSI to study cholesterol, its precursors, and its metabolites in animal models and from human biopsies will be discussed.
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Affiliation(s)
| | - Eylan Yutuc
- Swansea University Medical School, Swansea, Wales, UK
| | - Yuqin Wang
- Swansea University Medical School, Swansea, Wales, UK
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5
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Wang H, Li Z, Cao G, Tang L, Zhou R, Li C, Zhang J, Wu H, Li X, Yang H. Targeted Energy Metabolomics Combined with Spatial Metabolomics Study on the Efficacy of Guhong Injection Against Cerebral Ischemia Reperfusion. Mol Neurobiol 2023; 60:5533-5547. [PMID: 37328677 DOI: 10.1007/s12035-023-03403-x] [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: 02/05/2023] [Accepted: 05/23/2023] [Indexed: 06/18/2023]
Abstract
Optimizing the metabolic phenotype to improve cerebral function is critical for treatment of cerebral ischemia-reperfusion (I/R) injury. Guhong injection (GHI), which comprised safflower extract and aceglutamide, is widely prescribed in Chinese medicine for the treatment of cerebrovascular diseases. In this study, a combination of LC-QQQ-MS and MALDI-MSI were utilized to explore tissue-specific metabolic alterations in the brain of I/R, as well as to evaluate the therapeutic effect of GHI. Pharmacological evaluation demonstrated that GHI can significantly improve infarction rate, neurological deficit, cerebral blood flow, and neuronal damage in I/R rats. Based on LC-QQQ-MS, 23 energy metabolites were found to be significantly altered in the I/R group compared to the sham group (P < 0.05). After GHI treatment, 12 metabolites, including G6P, TPP, NAD, citrate, succinate, malate, ATP, GTP, GDP, ADP, NADP, and FMN showed a significant tendency of returning to baseline values (P < 0.05). Based on MALDI-MSI, 4 metabolites in glycolysis and TCA, 4 metabolites in nucleic acid metabolism, 4 amino acid metabolites, and 6 metabolites were discovered and compared between the different groups in the four special regions of cortex, hippocampus, hypothalamus, and striatum. Parts of these were found to have significant changes after I/R in the special brain region, and were regulated by GHI. The study provides comprehensive and detailed information for specific metabolic reprogramming of brain tissue in rats with I/R, and the therapeutic effect of GHI. Schema describing the discovery strategies of integrated LC-MS and MALDI-MSI to identify cerebral ischemia reperfusion metabolic reprogramming and GHI therapeutic effects.
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Affiliation(s)
- Huanhuan Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong Nei Nan Xiao Jie 16, Beijing, 100700, China
| | - Zhenkun Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong Nei Nan Xiao Jie 16, Beijing, 100700, China
| | - Guangzhao Cao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong Nei Nan Xiao Jie 16, Beijing, 100700, China
| | - Liying Tang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong Nei Nan Xiao Jie 16, Beijing, 100700, China.
| | - Rui Zhou
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong Nei Nan Xiao Jie 16, Beijing, 100700, China
| | - Caifeng Li
- Experimental Research Centre, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jingjing Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong Nei Nan Xiao Jie 16, Beijing, 100700, China.
- Chinese Institute for Brain Research, Beijing, 102206, China.
| | - Hongwei Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dong Nei Nan Xiao Jie 16, Beijing, 100700, China.
| | - Xianyu Li
- Experimental Research Centre, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hongjun Yang
- Experimental Research Centre, China Academy of Chinese Medical Sciences, Beijing, 100700, China
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6
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Khamidova N, Pergande MR, Pathmasiri KC, Khan R, Mohr JT, Cologna SM. DBDA matrix increases ion abundance of fatty acids and sulfatides in MALDI-TOF and mass spectrometry imaging studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.524013. [PMID: 36711800 PMCID: PMC9882223 DOI: 10.1101/2023.01.13.524013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
MALDI-TOF MS is a powerful tool to analyze biomolecules owing to its soft ionization nature and generally results in simple spectra of singly charged ions. Moreover, implementation of the technology in imaging mode provides a means to spatially map analytes in situ. Recently, a new matrix, DBDA (N1,N4-dibenzylidenebenzene-1,4-diamine) was reported to facilitate the ionization of free fatty acids in the negative ion mode. Building on this finding, we sought to implement DBDA for MALDI mass spectrometry imaging studies in brain tissue and successfully map oleic acid, palmitic acid, stearic acid, docosahexaenoic acid and arachidonic acid using mouse brain sections. Moreover, we hypothesized that DBDA would provide superior ionization for sulfatides, a class of sulfolipids, with multiple biological functions. Herein we also demonstrate that DBDA is ideal for MALDI mass spectrometry imaging of fatty acids and sulfatides in brain tissue sections. Additionally, we show enhanced ionization of sulfatides using DBDA compared to three different traditionally used MALDI matrices. Together these results provide new opportunities for studies to measure sulfatides by MALDI-TOF MS including in imaging modes.
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7
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Cologna SM, Pathmasiri KC, Pergande MR, Rosenhouse-Dantsker A. Alterations in Cholesterol and Phosphoinositides Levels in the Intracellular Cholesterol Trafficking Disorder NPC. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:143-165. [PMID: 36988880 DOI: 10.1007/978-3-031-21547-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Lipid mistrafficking is a biochemical hallmark of Niemann-Pick Type C (NPC) disease and is classically characterized with endo/lysosomal accumulation of unesterified cholesterol due to genetic mutations in the cholesterol transporter proteins NPC1 and NPC2. Storage of this essential signaling lipid leads to a sequence of downstream events, including oxidative stress, calcium imbalance, neuroinflammation, and progressive neurodegeneration, another hallmark of NPC disease. These observations have been validated in a growing number of studies ranging from NPC cell cultures and animal models to patient specimens. In recent reports, alterations in the levels of another class of critical signaling lipids, namely phosphoinositides, have been described in NPC disease. Focusing on cholesterol and phosphoinositides, the chapter begins by reviewing the interactions of NPC proteins with cholesterol and their role in cholesterol transport. It then continues to describe the modulation of cholesterol efflux in NPC disease. The chapter concludes with a summary of findings related to the functional consequences of perturbations in phosphoinositides in this fatal disease.
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Affiliation(s)
| | | | - Melissa R Pergande
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
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8
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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9
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Schnackenberg LK, Thorn DA, Barnette D, Jones EE. MALDI imaging mass spectrometry: an emerging tool in neurology. Metab Brain Dis 2022; 37:105-121. [PMID: 34347208 DOI: 10.1007/s11011-021-00797-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/11/2021] [Indexed: 12/24/2022]
Abstract
Neurological disease and disorders remain a large public health threat. Thus, research to improve early detection and/or develop more effective treatment approaches are necessary. Although there are many common techniques and imaging modalities utilized to study these diseases, existing approaches often require a label which can be costly and time consuming. Matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS) is a label-free, innovative and emerging technique that produces 2D ion density maps representing the distribution of an analyte(s) across a tissue section in relation to tissue histopathology. One main advantage of MALDI IMS over other imaging modalities is its ability to determine the spatial distribution of hundreds of analytes within a single imaging run, without the need for a label or any a priori knowledge. Within the field of neurology and disease there have been several impactful studies in which MALDI IMS has been utilized to better understand the cellular pathology of the disease and or severity. Furthermore, MALDI IMS has made it possible to map specific classes of analytes to regions of the brain that otherwise may have been lost using more traditional methods. This review will highlight key studies that demonstrate the potential of this technology to elucidate previously unknown phenomenon in neurological disease.
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Affiliation(s)
- Laura K Schnackenberg
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - David A Thorn
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - Dustyn Barnette
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA
| | - E Ellen Jones
- Division of Systems Biology, National Center for Toxicological Research/FDA, 3900 NCTR Rd, Jefferson, AR, USA.
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10
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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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11
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Bos AV, Erkelens MN, Koenders STA, van der Stelt M, van Egmond M, Mebius RE. Clickable Vitamins as a New Tool to Track Vitamin A and Retinoic Acid in Immune Cells. Front Immunol 2021; 12:671283. [PMID: 34305901 PMCID: PMC8298001 DOI: 10.3389/fimmu.2021.671283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/02/2021] [Indexed: 01/24/2023] Open
Abstract
The vitamin A derivative, retinoid acid (RA) is key player in guiding adaptive mucosal immune responses. However, data on the uptake and metabolism of vitamin A within human immune cells has remained largely elusive because retinoids are small, lipophilic molecules which are difficult to detect. To overcome this problem and to be able to study the effect of vitamin A metabolism in human immune cell subsets, we have synthesized novel bio-orthogonal retinoid-based probes (clickable probes), which are structurally and functionally indistinguishable from vitamin A. The probes contain a functional group (an alkyne) to conjugate to a fluorogenic dye to monitor retinoid molecules in real-time in immune cells. We demonstrate, by using flow cytometry and microscopy, that multiple immune cells have the capacity to internalize retinoids to varying degrees, including human monocyte-derived dendritic cells (DCs) and naïve B lymphocytes. We observed that naïve B cells lack the enzymatic machinery to produce RA, but use exogenous retinoic acid to enhance CD38 expression. Furthermore, we showed that human DCs metabolize retinal into retinoic acid, which in co-culture with naïve B cells led to of the induction of CD38 expression. These data demonstrate that in humans, DCs can serve as an exogenous source of RA for naïve B cells. Taken together, through the use of clickable vitamins our data provide valuable insight in the mechanism of vitamin A metabolism and its importance for human adaptive immunity.
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Affiliation(s)
- Amelie V Bos
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center, location VUmc, Amsterdam, Netherlands
| | - Martje N Erkelens
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center, location VUmc, Amsterdam, Netherlands
| | - Sebastiaan T A Koenders
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Marjolein van Egmond
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center, location VUmc, Amsterdam, Netherlands.,Department of Surgery, Amsterdam University Medical Center, location VUmc, Amsterdam, Netherlands
| | - Reina E Mebius
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center, location VUmc, Amsterdam, Netherlands
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12
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Liang X, Cao S, Xie P, Hu X, Lin Y, Liang J, Zhang S, Xian B, Cao H, Luan T, Cai Z. Three-Dimensional Imaging of Whole-Body Zebrafish Revealed Lipid Disorders Associated with Niemann-Pick Disease Type C1. Anal Chem 2021; 93:8178-8187. [PMID: 34061502 DOI: 10.1021/acs.analchem.1c00196] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Imaging of lipids of whole-body specimens in two-dimensional (2D) analysis provides a global picture of the lipid changes in lipid-disturbed diseases, enabling a better understanding of lipid functions and lipid-modulation processes in different organs. However, 2D imaging of a single cross section can hardly characterize the whole-body lipid alterations. In this work, a three-dimensional matrix-assisted laser desorption/ionization mass spectrometry imaging (3D MALDI-MSI) approach was developed for analysis of whole-body zebrafish, for the first time, and applied to identify altered lipids and map their spatial distributions by using a zebrafish model of Niemann-Pick disease type C1 (NPC1), a neurovisceral lipid storage disorder causing both neurodegenerative disorder and visceral organ damage. The constructed 3D fish model provided comprehensive information on the 3D distribution of lipids of interest and allowed direct correlations between these lipids and organs of the fish. Obtained results revealed that several sphingolipids and phospholipids showed significant alterations and exhibited different localization patterns in various organs such as the brain, spinal cord, intestines, and liver-spleen region in the npc1 gene mutant fish compared to those of the wild type. The whole-body 3D MALDI-MSI approach revealed unique lipid signatures for different NPC1-affected organs, which might offer insights into the link between the impaired lipid storage and subsequent clinical symptoms, such as neurodegeneration and hepatosplenomegaly.
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Affiliation(s)
- Xiaoping Liang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Shengxi Cao
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Peisi Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, China
| | - Xudong Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yusheng Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiehua Liang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Shengqi Zhang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Bai Xian
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Hong Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Tiangang Luan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Zongwei Cai
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.,State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, China
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13
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Angelini R, Yutuc E, Wyatt MF, Newton J, Yusuf FA, Griffiths L, Cooze BJ, El Assad D, Frache G, Rao W, Allen LB, Korade Z, Nguyen TTA, Rathnayake RAC, Cologna SM, Howell OW, Clench MR, Wang Y, Griffiths WJ. Visualizing Cholesterol in the Brain by On-Tissue Derivatization and Quantitative Mass Spectrometry Imaging. Anal Chem 2021; 93:4932-4943. [PMID: 33687199 PMCID: PMC7992047 DOI: 10.1021/acs.analchem.0c05399] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Despite being a critical
molecule in the brain, mass spectrometry
imaging (MSI) of cholesterol has been under-reported compared to
other lipids due to the difficulty in ionizing the sterol molecule.
In the present work, we have employed an on-tissue enzyme-assisted
derivatization strategy to improve detection of cholesterol in brain
tissue sections. We report distribution and levels of cholesterol
across specific structures of the mouse brain, in a model of Niemann-Pick
type C1 disease, and during brain development. MSI revealed that in
the adult mouse, cholesterol is the highest in the pons and medulla
and how its distribution changes during development. Cholesterol was
significantly reduced in the corpus callosum and other brain regions
in the Npc1 null mouse, confirming hypomyelination
at the molecular level. Our study demonstrates the potential of MSI
to the study of sterols in neuroscience.
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Affiliation(s)
- Roberto Angelini
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
| | - Eylan Yutuc
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
| | - Mark F Wyatt
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
| | - Jillian Newton
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, U.K
| | - Fowzi A Yusuf
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
| | - Lauren Griffiths
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
| | - Benjamin J Cooze
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
| | - Dana El Assad
- Materials Research and Technology, Luxembourg Institute of Science and Technology, Belvaux L-4422, Luxembourg
| | - Gilles Frache
- Materials Research and Technology, Luxembourg Institute of Science and Technology, Belvaux L-4422, Luxembourg
| | - Wei Rao
- European Application Laboratory, Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, U.K
| | - Luke B Allen
- Departments of Pediatrics and Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Zeljka Korade
- Departments of Pediatrics and Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Thu T A Nguyen
- Department of Chemistry and Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Rathnayake A C Rathnayake
- Department of Chemistry and Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Stephanie M Cologna
- Department of Chemistry and Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Owain W Howell
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomolecular Research Centre, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, U.K
| | - Yuqin Wang
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
| | - William J Griffiths
- Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, U.K
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14
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Luu GT, Condren AR, Kahl LJ, Dietrich LE, Sanchez LM. Evaluation of Data Analysis Platforms and Compatibility with MALDI-TOF Imaging Mass Spectrometry Data Sets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1313-1320. [PMID: 32329613 PMCID: PMC7275808 DOI: 10.1021/jasms.0c00039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Imaging mass spectrometry (IMS) has proven to be a useful tool when investigating the spatial distributions of metabolites and proteins in a biological system. One of the biggest advantages of IMS is the ability to maintain the 3D chemical composition of a sample and analyze it in a label-free manner. However, acquiring the spatial information leads to an increase in data size. Due to the increased availability of commercial mass spectrometers capable of IMS, there has been an exciting development of different statistical tools that can help decipher the spatial relevance of an analyte in a biological sample. To address this need, software packages like SCiLS and the open source R package Cardinal have been designed to perform unbiased spectral grouping based on the similarity of spectra in an IMS data set. In this note, we evaluate SCiLS and Cardinal compatibility with MALDI-TOF IMS data sets of the Gram-negative pathogen Pseudomonas aeruginosa PA14. Both software were able to perform unsupervised segmentation with similar performance. There were a few notable differences which are discussed related to the identification of statistically significant features which required optimization of preprocessing steps, region of interest, and manual analysis.
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Affiliation(s)
- Gordon T. Luu
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612
| | - Alanna R. Condren
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612
| | - Lisa Juliane Kahl
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Laura M. Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60612
- Corresponding Author,
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15
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Andres DA, Young LEA, Gentry MS, Sun RC. Spatial profiling of gangliosides in mouse brain by mass spectrometry imaging. J Lipid Res 2020; 61:1537. [PMID: 32482716 DOI: 10.1194/jlr.ilr120000870] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Douglas A Andres
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Lyndsay E A Young
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Ramon C Sun
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA
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16
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Pathmasiri KC, Pergande MR, Tobias F, Rebiai R, Rosenhouse-Dantsker A, Bongarzone ER, Cologna SM. Mass spectrometry imaging and LC/MS reveal decreased cerebellar phosphoinositides in Niemann-Pick type C1-null mice. J Lipid Res 2020; 61:1004-1013. [PMID: 32371566 DOI: 10.1194/jlr.ra119000606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/21/2020] [Indexed: 12/18/2022] Open
Abstract
Niemann-Pick disease type C1 (NPC1) is a lipid storage disorder in which cholesterol and glycosphingolipids accumulate in late endosomal/lysosomal compartments because of mutations in the NPC1 gene. A hallmark of NPC1 is progressive neurodegeneration of the cerebellum as well as visceral organ damage; however, the mechanisms driving this disease pathology are not fully understood. Phosphoinositides are phospholipids that play distinct roles in signal transduction and vesicle trafficking. Here, we utilized a consensus spectra analysis of MS imaging data sets and orthogonal LC/MS analyses to evaluate the spatial distribution of phosphoinositides and quantify them in cerebellar tissue from Npc1-null mice. Our results suggest significant depletion of multiple phosphoinositide species, including PI, PIP, and PIP2, in the cerebellum of the Npc1-null mice in both whole-tissue lysates and myelin-enriched fractions. Additionally, we observed altered levels of the regulatory enzyme phosphatidylinositol 4-kinase type 2α in Npc1-null mice. In contrast, the levels of related kinases, phosphatases, and transfer proteins were unaltered in the Npc1-null mouse model, as observed by Western blot analysis. Our discovery of phosphoinositide lipid biomarkers for NPC1 opens new perspectives on the pathophysiology underlying this fatal neurodegenerative disease.
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Affiliation(s)
| | | | - Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL
| | - Rima Rebiai
- Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL
| | | | - Ernesto R Bongarzone
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL; Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL. mailto:
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17
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Andrews WT, Donahue D, Holmes A, Balsara R, Castellino FJ, Hummon AB. In situ metabolite and lipid analysis of GluN2D -/- and wild-type mice after ischemic stroke using MALDI MSI. Anal Bioanal Chem 2020; 412:6275-6285. [PMID: 32107573 DOI: 10.1007/s00216-020-02477-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/27/2020] [Accepted: 01/31/2020] [Indexed: 02/06/2023]
Abstract
The N-methyl-D-aspartate (NMDA) receptor is a crucial mediator of pathological glutamate-driven excitotoxicity and subsequent neuronal death in acute ischemic stroke. Although the roles of the NMDAR's composite GluN2A-C subunits have been investigated in this phenomenon, the relative importance of the GluN2D subunit has yet to be evaluated. Herein, GluN2D-/- mice were studied in a model of ischemic stroke using MALDI FT-ICR mass spectrometry imaging to investigate the role of the GluN2D subunit of the NMDA receptor in brain ischemia. GluN2D-/- mice underwent middle cerebral artery occlusion (MCAO) and brain tissue was subsequently harvested, frozen, and cryosectioned. Tissue sections were analyzed via MALDI FT-ICR mass spectrometry imaging. MALDI analyses revealed increases in several calcium-related species, namely vitamin D metabolites, LysoPC, and several PS species, in wild-type mouse brain tissue when compared to wild type. In addition, GluN2D-/- mice also displayed an increase in PC, as well as a decrease in DG, suggesting reduced free fatty acid release from brain ischemia. These trends indicate that GluN2D-/- mice show enhanced rates of neurorecovery and neuroprotection from ischemic strokes compared to wild-type mice. The cause of neuroprotection may be the result of an increase in PGP in knockout mice, contributing to greater cardiolipin synthesis and decreased sensitivity to apoptotic signals. Graphical abstract.
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Affiliation(s)
- William T Andrews
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Cavanaugh Dr, Notre Dame, IN, 46556, USA.
| | - Deborah Donahue
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Cavanaugh Dr, Notre Dame, IN, 46556, USA
| | - Adam Holmes
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Cavanaugh Dr, Notre Dame, IN, 46556, USA
| | - Rashna Balsara
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Cavanaugh Dr, Notre Dame, IN, 46556, USA
| | - Francis J Castellino
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Cavanaugh Dr, Notre Dame, IN, 46556, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry and the Comprehensive Cancer Center, The Ohio State University, 414 Biomedical Research Tower, 460 W 12th Ave, Columbus, OH, 43210, USA.
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18
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Aerts JMFG, Artola M, van Eijk M, Ferraz MJ, Boot RG. Glycosphingolipids and Infection. Potential New Therapeutic Avenues. Front Cell Dev Biol 2019; 7:324. [PMID: 31867330 PMCID: PMC6908816 DOI: 10.3389/fcell.2019.00324] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
Glycosphingolipids (GSLs), the main topic of this review, are a subclass of sphingolipids. With their glycans exposed to the extracellular space, glycosphingolipids are ubiquitous components of the plasma membrane of cells. GSLs are implicated in a variety of biological processes including specific infections. Several pathogens use GSLs at the surface of host cells as binding receptors. In addition, lipid-rafts in the plasma membrane of host cells may act as platform for signaling the presence of pathogens. Relatively common in man are inherited deficiencies in lysosomal glycosidases involved in the turnover of GSLs. The associated storage disorders (glycosphingolipidoses) show lysosomal accumulation of substrate(s) of the deficient enzyme. In recent years compounds have been identified that allow modulation of GSLs levels in cells. Some of these agents are well tolerated and already used to treat lysosomal glycosphingolipidoses. This review summarizes present knowledge on the role of GSLs in infection and subsequent immune response. It concludes with the thought to apply glycosphingolipid-lowering agents to prevent and/or combat infections.
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Affiliation(s)
| | - M Artola
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - M van Eijk
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - M J Ferraz
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - R G Boot
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
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19
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Pergande MR, Serna‐Perez F, Mohsin SB, Hanek J, Cologna SM. Lipidomic Analysis Reveals Altered Fatty Acid Metabolism in the Liver of the Symptomatic Niemann–Pick, Type C1 Mouse Model. Proteomics 2019; 19:e1800285. [DOI: 10.1002/pmic.201800285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/22/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Melissa R. Pergande
- Department of ChemistryUniversity of Illinois at Chicago Chicago IL 60607 USA
| | - Fidel Serna‐Perez
- Department of ChemistryUniversity of Illinois at Chicago Chicago IL 60607 USA
| | | | - Jonathon Hanek
- Department of ChemistryUniversity of Illinois at Chicago Chicago IL 60607 USA
| | - Stephanie M. Cologna
- Department of ChemistryUniversity of Illinois at Chicago Chicago IL 60607 USA
- Department of ChemistryLaboratory for Integrative NeuroscienceUniversity of Illinois at Chicago Chicago IL 60607 USA
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20
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Mass spectrometry imaging reveals ganglioside and ceramide localization patterns during cerebellar degeneration in the Npc1−/− mouse model. Anal Bioanal Chem 2019; 411:5659-5668. [DOI: 10.1007/s00216-019-01989-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 06/01/2019] [Accepted: 06/17/2019] [Indexed: 02/08/2023]
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21
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Standard-flow LC and thermal focusing ESI elucidates altered liver proteins in late stage Niemann-Pick, type C1 disease. Bioanalysis 2019; 11:1067-1083. [PMID: 31251104 PMCID: PMC9933893 DOI: 10.4155/bio-2018-0232] [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] [Indexed: 02/08/2023] Open
Abstract
Aim: Mass spectrometry (MS)-based proteomics, particularly with the development of nano-ESI, have been invaluable to our understanding of altered proteins related to human disease. Niemann-Pick, type C1 (NPC1) disease is a fatal, autosomal recessive, neurodegenerative disorder. The resulting defects include unesterified cholesterol and sphingolipids accumulation in the late endosomal/lysosomal system resulting in organ dysfunction including liver disease. Materials & methods: First, we performed MS analysis of a complex mammalian proteome using both nano- and standard-flow ESI with the intent of developing a differential proteomics platform using standard-flow ESI. Next, we measured the differential liver proteome in the NPC1 mouse model via label-free quantitative MS using standard-flow ESI. Results: Using the standard-flow ESI approach, we found altered protein levels including, increased Limp2 and Rab7a in liver tissue of Npc1-/- compared to control mice. Conclusion: Standard-flow ESI can be a tool for quantitative proteomic studies when sample amount is not limited. Using this method, we have identified new protein markers of NPC1.
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22
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Ucal Y, Coskun A, Ozpinar A. Quality will determine the future of mass spectrometry imaging in clinical laboratories: the need for standardization. Expert Rev Proteomics 2019; 16:521-532. [DOI: 10.1080/14789450.2019.1624165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yasemin Ucal
- School of Medicine, Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Abdurrahman Coskun
- School of Medicine, Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Aysel Ozpinar
- School of Medicine, Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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