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Xie Q, Li Z, Chen Y, Zhao Y, Xu Y, Hong Z, Chen Z, Zhang Z, Xu H, Yin Z, Wu X. Mass Spectrometry Imaging Reveals the Morphology-Dependent Toxicological Effects of Nanosilvers on Multiple Organs of Adult Zebrafish ( Danio rerio). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 38798012 DOI: 10.1021/acs.est.4c00655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Nanosilvers with multifarious morphologies have been extensively used in many fields, but their morphology-dependent toxicity toward nontarget aquatic organisms remains largely unclear. Herein, we used matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to investigate the toxicological effects of silver nanomaterials with various morphologies on spatially resolved lipid profiles within multiple organs in adult zebrafish, especially for the gill, liver, and intestine. Integrated with histopathology, enzyme activity, accumulated Ag contents and amounts, as well as MSI results, we found that nanosilvers exhibit morphology-dependent nanotoxicity by disrupting lipid levels and producing oxidative stress. Silver nanospheres (AgNSs) had the highest toxicity toward adult zebrafish, whereas silver nanoflakes (AgNFs) exhibited greater toxicity than silver nanowires (AgNWs). Levels of differential phospholipids, such as PC, PE, PI, and PS, were associated with nanosilver morphology. Notably, we found that AgNSs induced greater toxicity in multiple organs, such as the brain, gill, and liver, while AgNWs and AgNFs caused greater toxicity in the intestine than AgNSs. Lipid functional disturbance and oxidative stress further caused inflammation and membrane damage after exposure to nanosilvers, especially with respect to sphere morphology. Taken together, these findings will contribute to clarifying the toxicological effects and mechanisms of different morphologies of nanosilvers in adult zebrafish.
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Affiliation(s)
- Qingrong Xie
- National Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yingying Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yuhui Zhao
- National Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yizhu Xu
- National Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Zhouyi Hong
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zilong Chen
- Instrumental Analysis and Research Center, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhixiang Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Hanhong Xu
- National Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Zhibin Yin
- Institute of Advanced Science Facilities, Shenzhen 518107, China
| | - Xinzhou Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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Xie YR, Castro DC, Rubakhin SS, Trinklein TJ, Sweedler JV, Lam F. Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry. Nat Methods 2024; 21:521-530. [PMID: 38366241 PMCID: PMC10927565 DOI: 10.1038/s41592-024-02171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
Spatial omics technologies can reveal the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive biochemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping using MEISTER, an integrative experimental and computational mass spectrometry (MS) framework. Our framework integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating three-dimensional (3D) molecular distributions and a data integration method fitting cell-specific mass spectra to 3D datasets. We imaged detailed lipid profiles in tissues with millions of pixels and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future development of multiscale technologies for biochemical characterization of the brain.
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Affiliation(s)
- Yuxuan Richard Xie
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Daniel C Castro
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stanislav S Rubakhin
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Timothy J Trinklein
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Fan Lam
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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Yilmaz A, Liraz-Zaltsman S, Shohami E, Gordevičius J, Kerševičiūtė I, Sherman E, Bahado-Singh RO, Graham SF. The longitudinal biochemical profiling of TBI in a drop weight model of TBI. Sci Rep 2023; 13:22260. [PMID: 38097614 PMCID: PMC10721861 DOI: 10.1038/s41598-023-48539-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Traumatic brain injury (TBI) is a major cause of mortality and disability worldwide, particularly among individuals under the age of 45. It is a complex, and heterogeneous disease with a multifaceted pathophysiology that remains to be elucidated. Metabolomics has the potential to identify metabolic pathways and unique biochemical profiles associated with TBI. Herein, we employed a longitudinal metabolomics approach to study TBI in a weight drop mouse model to reveal metabolic changes associated with TBI pathogenesis, severity, and secondary injury. Using proton nuclear magnetic resonance (1H NMR) spectroscopy, we biochemically profiled post-mortem brain from mice that suffered mild TBI (N = 25; 13 male and 12 female), severe TBI (N = 24; 11 male and 13 female) and sham controls (N = 16; 11 male and 5 female) at baseline, day 1 and day 7 following the injury. 1H NMR-based metabolomics, in combination with bioinformatic analyses, highlights a few significant metabolites associated with TBI severity and perturbed metabolism related to the injury. We report that the concentrations of taurine, creatinine, adenine, dimethylamine, histidine, N-Acetyl aspartate, and glucose 1-phosphate are all associated with TBI severity. Longitudinal metabolic observation of brain tissue revealed that mild TBI and severe TBI lead distinct metabolic profile changes. A multi-class model was able to classify the severity of injury as well as time after TBI with estimated 86% accuracy. Further, we identified a high degree of correlation between respective hemisphere metabolic profiles (r > 0.84, p < 0.05, Pearson correlation). This study highlights the metabolic changes associated with underlying TBI severity and secondary injury. While comprehensive, future studies should investigate whether: (a) the biochemical pathways highlighted here are recapitulated in the brain of TBI sufferers and (b) if the panel of biomarkers are also as effective in less invasively harvested biomatrices, for objective and rapid identification of TBI severity and prognosis.
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Affiliation(s)
- Ali Yilmaz
- Metabolomics Department, Beaumont Research Institute, Beaumont Health, Royal Oak, MI, 48073, USA
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA
| | - Sigal Liraz-Zaltsman
- Department of Pharmacology, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Ramat-Gan, Israel
- Department of Sports Therapy, Institute for Health and Medical Professions, Ono Academic College, Qiryat Ono, Israel
| | - Esther Shohami
- Department of Pharmacology, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Juozas Gordevičius
- VUGENE LLC, 625 EKenmoor Avenue Southeast, Suite 301, PMB 96578, Grand Rapids, MI, 49546, USA
| | - Ieva Kerševičiūtė
- VUGENE LLC, 625 EKenmoor Avenue Southeast, Suite 301, PMB 96578, Grand Rapids, MI, 49546, USA
| | - Eric Sherman
- Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Ray O Bahado-Singh
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA
| | - Stewart F Graham
- Metabolomics Department, Beaumont Research Institute, Beaumont Health, Royal Oak, MI, 48073, USA.
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48073, USA.
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Li H, Zhang S, Zhao Y, He J, Chen X. Identification of raffinose family oligosaccharides in processed Rehmannia glutinosa Libosch using matrix-assisted laser desorption/ionization mass spectrometry image combined with machine learning. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9635. [PMID: 37817339 DOI: 10.1002/rcm.9635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/07/2023] [Accepted: 08/20/2023] [Indexed: 10/12/2023]
Abstract
RATIONALE Currently, research on oligosaccharides primarily focuses on the physiological activity and function, with a few studies elaborating on the spatial distribution characterization and variation in the processing of Rehmannia glutinosa Libosch. Thus, imaging the spatial distributions and dynamic changes in oligosaccharides during the steaming process is significant for characterizing the metabolic networks of R. glutinosa. It will be beneficial to characterize the impact of steaming on the active ingredients and distribution patterns in different parts of the plant. METHODS A highly sensitive matrix-assisted laser desorption/ionization mass spectrometry image (MALDI-MSI) method was used to visualize the spatial distribution of oligosaccharides in processed R. glutinosa. Furthermore, machine learning was used to distinguish the processed R. glutinosa samples obtained under different steaming conditions. RESULTS Imaging results showed that the oligosaccharides in the fresh R. glutinosa were mainly distributed in the cortex and xylem. As steaming progressed, the tetra- and pentasaccharides were hydrolyzed and diffused gradually into the tissue section. MALDI-MS profiling combined with machine learning was used to identify the processed R. glutinosa samples accurately at different steaming intervals. Eight algorithms were used to build classification machine learning models, which were evaluated for accuracy, precision, recall, and F1 score. The linear discriminant analysis and random forest models performed the best, with prediction accuracies of 0.98 and 0.97, respectively, and thus can be considered for identifying the steaming durations of R. glutinosa. CONCLUSIONS MALDI-MSI combined with machine learning can be used to visualize the distribution of oligosaccharides and identify the processed samples after steaming for different durations. This can enhance our understanding of the metabolic changes that occur during the steaming process of R. glutinosa; meanwhile, it is expected to provide a theoretical reference for the standardization and modernization of processing in the field of medicinal plants.
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Affiliation(s)
- Huizhi Li
- Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences, Shandong University of Traditional Chinese Medicine, Jinan, China
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shishan Zhang
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yanfang Zhao
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Jixiang He
- Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiangfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
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5
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Bender K, Wang Y, Zhai CY, Saenz Z, Wang A, Neumann EK. Sample Preparation Method for MALDI Mass Spectrometry Imaging of Fresh-Frozen Spines. Anal Chem 2023; 95:17337-17346. [PMID: 37886878 PMCID: PMC10688227 DOI: 10.1021/acs.analchem.3c03672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
Technologies assessing the lipidomics, genomics, epigenomics, transcriptomics, and proteomics of tissue samples at single-cell resolution have deepened our understanding of physiology and pathophysiology at an unprecedented level of detail. However, the study of single-cell spatial metabolomics in undecalcified bones faces several significant challenges, such as the fragility of bone, which often requires decalcification or fixation leading to the degradation or removal of lipids and other molecules. As such, we describe a method for performing mass spectrometry imaging on undecalcified spine that is compatible with other spatial omics measurements. In brief, we use fresh-frozen rat spines and a system of carboxyl methylcellulose embedding, cryofilm, and polytetrafluoroethylene rollers to maintain tissue integrity while avoiding signal loss from variations in laser focus and artifacts from traditional tissue processing. This reveals various tissue types and lipidomic profiles of spinal regions at 10 μm spatial resolutions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We expect this method to be adapted and applied to the analysis of the spinal cord, shedding light on the mechanistic aspects of cellular heterogeneity, development, and disease pathogenesis underlying different bone-related conditions and diseases. This study furthers the methodology for high spatial metabolomics of spines and adds to the collective efforts to achieve a holistic understanding of diseases via single-cell spatial multiomics.
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Affiliation(s)
- Kayle
J. Bender
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Yongheng Wang
- Department
of Biomedical Engineering, University of
California, Davis, Davis, California 95616, United States
| | - Chuo Ying Zhai
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Zoe Saenz
- Department
of Surgery, School of Medicine, University
of California, Davis, Sacramento, California 95817, United States
| | - Aijun Wang
- Center
for Surgical Bioengineering, Department of Surgery, School of Medicine, University of California, Davis, Sacramento, California 95817, United States
- Institute
for Pediatric Regenerative Medicine, Shriners
Hospital for Children Northern California, UC Davis School of Medicine, Sacramento, California 96817, United States
| | - Elizabeth K. Neumann
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Schmitt R, Qayum S, Pliss A, Kuzmin AN, Muthaiah VPK, Kaliyappan K, Prasad PN, Mahajan SD. Mitochondrial Dysfunction and Apoptosis in Brain Microvascular Endothelial Cells Following Blast Traumatic Brain Injury. Cell Mol Neurobiol 2023; 43:3639-3651. [PMID: 37314617 DOI: 10.1007/s10571-023-01372-2] [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: 04/20/2022] [Accepted: 06/01/2023] [Indexed: 06/15/2023]
Abstract
Blood brain barrier (BBB) breakdown is a key driver of traumatic brain injury (TBI), contributing to prolonged neurological deficits and increased risk of death in TBI patients. Strikingly, the role of endothelium in the progression of BBB breakdown has not been sufficiently investigated, even though it constitutes the bulk of BBB structure. In the current study, we investigate TBI-induced changes in the brain endothelium at the subcellular level, particularly focusing on mitochondrial dysfunction, using a combination of confocal imaging, gene expression analysis, and molecular profiling by Raman spectrometry. Herein, we developed and applied an in-vitro blast-TBI (bTBI) model that employs an acoustic shock tube to deliver injury to cultured human brain microvascular endothelial cells (HBMVEC). We found that this injury results in aberrant expression of mitochondrial genes, as well as cytokines/ inflammasomes, and regulators of apoptosis. Furthermore, injured cells exhibit a significant increase in reactive oxygen species (ROS) and in Ca2+ levels. These changes are accompanied by overall reduction of intracellular proteins levels as well as profound transformations in mitochondrial proteome and lipidome. Finally, blast injury leads to a reduction in HBMVEC cell viability, with up to 50% of cells exhibiting signs of apoptosis following 24 h after injury. These findings led us to hypothesize that mitochondrial dysfunction in HBMVEC is a key component of BBB breakdown and TBI progression.
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Affiliation(s)
- Rebecca Schmitt
- Institute for Lasers, Photonics and Biophotonics, Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Sana Qayum
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, Clinical Translational Research Center, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Andrey N Kuzmin
- Institute for Lasers, Photonics and Biophotonics, Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Vijaya Prakash Krishnan Muthaiah
- Department of Rehabilitation Science, School of Public Health and Health Professions, The State University of New York, 633 Kimball Tower, Buffalo, NY, 14214, USA
| | - Kathiravan Kaliyappan
- Department of Rehabilitation Science, School of Public Health and Health Professions, The State University of New York, 633 Kimball Tower, Buffalo, NY, 14214, USA
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
| | - Supriya D Mahajan
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, Clinical Translational Research Center, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
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8
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Bender KJ, Wang Y, Zhai CY, Saenz Z, Wang A, Neumann EK. Spatial lipidomics of fresh-frozen spines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554488. [PMID: 37662353 PMCID: PMC10473750 DOI: 10.1101/2023.08.23.554488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Technologies assessing the lipidomics, genomics, epigenomics, transcriptomics, and proteomics of tissue samples at single-cell resolution have deepened our understanding of physiology and pathophysiology at an unprecedented level of detail. However, the study of single-cell spatial metabolomics in undecalcified bones faces several significant challenges, such as the fragility of bone which often requires decalcification or fixation leading to the degradation or removal of lipids and other molecules and. As such, we describe a method for performing mass spectrometry imaging on undecalcified spine that is compatible with other spatial omics measurements. In brief, we use fresh-freeze rat spines and a system of carboxyl methylcellulose embedding, cryofilm, and polytetrafluoroethylene rollers to maintain tissue integrity, while avoiding signal loss from variations in laser focus and artifacts from traditional tissue processing. This reveals various tissue types and lipidomic profiles of spinal regions at 10 μm spatial resolutions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We expect this method to be adapted and applied to the analysis of spinal cord, shedding light on the mechanistic aspects of cellular heterogeneity, development, and disease pathogenesis underlying different bone-related conditions and diseases. This study furthers the methodology for high spatial metabolomics of spines, as well as adds to the collective efforts to achieve a holistic understanding of diseases via single-cell spatial multi-omics.
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Affiliation(s)
- Kayle J. Bender
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Yongheng Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, United States
| | - Chuo Ying Zhai
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Zoe Saenz
- Department of Surgery, University of California, Davis, School of Medicine, Sacramento, CA 95817, United States
| | - Aijun Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, United States
- Department of Surgery, University of California, Davis, School of Medicine, Sacramento, CA 95817, United States
- Institute for Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, UC Davis School of Medicine, Sacramento, CA 96817, United States
| | - Elizabeth K. Neumann
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
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9
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Kaya I, Nilsson A, Luptáková D, He Y, Vallianatou T, Bjärterot P, Svenningsson P, Bezard E, Andrén PE. Spatial lipidomics reveals brain region-specific changes of sulfatides in an experimental MPTP Parkinson's disease primate model. NPJ Parkinsons Dis 2023; 9:118. [PMID: 37495571 PMCID: PMC10372136 DOI: 10.1038/s41531-023-00558-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Metabolism of MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) to the neurotoxin MPP+ in the brain causes permanent Parkinson's disease-like symptoms by destroying dopaminergic neurons in the pars compacta of the substantia nigra in humans and non-human primates. However, the complete molecular pathology underlying MPTP-induced parkinsonism remains poorly understood. We used dual polarity matrix-assisted laser desorption/ionization mass spectrometry imaging to thoroughly image numerous glycerophospholipids and sphingolipids in coronal brain tissue sections of MPTP-lesioned and control non-human primate brains (Macaca mulatta). The results revealed specific distributions of several sulfatide lipid molecules based on chain-length, number of double bonds, and importantly, hydroxylation stage. More specifically, certain long-chain hydroxylated sulfatides with polyunsaturated chains in the molecular structure were depleted within motor-related brain regions in the MPTP-lesioned animals, e.g., external and internal segments of globus pallidus and substantia nigra pars reticulata. In contrast, certain long-chain non-hydroxylated sulfatides were found to be elevated within the same brain regions. These findings demonstrate region-specific dysregulation of sulfatide metabolism within the MPTP-lesioned macaque brain. The depletion of long-chain hydroxylated sulfatides in the MPTP-induced pathology indicates oxidative stress and oligodendrocyte/myelin damage within the pathologically relevant brain regions. Hence, the presented findings improve our current understanding of the molecular pathology of MPTP-induced parkinsonism within primate brains, and provide a basis for further research regarding the role of dysregulated sulfatide metabolism in PD.
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Affiliation(s)
- Ibrahim Kaya
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Nilsson
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dominika Luptáková
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Yachao He
- Section of Neurology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Theodosia Vallianatou
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Patrik Bjärterot
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Svenningsson
- Section of Neurology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Erwan Bezard
- University of Bordeaux, CNRS, IMN, UMR 5293, F-33000, Bordeaux, France
| | - Per E Andrén
- Department of Pharmaceutical Biosciences, Spatial Mass Spectrometry, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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10
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Yang Z, Apiliogullari S, Fu Y, Istanbouli A, Kaur S, Jabbal IS, Moghieb A, Irfan Z, Patterson RL, Kurup M, Morrow L, Cohn M, Zhang Z, Zhu J, Hayes RL, Bramlett HM, Bullock MR, Dietrich WD, Wang MY, Kobeissy F, Wang KW. Association between Cerebrospinal Fluid and Serum Biomarker Levels and Diagnosis, Injury Severity, and Short-Term Outcomes in Patients with Acute Traumatic Spinal Cord Injury. Diagnostics (Basel) 2023; 13:diagnostics13101814. [PMID: 37238298 DOI: 10.3390/diagnostics13101814] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Acute traumatic spinal cord injury (SCI) is recognized as a global problem that can lead to a range of acute and secondary complications impacting morbidity and mortality. There is still a lack of reliable diagnostic and prognostic biomarkers in patients with SCI that could help guide clinical care and identify novel therapeutic targets for future drug discovery. The aim of this prospective controlled study was to determine the cerebral spinal fluid (CSF) and serum profiles of 10 biomarkers as indicators of SCI diagnosis, severity, and prognosis to aid in assessing appropriate treatment modalities. CSF and serum samples of 15 SCI and ten healthy participants were included in the study. The neurological assessments were scored on admission and at discharge from the hospital using the American Spinal Injury Association Impairment Score (AIS) grades. The CSF and serum concentrations of SBDP150, S100B, GFAP, NF-L, UCHL-1, Tau, and IL-6 were significantly higher in SCI patients when compared with the control group. The CSF GBDP 38/44K, UCHL-L1, S100B, GFAP, and Tau levels were significantly higher in the AIS A patients. This study demonstrated a strong correlation between biomarker levels in the diagnosis and injury severity of SCI but no association with short-term outcomes. Future prospective controlled studies need to be done to support the results of this study.
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Affiliation(s)
- Zhihui Yang
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Seza Apiliogullari
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr SW, Atlanta, GA 30310, USA
| | - Yueqiang Fu
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Ayah Istanbouli
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Sehajpreet Kaur
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Iktej Singh Jabbal
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Ahmed Moghieb
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Zoha Irfan
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Robert Logan Patterson
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Milin Kurup
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Lindsey Morrow
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Michael Cohn
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Zhiqun Zhang
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jiepei Zhu
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr SW, Atlanta, GA 30310, USA
| | - Ronald L Hayes
- Banyan Biomarkers, Inc., 16470 West Bernardo Drive, Suite 100, San Diego, CA 92127, USA
| | - Helen M Bramlett
- Department of Neurological Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - M Ross Bullock
- Department of Neurological Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - W Dalton Dietrich
- Department of Neurological Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Michael Y Wang
- Department of Neurological Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr SW, Atlanta, GA 30310, USA
| | - Kevin W Wang
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr SW, Atlanta, GA 30310, USA
- Brain Rehabilitation Research Center, Malcom Randall Veterans Affairs Medical Center (VAMC), 1601, The Archer Rd., Gainesville, FL 32608, USA
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11
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Guo L, Dong J, Xu X, Wu Z, Zhang Y, Wang Y, Li P, Tang Z, Zhao C, Cai Z. Divide and Conquer: A Flexible Deep Learning Strategy for Exploring Metabolic Heterogeneity from Mass Spectrometry Imaging Data. Anal Chem 2023; 95:1924-1932. [PMID: 36633187 PMCID: PMC9878502 DOI: 10.1021/acs.analchem.2c04045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023]
Abstract
Research on metabolic heterogeneity provides an important basis for the study of the molecular mechanism of a disease and personalized treatment. The screening of metabolism-related sub-regions that affect disease development is essential for the more focused exploration on disease progress aberrant phenotypes, even carcinogenesis and metastasis. The mass spectrometry imaging (MSI) technique has distinct advantages to reveal the heterogeneity of an organism based on in situ molecular profiles. The challenge of heterogeneous analysis has been to perform an objective identification among biological tissues with different characteristics. By introducing the divide-and-conquer strategy to architecture design and application, we establish here a flexible unsupervised deep learning model, called divide-and-conquer (dc)-DeepMSI, for metabolic heterogeneity analysis from MSI data without prior knowledge of histology. dc-DeepMSI can be used to identify either spatially contiguous regions of interest (ROIs) or spatially sporadic ROIs by designing two specific modes, spat-contig and spat-spor. Comparison results on fetus mouse data demonstrate that the dc-DeepMSI outperforms state-of-the-art MSI segmentation methods. We demonstrate that the novel learning strategy successfully obtained sub-regions that are statistically linked to the invasion status and molecular phenotypes of breast cancer as well as organizing principles during developmental phase.
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Affiliation(s)
- Lei Guo
- Department
of Electronic Science, National Institute
for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Jiyang Dong
- Department
of Electronic Science, National Institute
for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiangnan Xu
- School
of Mathematics and Statistics, The University
of Sydney, Sydney, NSW 2006, Australia
| | - Zhichao Wu
- School
of Artificial Intelligence, Beijing Normal
University, Beijing 100875, China
| | - Yinbin Zhang
- Department
of Oncology, The Second Affiliated Hospital
of Medical College, Xi’an Jiaotong University, Xi’an, Shaanxi 710004, China
| | - Yongwei Wang
- Bruker
Scientific Technology Co., Ltd., Beijing 100086, China
| | - Pengfei Li
- Bruker
Scientific Technology Co., Ltd., Beijing 100086, China
| | - Zhi Tang
- School
of Public Health, Dongguan Key Laboratory of Environmental Medicine, Institute of Environmental Health, Guangdong Medical
University, Dongguan, Guangdong 523808, China
| | - Chao Zhao
- Bionic
Sensing and Intelligence Center, Institute of Biomedical and Health
Engineering, Shenzhen Institute of Advanced
Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Zongwei Cai
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong SAR 999077, China
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12
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Mallah K, Zibara K, Kerbaj C, Eid A, Khoshman N, Ousseily Z, Kobeissy A, Cardon T, Cizkova D, Kobeissy F, Fournier I, Salzet M. Neurotrauma investigation through spatial omics guided by mass spectrometry imaging: Target identification and clinical applications. MASS SPECTROMETRY REVIEWS 2023; 42:189-205. [PMID: 34323300 DOI: 10.1002/mas.21719] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/04/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Traumatic brain injury (TBI) represents one of the major public health concerns worldwide due to the increase in TBI incidence as a result of injuries from daily life accidents such as sports and motor vehicle transportation as well as military-related practices. This type of central nervous system trauma is known to predispose patients to several neurological disorders such as Parkinson's disease, Alzheimer's disease, chronic trauamatic encephalopathy, and age-related Dementia. Recently, several proteomic and lipidomic platforms have been applied on different TBI studies to investigate TBI-related mechanisms that have broadened our understanding of its distinct neuropathological complications. In this study, we provide an updated comprehensive overview of the current knowledge and novel perspectives of the spatially resolved microproteomics and microlipidomics approaches guided by mass spectrometry imaging used in TBI studies and its applications in the neurotrauma field. In this regard, we will discuss the use of the spatially resolved microproteomics and assess the different microproteomic sampling methods such as laser capture microdissection, parafilm assisted microdissection, and liquid microjunction extraction as accurate and precise techniques in the field of neuroproteomics. Additionally, we will highlight lipid profiling applications and their prospective potentials in characterizing molecular processes involved in the field of TBI. Specifically, we will discuss the phospholipid metabolism acting as a precursor for proinflammatory molecules such as eicosanoids. Finally, we will survey the current state of spatial neuroproteomics and microproteomics applications and present the various studies highlighting their findings in these fields.
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Affiliation(s)
- Khalil Mallah
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- PRASE, Lebanese University, Beirut, Lebanon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Kazem Zibara
- PRASE, Lebanese University, Beirut, Lebanon
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Coline Kerbaj
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Ali Eid
- Department of Basic Medical Sciences, QU Health, Qatar University, Doha, Qatar
| | - Nour Khoshman
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Zahraa Ousseily
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Abir Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Tristan Cardon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Dasa Cizkova
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Center for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Isabelle Fournier
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
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13
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Yang Z, Arja RD, Zhu T, Sarkis GA, Patterson RL, Romo P, Rathore DS, Moghieb A, Abbatiello S, Robertson CS, Haskins WE, Kobeissy F, Wang KKW. Characterization of Calpain and Caspase-6-Generated Glial Fibrillary Acidic Protein Breakdown Products Following Traumatic Brain Injury and Astroglial Cell Injury. Int J Mol Sci 2022; 23:8960. [PMID: 36012232 PMCID: PMC9409281 DOI: 10.3390/ijms23168960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 12/03/2022] Open
Abstract
Glial fibrillary acidic protein (GFAP) is the major intermediate filament III protein of astroglia cells which is upregulated in traumatic brain injury (TBI). Here we reported that GFAP is truncated at both the C- and N-terminals by cytosolic protease calpain to GFAP breakdown products (GBDP) of 46-40K then 38K following pro-necrotic (A23187) and pro-apoptotic (staurosporine) challenges to primary cultured astroglia or neuron-glia mixed cells. In addition, with another pro-apoptotic challenge (EDTA) where caspases are activated but not calpain, GFAP was fragmented internally, generating a C-terminal GBDP of 20 kDa. Following controlled cortical impact in mice, GBDP of 46-40K and 38K were formed from day 3 to 28 post-injury. Purified GFAP protein treated with calpain-1 and -2 generates (i) major N-terminal cleavage sites at A-56*A-61 and (ii) major C-terminal cleavage sites at T-383*Q-388, producing a limit fragment of 38K. Caspase-6 treated GFAP was cleaved at D-78/R-79 and D-225/A-226, where GFAP was relatively resistant to caspase-3. We also derived a GBDP-38K N-terminal-specific antibody which only labels injured astroglia cell body in both cultured astroglia and mouse cortex and hippocampus after TBI. As a clinical translation, we observed that CSF samples collected from severe human TBI have elevated levels of GBDP-38K as well as two C-terminally released GFAP peptides (DGEVIKES and DGEVIKE). Thus, in addition to intact GFAP, both the GBDP-38K as well as unique GFAP released C-terminal proteolytic peptides species might have the potential in tracking brain injury progression.
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Affiliation(s)
- Zhihui Yang
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- The Departments of Psychiatry, University of Florida, Gainesville, FL 32611, USA
| | - Rawad Daniel Arja
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- The Departments of Psychiatry, University of Florida, Gainesville, FL 32611, USA
| | - Tian Zhu
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- The Departments of Psychiatry, University of Florida, Gainesville, FL 32611, USA
- Department of Pediatrics, Daping Hospital, Third Military Medical University, Chongqing 400038, China
| | - George Anis Sarkis
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- The Departments of Chemistry, University of Florida, Gainesville, FL 32611, USA
- National Laboratory, Biological Sciences Division/Integrative Omics, Pacific Northwest, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Robert Logan Patterson
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pammela Romo
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Disa S. Rathore
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Ahmed Moghieb
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- The Departments of Chemistry, University of Florida, Gainesville, FL 32611, USA
- National Laboratory, Biological Sciences Division/Integrative Omics, Pacific Northwest, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Susan Abbatiello
- The Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
| | | | - William E. Haskins
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080, USA
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- The Departments of Psychiatry, University of Florida, Gainesville, FL 32611, USA
| | - Kevin K. W. Wang
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- The Departments of Psychiatry, University of Florida, Gainesville, FL 32611, USA
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080, USA
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14
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Baijnath S, Kaya I, Nilsson A, Shariatgorji R, Andrén PE. Advances in spatial mass spectrometry enable in-depth neuropharmacodynamics. Trends Pharmacol Sci 2022; 43:740-753. [DOI: 10.1016/j.tips.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/06/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022]
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15
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Zhao C, Cai Z. Three-dimensional quantitative mass spectrometry imaging in complex system: From subcellular to whole organism. MASS SPECTROMETRY REVIEWS 2022; 41:469-487. [PMID: 33300181 DOI: 10.1002/mas.21674] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
Mass spectrometry imaging (MSI) has been applied for label-free three-dimensional (3D) imaging from position array across the whole organism, which provides high-dimensional quantitative data of inorganic or organic compounds that may play an important role in the regulation of cellular signaling, including metals, metabolites, lipids, drugs, peptides, and proteins. While MSI is suitable for investigation of the spatial distribution of molecules, it has a limitation with visualization and quantification of multiple molecules. 3D-MSI, however, can be applied toward exploring metabolic pathway as well as the interactions of lipid-protein, protein-protein, and metal-protein in complex systems from subcellular to the whole organism through an untargeted methodology. In this review, we highlight the methods and applications of MS-based 3D imaging to address the complexity of molecular interaction from nano- to micrometer lateral resolution, with particular focus on: (a) common and hybrid 3D-MSI techniques; (b) quantitative MSI methodology, including the methods using a stable isotope labeling internal standard (SILIS) and SILIS-free approaches with tissue extinction coefficient or virtual calibration; (c) reconstruction of the 3D organ; (d) application of 3D-MSI for biomarker screening and environmental toxicological research. 3D-MSI quantitative analysis provides accurate spatial information and quantitative variation of biomolecules, which may be valuable for the exploration of the molecular mechanism of the disease progresses and toxicological assessment of environmental pollutants in the whole organism. Additionally, we also discuss the challenges and perspectives on the future of 3D quantitative MSI.
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Affiliation(s)
- Chao Zhao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
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16
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Stevens AR, Stickland CA, Harris G, Ahmed Z, Goldberg Oppenheimer P, Belli A, Davies DJ. Raman Spectroscopy as a Neuromonitoring Tool in Traumatic Brain Injury: A Systematic Review and Clinical Perspectives. Cells 2022; 11:1227. [PMID: 35406790 PMCID: PMC8997459 DOI: 10.3390/cells11071227] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022] Open
Abstract
Traumatic brain injury (TBI) is a significant global health problem, for which no disease-modifying therapeutics are currently available to improve survival and outcomes. Current neuromonitoring modalities are unable to reflect the complex and changing pathophysiological processes of the acute changes that occur after TBI. Raman spectroscopy (RS) is a powerful, label-free, optical tool which can provide detailed biochemical data in vivo. A systematic review of the literature is presented of available evidence for the use of RS in TBI. Seven research studies met the inclusion/exclusion criteria with all studies being performed in pre-clinical models. None of the studies reported the in vivo application of RS, with spectral acquisition performed ex vivo and one performed in vitro. Four further studies were included that related to the use of RS in analogous brain injury models, and a further five utilised RS in ex vivo biofluid studies for diagnosis or monitoring of TBI. RS is identified as a potential means to identify injury severity and metabolic dysfunction which may hold translational value. In relation to the available evidence, the translational potentials and barriers are discussed. This systematic review supports the further translational development of RS in TBI to fully ascertain its potential for enhancing patient care.
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Affiliation(s)
- Andrew R. Stevens
- Neuroscience, Trauma and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; (Z.A.); (A.B.); (D.J.D.)
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham B15 2TH, UK
| | - Clarissa A. Stickland
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK; (C.A.S.); (G.H.); (P.G.O.)
| | - Georgia Harris
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK; (C.A.S.); (G.H.); (P.G.O.)
| | - Zubair Ahmed
- Neuroscience, Trauma and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; (Z.A.); (A.B.); (D.J.D.)
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham B15 2TH, UK
- Centre for Trauma Science Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Pola Goldberg Oppenheimer
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK; (C.A.S.); (G.H.); (P.G.O.)
| | - Antonio Belli
- Neuroscience, Trauma and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; (Z.A.); (A.B.); (D.J.D.)
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham B15 2TH, UK
- Centre for Trauma Science Research, University of Birmingham, Birmingham B15 2TT, UK
| | - David J. Davies
- Neuroscience, Trauma and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; (Z.A.); (A.B.); (D.J.D.)
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham B15 2TH, UK
- Centre for Trauma Science Research, University of Birmingham, Birmingham B15 2TT, UK
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17
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DeLaney K, Phetsanthad A, Li L. ADVANCES IN HIGH-RESOLUTION MALDI MASS SPECTROMETRY FOR NEUROBIOLOGY. MASS SPECTROMETRY REVIEWS 2022; 41:194-214. [PMID: 33165982 PMCID: PMC8106695 DOI: 10.1002/mas.21661] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/13/2020] [Indexed: 05/08/2023]
Abstract
Research in the field of neurobiology and neurochemistry has seen a rapid expansion in the last several years due to advances in technologies and instrumentation, facilitating the detection of biomolecules critical to the complex signaling of neurons. Part of this growth has been due to the development and implementation of high-resolution Fourier transform (FT) mass spectrometry (MS), as is offered by FT ion cyclotron resonance (FTICR) and Orbitrap mass analyzers, which improves the accuracy of measurements and helps resolve the complex biological mixtures often analyzed in the nervous system. The coupling of matrix-assisted laser desorption/ionization (MALDI) with high-resolution MS has drastically expanded the information that can be obtained with these complex samples. This review discusses notable technical developments in MALDI-FTICR and MALDI-Orbitrap platforms and their applications toward molecules in the nervous system, including sequence elucidation and profiling with de novo sequencing, analysis of post-translational modifications, in situ analysis, key advances in sample preparation and handling, quantitation, and imaging. Notable novel applications are also discussed to highlight key developments critical to advancing our understanding of neurobiology and providing insight into the exciting future of this field. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
- To whom correspondence should be addressed. , Phone: (608) 265-8491, Fax: (608) 262-5345., Mailing Address: 5125 Rennebohm Hall, 777 Highland Avenue, Madison, WI 53706
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18
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Gier EC, Pulliam AN, Gaul DA, Moore SG, LaPlaca MC, Fernández FM. Lipidome Alterations following Mild Traumatic Brain Injury in the Rat. Metabolites 2022; 12:150. [PMID: 35208224 PMCID: PMC8878543 DOI: 10.3390/metabo12020150] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 12/10/2022] Open
Abstract
Traumatic brain injury (TBI) poses a major health challenge, with tens of millions of new cases reported globally every year. Brain damage resulting from TBI can vary significantly due to factors including injury severity, injury mechanism and exposure to repeated injury events. Therefore, there is need for robust blood biomarkers. Serum from Sprague Dawley rats was collected at several timepoints within 24 h of mild single or repeat closed head impacts. Serum samples were analyzed via ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) in positive and negative ion modes. Known lipid species were identified through matching to in-house tandem MS databases. Lipid biomarkers have a unique potential to serve as objective molecular measures of injury response as they may be liberated to circulation more readily than larger protein markers. Machine learning and feature selection approaches were used to construct lipid panels capable of distinguishing serum from injured and uninjured rats. The best multivariate lipid panels had over 90% cross-validated sensitivity, selectivity, and accuracy. These mapped onto sphingolipid signaling, autophagy, necroptosis and glycerophospholipid metabolism pathways, with Benjamini adjusted p-values less than 0.05. The novel lipid biomarker candidates identified provide insight into the metabolic pathways altered within 24 h of mild TBI.
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Affiliation(s)
- Eric C. Gier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (E.C.G.); (D.A.G.); (S.G.M.)
| | - Alexis N. Pulliam
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA 30332, USA;
| | - David A. Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (E.C.G.); (D.A.G.); (S.G.M.)
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Samuel G. Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (E.C.G.); (D.A.G.); (S.G.M.)
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michelle C. LaPlaca
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA 30332, USA;
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; (E.C.G.); (D.A.G.); (S.G.M.)
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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19
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Balluff B, Heeren RM, Race AM. An overview of image registration for aligning mass spectrometry imaging with clinically relevant imaging modalities. J Mass Spectrom Adv Clin Lab 2022; 23:26-38. [PMID: 35156074 PMCID: PMC8821033 DOI: 10.1016/j.jmsacl.2021.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 01/25/2023] Open
Abstract
Mass spectrometry imaging (MSI) is a powerful molecular imaging technique. Integration with other imaging modalities is essential in clinical MSI. Image integration is performed by image registration techniques. Technical potential of image registration in MSI has not been fully exploited. Roadmap proposed to improve registration accuracy.
Mass spectrometry imaging (MSI) is used in many aspects of clinical research, including pharmacokinetics, toxicology, personalised medicine, and surgical decision-making. Maximising its potential requires the spatial integration of MSI images with imaging data from existing clinical imaging modalities, such as histology and MRI. To ensure that the information is properly integrated, all contributing images must be accurately aligned. This process is called image registration and is the focus of this review. In light of the ever-increasing spatial resolution of MSI instrumentation and a diversification of multi-modal MSI studies (e.g., spatial omics, 3D-MSI), the accuracy, versatility, and precision of image registration must increase accordingly. We review the application of image registration to align MSI data with different clinically relevant ex vivo and in vivo imaging techniques. Based on this, we identify steps in the current image registration processes where there is potential for improvement. Finally, we propose a roadmap for community efforts to address these challenges in order to increase registration quality and help MSI to fully exploit its multi-modal potential.
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20
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Li X, Hang L, Wang T, Leng Y, Zhang H, Meng Y, Yin Z, Hang W. Nanoscale Three-Dimensional Imaging of Drug Distributions in Single Cells via Laser Desorption Post-Ionization Mass Spectrometry. J Am Chem Soc 2021; 143:21648-21656. [PMID: 34913337 DOI: 10.1021/jacs.1c10081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exploring the three-dimensional (3D) drug distribution within a single cell at nanoscale resolution with mass spectrometry imaging (MSI) techniques is crucial in cellular biology, yet it remains a great challenge due to limited lateral resolution, detection sensitivities, and reconstruction problems. Herein, a microlensed fiber laser desorption post-ionization time-of-flight mass spectrometer (MLF-LDPI-TOFMS) was developed for the 3D imaging of two anticancer drugs within single cells at a 500 × 500 × 500 nm3 voxel resolution. Nanoscale desorption was obtained with a microlensed fiber (MLF), and a 157 nm post-ionization laser was introduced to enhance the ionization yield. Furthermore, a new type of alignment method for 3D reconstruction was developed on the basis of our embedded uniform circular polystyrene microspheres (PMs). Our findings demonstrate that this 3D imaging technique has the potential to provide information about the 3D distributions of specific molecules at the nanoscale level.
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Affiliation(s)
- Xiaoping Li
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Le Hang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Tongtong Wang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yixin Leng
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Heng Zhang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yifan Meng
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhibin Yin
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wei Hang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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21
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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: 2] [Impact Index Per Article: 0.7] [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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22
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Javaid S, Farooq T, Rehman Z, Afzal A, Ashraf W, Rasool MF, Alqahtani F, Alsanea S, Alasmari F, Alanazi MM, Alharbi M, Imran I. Dynamics of Choline-Containing Phospholipids in Traumatic Brain Injury and Associated Comorbidities. Int J Mol Sci 2021; 22:ijms222111313. [PMID: 34768742 PMCID: PMC8583393 DOI: 10.3390/ijms222111313] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 01/01/2023] Open
Abstract
The incidences of traumatic brain injuries (TBIs) are increasing globally because of expanding population and increased dependencies on motorized vehicles and machines. This has resulted in increased socio-economic burden on the healthcare system, as TBIs are often associated with mental and physical morbidities with lifelong dependencies, and have severely limited therapeutic options. There is an emerging need to identify the molecular mechanisms orchestrating these injuries to life-long neurodegenerative disease and a therapeutic strategy to counter them. This review highlights the dynamics and role of choline-containing phospholipids during TBIs and how they can be used to evaluate the severity of injuries and later targeted to mitigate neuro-degradation, based on clinical and preclinical studies. Choline-based phospholipids are involved in maintaining the structural integrity of the neuronal/glial cell membranes and are simultaneously the essential component of various biochemical pathways, such as cholinergic neuronal transmission in the brain. Choline or its metabolite levels increase during acute and chronic phases of TBI because of excitotoxicity, ischemia and oxidative stress; this can serve as useful biomarker to predict the severity and prognosis of TBIs. Moreover, the effect of choline-replenishing agents as a post-TBI management strategy has been reviewed in clinical and preclinical studies. Overall, this review determines the theranostic potential of choline phospholipids and provides new insights in the management of TBI.
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Affiliation(s)
- Sana Javaid
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan; (S.J.); (T.F.); (Z.R.); (A.A.); (W.A.); (I.I.)
- Department of Pharmacy, The Women University, Multan 60000, Pakistan
| | - Talha Farooq
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan; (S.J.); (T.F.); (Z.R.); (A.A.); (W.A.); (I.I.)
| | - Zohabia Rehman
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan; (S.J.); (T.F.); (Z.R.); (A.A.); (W.A.); (I.I.)
| | - Ammara Afzal
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan; (S.J.); (T.F.); (Z.R.); (A.A.); (W.A.); (I.I.)
| | - Waseem Ashraf
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan; (S.J.); (T.F.); (Z.R.); (A.A.); (W.A.); (I.I.)
| | - Muhammad Fawad Rasool
- Department of Pharmacy Practice, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Faleh Alqahtani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (F.A.); (M.M.A.); (M.A.)
- Correspondence: ; Tel.: +966-114697749
| | - Sary Alsanea
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (F.A.); (M.M.A.); (M.A.)
| | - Fawaz Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (F.A.); (M.M.A.); (M.A.)
| | - Mohammed Mufadhe Alanazi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (F.A.); (M.M.A.); (M.A.)
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (F.A.); (M.M.A.); (M.A.)
| | - Imran Imran
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan; (S.J.); (T.F.); (Z.R.); (A.A.); (W.A.); (I.I.)
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23
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Liu H, Han M, Li J, Qin L, Chen L, Hao Q, Jiang D, Chen D, Ji Y, Han H, Long C, Zhou Y, Feng J, Wang X. A Caffeic Acid Matrix Improves In Situ Detection and Imaging of Proteins with High Molecular Weight Close to 200,000 Da in Tissues by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Anal Chem 2021; 93:11920-11928. [PMID: 34405989 DOI: 10.1021/acs.analchem.0c05480] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To our knowledge, this was the first study in which caffeic acid (CA) was successfully evaluated as a matrix to enhance the in situ detection and imaging of endogenous proteins in three biological tissue sections (i.e., a rat brain and Capparis masaikai and germinating soybean seeds) by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Our results show several properties of CA, including strong ultraviolet absorption, a super-wide MS detection mass range close to 200,000 Da, micrometer-sized matrix crystals, uniform matrix deposition, and high ionization efficiency. More high-molecular-weight (HMW) protein ion signals (m/z > 30,000) could be clearly detected in biological tissues with the use of CA, compared to two commonly used MALDI matrices, i.e., sinapinic acid (SA) and ferulic acid (FA). Notably, CA shows excellent performance for HMW protein in situ detection from biological tissues in the mass range m/z > 80,000, compared to the use of SA and FA. Furthermore, the use of a CA matrix also significantly enhanced the imaging of proteins on the surface of selected biological tissue sections. Three HMW protein ion signals (m/z 50,419, m/z 65,874, and m/z 191,872) from a rat brain, two sweet proteins (mabinlin-2 and mabinlin-4) from a Capparis masaikai seed, and three HMW protein ion signals (m/z 94,838, m/z 134,204, and m/z 198,738) from a germinating soybean seed were successfully imaged for the first time. Our study proves that CA has the potential to become a standard organic acid matrix for enhanced tissue imaging of HMW proteins by MALDI-MSI in both animal and plant tissues.
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Affiliation(s)
- Haiqiang Liu
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Manman Han
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Jinming Li
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Liang Qin
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Lulu Chen
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Qichen Hao
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Dongxu Jiang
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Difan Chen
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yuanyuan Ji
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Hang Han
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Chunlin Long
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yijun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Jinchao Feng
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xiaodong Wang
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing 100081, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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24
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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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25
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Liu H, Wang S, Lin JM, Lin Z, Li HF. Investigation of the lipidomic changes in differentiated glioblastoma cells after drug treatment using MALDI-MS. Talanta 2021; 233:122570. [PMID: 34215066 DOI: 10.1016/j.talanta.2021.122570] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 01/10/2023]
Abstract
Lipids differences between tumor and normal tissue have been proved to be of diagnostic and therapeutic significance. The research of lipidomics in tumor is more and more important. Mass spectrometry like matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) can be more convenient and informative for lipids researching in biological and clinical researches. Most of malignant tumors like glioblastoma are characterized by incomplete differentiation, so differentiation therapy has made important progress in tumor treatment. Lipid profiles changes after therapy are worthy investigating. In our study, glioblastoma cell line U87-MG cells were treated by inducers of sodium phenylbutyrate (SPB) and all-trans retinoic acid (ATRA). The changes in lipids on cell membrane were profiled by MALDI-MS. The differentiation degree was assessed by cell proliferation, cell cycle, morphology and protein expression before MALDI-MS analysis. Comparing the inducer treated and untreated U87-MG cells, reduced proliferation rate, blocked cell cycle, benign nucleus morphology and changed expression of protein CD133 and glial fibrillary acidic protein (GFAP), were found after drug treatment. Moreover, the lipids of cell membrane presented distinguished differences in the drug treated cells. Most of the glycerophosphocholines (PC) with an increasing abundance are unsaturated PCs (PC (38:1), 816 m/z; PC (36:1), 788 m/z; PC (31:1), 725 m/z), and those decreasing are saturated PCs (PC (32:0), 734 m/z). These results provide the lipidomic differentiation which may be a significant guidance for evaluating the therapeutic effect of tumor therapy.
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Affiliation(s)
- Hongxing Liu
- Department of Neurosurgery, Beijing Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China; Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing, 100084, China
| | - Shiqi Wang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing, 100084, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing, 100084, China
| | - Zhixiong Lin
- Department of Neurosurgery, Beijing Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China.
| | - Hai-Fang Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Tsinghua University, Beijing, 100084, China.
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26
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Postolache TT, Wadhawan A, Can A, Lowry CA, Woodbury M, Makkar H, Hoisington AJ, Scott AJ, Potocki E, Benros ME, Stiller JW. Inflammation in Traumatic Brain Injury. J Alzheimers Dis 2021; 74:1-28. [PMID: 32176646 DOI: 10.3233/jad-191150] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is an increasing evidence that inflammation contributes to clinical and functional outcomes in traumatic brain injury (TBI). Many successful target-engaging, lesion-reducing, symptom-alleviating, and function-improving interventions in animal models of TBI have failed to show efficacy in clinical trials. Timing and immunological context are paramount for the direction, quality, and intensity of immune responses to TBI and the resulting neuroanatomical, clinical, and functional course. We present components of the immune system implicated in TBI, potential immune targets, and target-engaging interventions. The main objective of our article is to point toward modifiable molecular and cellular mechanisms that may modify the outcomes in TBI, and contribute to increasing the translational value of interventions that have been identified in animal models of TBI.
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Affiliation(s)
- Teodor T Postolache
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.,Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 19, Aurora, CO, USA.,Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA.,Mental Illness Research, Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 5, VA Capitol Health Care Network, Baltimore, MD, USA
| | - Abhishek Wadhawan
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.,Saint Elizabeths Hospital, Department of Psychiatry, Washington, DC, USA
| | - Adem Can
- School of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Christopher A Lowry
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 19, Aurora, CO, USA.,Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA.,Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, Boulder, CO, USA.,Department of Physical Medicine and Rehabilitation and Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Margaret Woodbury
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.,VA Maryland Healthcare System, Baltimore VA Medical Center, Baltimore, MD, USA
| | - Hina Makkar
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew J Hoisington
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 19, Aurora, CO, USA.,Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson AFB, OH, USA
| | - Alison J Scott
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Eileen Potocki
- VA Maryland Healthcare System, Baltimore VA Medical Center, Baltimore, MD, USA
| | - Michael E Benros
- Copenhagen Research Center for Mental Health-CORE, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - John W Stiller
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.,Maryland State Athletic Commission, Baltimore, MD, USA.,Saint Elizabeths Hospital, Neurology Consultation Services, Washington, DC, USA
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27
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Li Y, Wu Q, Hu E, Wang Y, Lu H. Quantitative Mass Spectrometry Imaging of Metabolomes and Lipidomes for Tracking Changes and Therapeutic Response in Traumatic Brain Injury Surrounding Injured Area at Chronic Phase. ACS Chem Neurosci 2021; 12:1363-1375. [PMID: 33793210 DOI: 10.1021/acschemneuro.1c00002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Traumatic brain injury (TBI) is a complex disease process that may contribute to temporary or permanent disability. Tracking spatial changes of lipids and metabolites in the brain helps unveil the underlying mechanisms of the disease procession and therapeutic response. Here, the liquid microjunction surface sampling technique was used for mass spectrometry imaging of both lipids and metabolites in rat models of controlled cortical impact with and without XueFu ZhuYu decoction treatment, and the work was focused on the diffuse changes outside the injured area at chronic phase (14 days after injury). Quantitative information was provided for phosphotidylcholines and cerebrosides by adding internal standards in the sampling solvent. With principal component analysis for the imaging data, the midbrain was found to be the region with the largest diffuse changes following TBI outside the injured area. In detail, several phosphatidylcholines, phosphatidylethanolamines, phosphatidic acids, and diacylglycerols were found to be significantly up-regulated particularly in midbrain and thalamus after TBI and XFZY treatment. It is associated with the reported "self-repair" mechanisms at the chronic phase of TBI activated by neuroinflammation. Several glycosphingolipids were found to be increased in most of brain regions after TBI, which was inferred to be associated with neuroinflammation and oxidative stress triggered by TBI. Moreover, different classes of small matabolites were significantly changed after TBI, including fatty acids, amino acids, and purines. All these compounds were involved in 10 metabolic pathway networks, and 6 target proteins of XFZY were found related to the impacted pathways. These results shed light on the molecular mechanisms of TBI pathologic processes and therapeutic response.
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Affiliation(s)
- Youmei Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Qian Wu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - En Hu
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P. R. China
| | - Yang Wang
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P. R. China
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
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Vos DRN, Ellis SR, Balluff B, Heeren RMA. Experimental and Data Analysis Considerations for Three-Dimensional Mass Spectrometry Imaging in Biomedical Research. Mol Imaging Biol 2021; 23:149-159. [PMID: 33025328 PMCID: PMC7910367 DOI: 10.1007/s11307-020-01541-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/12/2020] [Accepted: 09/10/2020] [Indexed: 10/26/2022]
Abstract
Mass spectrometry imaging (MSI) enables the visualization of molecular distributions on complex surfaces. It has been extensively used in the field of biomedical research to investigate healthy and diseased tissues. Most of the MSI studies are conducted in a 2D fashion where only a single slice of the full sample volume is investigated. However, biological processes occur within a tissue volume and would ideally be investigated as a whole to gain a more comprehensive understanding of the spatial and molecular complexity of biological samples such as tissues and cells. Mass spectrometry imaging has therefore been expanded to the 3D realm whereby molecular distributions within a 3D sample can be visualized. The benefit of investigating volumetric data has led to a quick rise in the application of single-sample 3D-MSI investigations. Several experimental and data analysis aspects need to be considered to perform successful 3D-MSI studies. In this review, we discuss these aspects as well as ongoing developments that enable 3D-MSI to be routinely applied to multi-sample studies.
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Affiliation(s)
- D R N Vos
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - S R Ellis
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - B Balluff
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - R M A Heeren
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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29
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Nessel I, Michael-Titus AT. Lipid profiling of brain tissue and blood after traumatic brain injury. Semin Cell Dev Biol 2021; 112:145-156. [DOI: 10.1016/j.semcdb.2020.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 11/15/2022]
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30
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Removal of optimal cutting temperature (O.C.T.) compound from embedded tissue for MALDI imaging of lipids. Anal Bioanal Chem 2021; 413:2695-2708. [PMID: 33564925 DOI: 10.1007/s00216-020-03128-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/27/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is a common molecular imaging modality used to characterise the abundance and spatial distribution of lipids in situ. There are several technical challenges predominantly involving sample pre-treatment and preparation which have complicated the analysis of clinical tissues by MALDI-MSI. Firstly, the common embedding of samples in optimal cutting temperature (O.C.T.), which contains high concentrations of polyethylene glycol (PEG) polymers, causes analyte signal suppression during mass spectrometry (MS) by competing for available ions during ionisation. This suppressive effect has constrained the application of MALDI-MSI for the molecular mapping of clinical tissues. Secondly, the complexity of the mass spectra is obtained by the formation of multiple adduct ions. The process of analyte ion formation during MALDI can generate multiple m/z peaks from a single lipid species due to the presence of alkali salts in tissues, resulting in the suppression of protonated adduct formation and the generation of multiple near isobaric ions which produce overlapping spatial distributions. Presented is a method to simultaneously remove O.C.T. and endogenous salts. This approach was applied to lipid imaging in order to prevent analyte suppression, simplify data interpretation, and improve sensitivity by promoting lipid protonation and reducing the formation of alkali adducts.
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31
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Veličković D, Chu RK, Henkel C, Nyhuis A, Tao N, Kyle JE, Adkins JN, Anderton CR, Paurus V, Bloodsworth K, Bramer LM, Cornett DS, Curtis WR, Burnum‐Johnson KE. Preserved and variable spatial-chemical changes of lipids across tomato leaves in response to central vein wounding reveals potential origin of linolenic acid in signal transduction cascade. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2021; 2:28-35. [PMID: 37283847 PMCID: PMC10168036 DOI: 10.1002/pei3.10038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/08/2023]
Abstract
Membrane lipids serve as substrates for the generation of numerous signaling lipids when plants are exposed to environmental stresses, and jasmonic acid, an oxidized product of 18-carbon unsaturated fatty acids (e.g., linolenic acid), has been recognized as the essential signal in wound-induced gene expression. Yet, the contribution of individual membrane lipids in linolenic acid generation is ill-defined. In this work, we performed spatial lipidomic experiments to track lipid changes that occur locally at the sight of leaf injury to better understand the potential origin of linolenic and linoleic acids from individual membrane lipids. The central veins of tomato leaflets were crushed using surgical forceps, leaves were cryosectioned and analyzed by two orthogonal matrix-assisted laser desorption/ionization mass spectrometry imaging platforms for insight into lipid spatial distribution. Significant changes in lipid composition are only observed 30 min after wounding, while after 60 min lipidome homeostasis has been re-established. Phosphatidylcholines exhibit a variable pattern of spatial behavior in individual plants. Among lysolipids, lysophosphatidylcholines strongly co-localize with the injured zone of wounded leaflets, while, for example, lysophosphatidylglycerol (LPG) (16:1) accumulated preferentially toward the apex in the injured zone of wounded leaflets. In contrast, two other LPGs (LPG [18:3] and LPG [18:2]) are depleted in the injured zone. Our high-resolution co-localization imaging analyses suggest that linolenic acids are predominantly released from PCs with 16_18 fatty acid composition along the entire leaf, while it seems that in the apex zone PG (16:1_18:3) significantly contributes to the linolenic acid pool. These results also indicate distinct localization and/or substrate preferences of phospholipase isoforms in leaf tissue.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | - Rosalie K. Chu
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | | | | | | | - Jennifer E. Kyle
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Joshua N. Adkins
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Christopher R. Anderton
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | - Vanessa Paurus
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Kent Bloodsworth
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Lisa M. Bramer
- Computing & Analytics DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | | | - Wayne R. Curtis
- Department of Chemical EngineeringThe Pennsylvania State UniversityUniversity ParkPAUSA
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Pinsky W, Harris A, Roseborough AD, Wang W, Khan AR, Jurcic K, Yeung KKC, Pasternak SH, Whitehead SN. Regional Lipid Expression Abnormalities Identified Using MALDI IMS Correspond to MRI-Defined White Matter Hyperintensities within Post-mortem Human Brain Tissues. Anal Chem 2021; 93:2652-2659. [PMID: 33464828 DOI: 10.1021/acs.analchem.0c05017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Periventricular white matter hyperintensities (pvWMHs) are a neurological feature detected with magnetic resonance imaging that are clinically associated with an increased risk of stroke and dementia. pvWMHs represent white matter lesions characterized by regions of myelin and axon rarefaction and as such likely involve changes in lipid composition; however, these alterations remain unknown. Lipids are critical in determining cell function and survival. Perturbations in lipid expression have previously been associated with neurological disorders. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is an emerging technique for untargeted, high-throughput investigation of lipid expression and spatial distribution in situ; however, the use of MALDI IMS has been previously been limited by the need for non-embedded, non-fixed, fresh-frozen samples. In the current study, we demonstrate the novel use of MALDI IMS to distinguish regional lipid abnormalities that correlate with magnetic resonance imaging (MRI) defined pvWMHs within ammonium formate washed, formalin-fixed human archival samples. MALDI IMS scans were conducted in positive or negative ion detection mode on tissues sublimated with 2,5-dihydroxybenzoic acid or 1,5-diaminonaphthalene matrices, respectively. Using a broad, untargeted approach to lipid analysis, we consistently detected 116 lipid ion species in 21 tissue blocks from 11 different post-mortem formalin-fixed human brains. Comparing the monoisotopic mass peaks of these lipid ions elucidated significant differences in lipid expression between pvWMHs and NAWM for 31 lipid ion species. Expanding our understanding of alterations in lipid composition will provide greater knowledge of molecular mechanisms underpinning ischemic white matter lesions and provides the potential for novel therapeutic interventions targeting lipid composition abnormalities.
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Affiliation(s)
- William Pinsky
- Vulnerable Brain Lab, Department of Anatomy and Cell Biology, University of Western Ontario, London, N6A 5C1 Ontario, Canada
| | - Aaron Harris
- Vulnerable Brain Lab, Department of Anatomy and Cell Biology, University of Western Ontario, London, N6A 5C1 Ontario, Canada
| | - Austyn D Roseborough
- Vulnerable Brain Lab, Department of Anatomy and Cell Biology, University of Western Ontario, London, N6A 5C1 Ontario, Canada
| | - Wenxuan Wang
- Vulnerable Brain Lab, Department of Anatomy and Cell Biology, University of Western Ontario, London, N6A 5C1 Ontario, Canada
| | - Ali R Khan
- Department of Medical Biophysics, University of Western Ontario, London, N6A 5C1 Ontario, Canada
| | - Kristina Jurcic
- MALDI Mass Spectrometry Facility, Department of Biochemistry, University of Western Ontario, London, N6A 5C1 Ontario, Canada
| | - Ken K-C Yeung
- Departments of Biochemistry and Chemistry, University of Western Ontario, London, N6A 5C1 Ontario, Canada
| | - Stephen H Pasternak
- Robarts Research Institute, Western University, London, N6A 3K7 Ontario, Canada
| | - Shawn N Whitehead
- Vulnerable Brain Lab, Department of Anatomy and Cell Biology, University of Western Ontario, London, N6A 5C1 Ontario, Canada
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33
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Flinders B, Morrell J, Marshall PS, Ranshaw LE, Heeren RMA, Clench MR. Monitoring the three-dimensional distribution of endogenous species in the lungs by matrix-assisted laser desorption/ionization mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8957. [PMID: 32990347 DOI: 10.1002/rcm.8957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is routinely employed to monitor the distribution of compounds in tissue sections and generate two-dimensional (2D) images. Whilst informative the images do not represent the distribution of the analyte of interest through the entire organ. The generation of 3D images is an exciting field that can provide a deeper view of the analyte of interest throughout an entire organ. METHODS Serial sections of mouse and rat lung tissue were obtained at 120 μm depth intervals and imaged individually. Homogenate registration markers were incorporated in order to aid the final 3D image construction. Using freely available software packages, the images were stacked together to generate a 3D image that showed the distribution of endogenous species throughout the lungs. RESULTS Preliminary tests were performed on 16 serial tissue sections of mouse lungs. A 3D model showing the distribution of phosphocholine at m/z 184.09 was constructed, which defined the external structure of the lungs and trachea. Later, a second experiment was performed using 24 serial tissue sections of the left lung of a rat. Two molecular markers, identified as [PC (32:1) + K]+ at m/z 770.51 and [PC (36:4) + K]+ at m/z 820.52, were used to generate 3D models of the parenchyma and airways, respectively. CONCLUSIONS A straightforward method to generate 3D MALDI-MS images of selected molecules in lung tissue has been presented. Using freely available imaging software, the 3D distributions of molecules related to different anatomical features were determined.
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Affiliation(s)
- Bryn Flinders
- Centre for Mass Spectrometry Imaging, Biomedical Research Centre, City Campus, Sheffield Hallam University, Sheffield, S1 1WB, UK
- Hair Diagnostix, Dutch Screening Group, Gaetano Martinolaan 63A, Maastricht, 6229 GS, The Netherlands
- Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, Maastricht, 6229 ER, The Netherlands
| | - Josie Morrell
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | | | - Lisa E Ranshaw
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, Maastricht, 6229 ER, The Netherlands
| | - Malcolm R Clench
- Centre for Mass Spectrometry Imaging, Biomedical Research Centre, City Campus, Sheffield Hallam University, Sheffield, S1 1WB, UK
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34
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Keating CE, Cullen DK. Mechanosensation in traumatic brain injury. Neurobiol Dis 2020; 148:105210. [PMID: 33259894 DOI: 10.1016/j.nbd.2020.105210] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/10/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Traumatic brain injury (TBI) is distinct from other neurological disorders because it is induced by a discrete event that applies extreme mechanical forces to the brain. This review describes how the brain senses, integrates, and responds to forces under both normal conditions and during injury. The response to forces is influenced by the unique mechanical properties of brain tissue, which differ by region, cell type, and sub-cellular structure. Elements such as the extracellular matrix, plasma membrane, transmembrane receptors, and cytoskeleton influence its properties. These same components also act as force-sensors, allowing neurons and glia to respond to their physical environment and maintain homeostasis. However, when applied forces become too large, as in TBI, these components may respond in an aberrant manner or structurally fail, resulting in unique pathological sequelae. This so-called "pathological mechanosensation" represents a spectrum of cellular responses, which vary depending on the overall biomechanical parameters of the injury and may be compounded by repetitive injuries. Such aberrant physical responses and/or damage to cells along with the resulting secondary injury cascades can ultimately lead to long-term cellular dysfunction and degeneration, often resulting in persistent deficits. Indeed, pathological mechanosensation not only directly initiates secondary injury cascades, but this post-physical damage environment provides the context in which these cascades unfold. Collectively, these points underscore the need to use experimental models that accurately replicate the biomechanics of TBI in humans. Understanding cellular responses in context with injury biomechanics may uncover therapeutic targets addressing various facets of trauma-specific sequelae.
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Affiliation(s)
- Carolyn E Keating
- Department of Neurosurgery, Center for Brain Injury and Repair, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Neurotrauma, Neurodegeneration, and Restoration, Corporal Michael J. Crescenz VA Medical Center, USA
| | - D Kacy Cullen
- Department of Neurosurgery, Center for Brain Injury and Repair, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA; Center for Neurotrauma, Neurodegeneration, and Restoration, Corporal Michael J. Crescenz VA Medical Center, USA.
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35
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Möginger U, Marcussen N, Jensen ON. Histo-molecular differentiation of renal cancer subtypes by mass spectrometry imaging and rapid proteome profiling of formalin-fixed paraffin-embedded tumor tissue sections. Oncotarget 2020; 11:3998-4015. [PMID: 33216824 PMCID: PMC7646834 DOI: 10.18632/oncotarget.27787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/10/2020] [Indexed: 12/24/2022] Open
Abstract
Pathology differentiation of renal cancer types is challenging due to tissue similarities or overlapping histological features of various tumor (sub) types. As assessment is often manually conducted outcomes can be prone to human error and therefore require high-level expertise and experience. Mass spectrometry can provide detailed histo-molecular information on tissue and is becoming increasingly popular in clinical settings. Spatially resolving technologies such as mass spectrometry imaging and quantitative microproteomics profiling in combination with machine learning approaches provide promising tools for automated tumor classification of clinical tissue sections. In this proof of concept study we used MALDI-MS imaging (MSI) and rapid LC-MS/MS-based microproteomics technologies (15 min/sample) to analyze formalin-fixed paraffin embedded (FFPE) tissue sections and classify renal oncocytoma (RO, n = 11), clear cell renal cell carcinoma (ccRCC, n = 12) and chromophobe renal cell carcinoma (ChRCC, n = 5). Both methods were able to distinguish ccRCC, RO and ChRCC in cross-validation experiments. MSI correctly classified 87% of the patients whereas the rapid LC-MS/MS-based microproteomics approach correctly classified 100% of the patients. This strategy involving MSI and rapid proteome profiling by LC-MS/MS reveals molecular features of tumor sections and enables cancer subtype classification. Mass spectrometry provides a promising complementary approach to current pathological technologies for precise digitized diagnosis of diseases.
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Affiliation(s)
- Uwe Möginger
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Present address: Global Research Technologies, Novo Nordisk A/S, Novo Nordisk Park, Bagsværd, Denmark
| | - Niels Marcussen
- Institute for Pathology, Odense University Hospital, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
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36
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Enzlein T, Cordes J, Munteanu B, Michno W, Serneels L, De Strooper B, Hanrieder J, Wolf I, Chávez-Gutiérrez L, Hopf C. Computational Analysis of Alzheimer Amyloid Plaque Composition in 2D- and Elastically Reconstructed 3D-MALDI MS Images. Anal Chem 2020; 92:14484-14493. [PMID: 33138378 DOI: 10.1021/acs.analchem.0c02585] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MALDI mass spectrometry imaging (MSI) enables label-free, spatially resolved analysis of a wide range of analytes in tissue sections. Quantitative analysis of MSI datasets is typically performed on single pixels or manually assigned regions of interest (ROIs). However, many sparse, small objects such as Alzheimer's disease (AD) brain deposits of amyloid peptides called plaques are neither single pixels nor ROIs. Here, we propose a new approach to facilitate the comparative computational evaluation of amyloid plaque-like objects by MSI: a fast PLAQUE PICKER tool that enables a statistical evaluation of heterogeneous amyloid peptide composition. Comparing two AD mouse models, APP NL-G-F and APP PS1, we identified distinct heterogeneous plaque populations in the NL-G-F model but only one class of plaques in the PS1 model. We propose quantitative metrics for the comparison of technical and biological MSI replicates. Furthermore, we reconstructed a high-accuracy 3D-model of amyloid plaques in a fully automated fashion, employing rigid and elastic MSI image registration using structured and plaque-unrelated reference ion images. Statistical single-plaque analysis in reconstructed 3D-MSI objects revealed the Aβ1-42Arc peptide to be located either in the core of larger plaques or in small plaques without colocalization of other Aβ isoforms. In 3D, a substantially larger number of small plaques were observed than that indicated by the 2D-MSI data, suggesting that quantitative analysis of molecularly diverse sparsely-distributed features may benefit from 3D-reconstruction. Data are available via ProteomeXchange with identifier PXD020824.
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Affiliation(s)
- Thomas Enzlein
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, Mannheim 68163, Germany.,KU Leuven-VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium.,Department of Neurosciences, Leuven Institute for Neuroscience and Disease, KU Leuven, Leuven 3000, Belgium
| | - Jonas Cordes
- Faculty of Computer Science, University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, Mannheim 68163, Germany
| | - Bogdan Munteanu
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, Mannheim 68163, Germany
| | - Wojciech Michno
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, House V3, Mölndal 43180, Sweden.,Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Lutgarde Serneels
- KU Leuven-VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium.,Department of Neurosciences, Leuven Institute for Neuroscience and Disease, KU Leuven, Leuven 3000, Belgium
| | - Bart De Strooper
- KU Leuven-VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium.,Department of Neurosciences, Leuven Institute for Neuroscience and Disease, KU Leuven, Leuven 3000, Belgium.,UK Dementia Research Institute at UCL, University College London, London WC1E 6BT U.K
| | - Jörg Hanrieder
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, House V3, Mölndal 43180, Sweden.,Department of Neurodegenerative Diseases, University College London Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom
| | - Ivo Wolf
- Faculty of Computer Science, University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, Mannheim 68163, Germany
| | - Lucía Chávez-Gutiérrez
- KU Leuven-VIB Center for Brain & Disease Research, VIB, Leuven 3000, Belgium.,Department of Neurosciences, Leuven Institute for Neuroscience and Disease, KU Leuven, Leuven 3000, Belgium
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack Str. 10, Mannheim 68163, Germany
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37
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Rose M, Duhamel M, Aboulouard S, Kobeissy F, Le Rhun E, Desmons A, Tierny D, Fournier I, Rodet F, Salzet M. The Role of a Proprotein Convertase Inhibitor in Reactivation of Tumor-Associated Macrophages and Inhibition of Glioma Growth. MOLECULAR THERAPY-ONCOLYTICS 2020; 17:31-46. [PMID: 32300641 PMCID: PMC7152595 DOI: 10.1016/j.omto.2020.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/20/2020] [Indexed: 02/07/2023]
Abstract
Tumors are characterized by the presence of malignant and non-malignant cells, such as immune cells including macrophages, which are preponderant. Macrophages impact the efficacy of chemotherapy and may lead to drug resistance. In this context and based on our previous work, we investigated the ability to reactivate macrophages by using a proprotein convertases inhibitor. Proprotein convertases process immature proteins into functional proteins, with several of them having a role in immune cell activation and tumorigenesis. Macrophages were treated with a peptidomimetic inhibitor targeting furin, PC1/3, PC4, PACE4, and PC5/6. Their anti-glioma activity was analyzed by mass spectrometry-based proteomics and viability assays in 2D and 3D in vitro cultures. Comparison with temozolomide, the drug used for glioma therapy, established that the inhibitor was more efficient for the reduction of cancer cell density. The inhibitor was also able to reactivate macrophages through the secretion of several immune factors with antitumor properties. Moreover, two proteins considered as good glioma patient survival indicators were also identified in 3D cultures treated with the inhibitor. Finally, we established that the proprotein convertases inhibitor has a dual role as an anti-glioma drug and anti-tumoral macrophage reactivation drug. This strategy could be used together with chemotherapy to increase therapy efficacy in glioma.
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Affiliation(s)
- Mélanie Rose
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France.,Oncovet Clinical Research (OCR), SIRIC ONCOLille, 59650 Villeneuve d'Ascq, France
| | - Marie Duhamel
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Soulaimane Aboulouard
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Firas Kobeissy
- Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Emilie Le Rhun
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Annie Desmons
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Dominique Tierny
- Oncovet Clinical Research (OCR), SIRIC ONCOLille, 59650 Villeneuve d'Ascq, France
| | - Isabelle Fournier
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Franck Rodet
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Michel Salzet
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
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Kaya I, Jennische E, Lange S, Tarik Baykal A, Malmberg P, Fletcher JS. Brain region-specific amyloid plaque-associated myelin lipid loss, APOE deposition and disruption of the myelin sheath in familial Alzheimer's disease mice. J Neurochem 2020; 154:84-98. [PMID: 32141089 DOI: 10.1111/jnc.14999] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/07/2020] [Accepted: 03/02/2020] [Indexed: 12/17/2022]
Abstract
There is emerging evidence that amyloid beta (Aβ) aggregates forming neuritic plaques lead to impairment of the lipid-rich myelin sheath and glia. In this study, we examined focal myelin lipid alterations and the disruption of the myelin sheath associated with amyloid plaques in a widely used familial Alzheimer's disease (AD) mouse model; 5xFAD. This AD mouse model has Aβ42 peptide-rich plaque deposition in the brain parenchyma. Matrix-assisted laser desorption/ionization imaging mass spectrometry of coronal brain tissue sections revealed focal Aβ plaque-associated depletion of multiple myelin-associated lipid species including sulfatides, galactosylceramides, and specific plasmalogen phopshatidylethanolamines in the hippocampus, cortex, and on the edges of corpus callosum. Certain phosphatidylcholines abundant in myelin were also depleted in amyloid plaques on the edges of corpus callosum. Further, lysophosphatidylethanolamines and lysophosphatidylcholines, implicated in neuroinflammation, were found to accumulate in amyloid plaques. Double staining of the consecutive sections with fluoromyelin and amyloid-specific antibody revealed amyloid plaque-associated myelin sheath disruption on the edges of the corpus callosum which is specifically correlated with plaque-associated myelin lipid loss only in this region. Further, apolipoprotein E, which is implicated in depletion of sulfatides in AD brain, is deposited in all the Aβ plaques which suggest apolipoprotein E might mediate sulfatide depletion as a consequence of an immune response to Aβ deposition. This high-spatial resolution matrix-assisted laser desorption/ionization imaging mass spectrometry study in combination with (immuno) fluorescence staining of 5xFAD mouse brain provides new understanding of morphological, molecular and immune signatures of Aβ plaque pathology-associated myelin lipid loss and myelin degeneration in a brain region-specific manner. Read the Editorial Highlight for this article on page 7.
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Affiliation(s)
- Ibrahim Kaya
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Eva Jennische
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Lange
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Per Malmberg
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - John S Fletcher
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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Holzlechner M, Eugenin E, Prideaux B. Mass spectrometry imaging to detect lipid biomarkers and disease signatures in cancer. Cancer Rep (Hoboken) 2019; 2:e1229. [PMID: 32729258 PMCID: PMC7941519 DOI: 10.1002/cnr2.1229] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Current methods to identify, classify, and predict tumor behavior mostly rely on histology, immunohistochemistry, and molecular determinants. However, better predictive markers are required for tumor diagnosis and evaluation. Due, in part, to recent technological advancements, metabolomics and lipid biomarkers have become a promising area in cancer research. Therefore, there is a necessity for novel and complementary techniques to identify and visualize these molecular markers within tumors and surrounding tissue. RECENT FINDINGS Since its introduction, mass spectrometry imaging (MSI) has proven to be a powerful tool for mapping analytes in biological tissues. By adding the label-free specificity of mass spectrometry to the detailed spatial information of traditional histology, hundreds of lipids can be imaged simultaneously within a tumor. MSI provides highly detailed lipid maps for comparing intra-tumor, tumor margin, and healthy regions to identify biomarkers, patterns of disease, and potential therapeutic targets. In this manuscript, recent advancement in sample preparation and MSI technologies are discussed with special emphasis on cancer lipid research to identify tumor biomarkers. CONCLUSION MSI offers a unique approach for biomolecular characterization of tumor tissues and provides valuable complementary information to histology for lipid biomarker discovery and tumor classification in clinical and research cancer applications.
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Affiliation(s)
- Matthias Holzlechner
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| | - Eliseo Eugenin
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| | - Brendan Prideaux
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
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Defining New Research Questions and Protocols in the Field of Traumatic Brain Injury through Public Engagement: Preliminary Results and Review of the Literature. Emerg Med Int 2019; 2019:9101235. [PMID: 31781399 PMCID: PMC6875310 DOI: 10.1155/2019/9101235] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/23/2019] [Indexed: 11/17/2022] Open
Abstract
Traumatic brain injury (TBI) is the most common cause of death and disability in the age group below 40 years. The financial cost of loss of earnings and medical care presents a massive burden to family, society, social care, and healthcare, the cost of which is estimated at £1 billion per annum (about brain injury (online)). At present, we still lack a full understanding on the pathophysiology of TBI, and biomarkers represent the next frontier of breakthrough discoveries. Unfortunately, many tenets limit their widespread adoption. Brain tissue sampling is the mainstay of diagnosis in neuro-oncology; following on this path, we hypothesise that information gleaned from neural tissue samples obtained in TBI patients upon hospital admission may correlate with outcome data in TBI patients, enabling an early, accurate, and more comprehensive pathological classification, with the intent of guiding treatment and future research. We proposed various methods of tissue sampling at opportunistic times: two methods rely on a dedicated sample being taken; the remainder relies on tissue that would otherwise be discarded. To gauge acceptance of this, and as per the guidelines set out by the National Research Ethics Service, we conducted a survey of TBI and non-TBI patients admitted to our Trauma ward and their families. 100 responses were collected between December 2017 and July 2018, incorporating two redesigns in response to patient feedback. 75.0% of respondents said that they would consent to a brain biopsy performed at the time of insertion of an intracranial pressure (ICP) bolt. 7.0% replied negatively and 18.0% did not know. 70.0% would consent to insertion of a jugular bulb catheter to obtain paired intracranial venous samples and peripheral samples for analysis of biomarkers. Over 94.0% would consent to neural tissue from ICP probes, external ventricular drains (EVD), and lumbar drains (LD) to be salvaged, and 95.0% would consent to intraoperative samples for further analysis.
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Mallah K, Quanico J, Raffo-Romero A, Cardon T, Aboulouard S, Devos D, Kobeissy F, Zibara K, Salzet M, Fournier I. Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging of Lipids in Experimental Model of Traumatic Brain Injury Detecting Acylcarnitines as Injury Related Markers. Anal Chem 2019; 91:11879-11887. [DOI: 10.1021/acs.analchem.9b02633] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Khalil Mallah
- Université de Lille, INSERM, U1192 - Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
- ER045, PRASE, Laboratory of Stem Cells, Department of Biology, Faculty of Sciences-I, Lebanese University, P. O. Box 6573/14 Badaro, Museum, Beirut, Lebanon
| | - Jusal Quanico
- Université de Lille, INSERM, U1192 - Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Antonella Raffo-Romero
- Université de Lille, INSERM, U1192 - Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Tristan Cardon
- Université de Lille, INSERM, U1192 - Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Soulaimane Aboulouard
- Université de Lille, INSERM, U1192 - Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - David Devos
- Department of Neurology, Expert Center for Parkinson’s Disease, Department of Pharmacology, University of Lille, CHU Lille, INSERM UMR_S 1171, LICEND, F-59000 Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Kazem Zibara
- ER045, PRASE, Laboratory of Stem Cells, Department of Biology, Faculty of Sciences-I, Lebanese University, P. O. Box 6573/14 Badaro, Museum, Beirut, Lebanon
| | - Michel Salzet
- Université de Lille, INSERM, U1192 - Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Isabelle Fournier
- Université de Lille, INSERM, U1192 - Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
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Mallah K, Quanico J, Raffo-Romero A, Cardon T, Aboulouard S, Devos D, Kobeissy F, Zibara K, Salzet M, Fournier I. Mapping Spatiotemporal Microproteomics Landscape in Experimental Model of Traumatic Brain Injury Unveils a link to Parkinson's Disease. Mol Cell Proteomics 2019; 18:1669-1682. [PMID: 31204315 PMCID: PMC6683007 DOI: 10.1074/mcp.ra119.001604] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Indexed: 12/14/2022] Open
Abstract
Traumatic brain injury (TBI) represents a major health concerns with no clinically-approved FDA drug available for therapeutic intervention. Several genomics and neuroproteomics studies have been employed to decipher the underlying pathological mechanisms involved that can serve as potential neurotherapeutic targets and unveil a possible underlying relation of TBI to other secondary neurological disorders. In this work, we present a novel high throughput systems biology approach using a spatially resolved microproteomics platform conducted on different brain regions in an experimental rat model of moderate of controlled cortical injury (CCI) at a temporal pattern postinjury (1 day, 3 days, 7 days, and 10 days). Mapping the spatiotemporal landscape of signature markers in TBI revealed an overexpression of major protein families known to be implicated in Parkinson's disease (PD) such as GPR158, HGMB1, synaptotagmin and glutamate decarboxylase in the ipsilateral substantia nigra. In silico bioinformatics docking experiments indicated the potential correlation between TBI and PD through alpha-synuclein. In an in vitro model, stimulation with palmitoylcarnitine triggered an inflammatory response in macrophages and a regeneration processes in astrocytes which also further confirmed the in vivo TBI proteomics data. Taken together, this is the first study to assess the microproteomics landscape in TBI, mainly in the substantia nigra, thus revealing a potential predisposition for PD or Parkinsonism post-TBI.
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Affiliation(s)
- Khalil Mallah
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; §ER045, PRASE, Laboratory of Stem Cells, Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Jusal Quanico
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Antonella Raffo-Romero
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Tristan Cardon
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Soulaimane Aboulouard
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - David Devos
- ¶Department of Neurology, Expert center for Parkinson's disease, Department of Pharmacology, University of Lille, CHU LILLE, INSERM UMR_S 1171, LICEND, France
| | - Firas Kobeissy
- ‖Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Kazem Zibara
- §ER045, PRASE, Laboratory of Stem Cells, Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Michel Salzet
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- ‡Université de Lille, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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Hoshi M. Tracking down a missing trigger for Alzheimer's disease by mass spectrometric imaging based on brain network analysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:25-55. [DOI: 10.1016/bs.pmbts.2019.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Fernández-Irigoyen J, Corrales F, Santamaría E. The Human Brain Proteome Project: Biological and Technological Challenges. Methods Mol Biol 2019; 2044:3-23. [PMID: 31432403 DOI: 10.1007/978-1-4939-9706-0_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Brain proteomics has become a method of choice that allows zooming-in where neuropathophysiological alterations are taking place, detecting protein mediators that might eventually be measured in cerebrospinal fluid (CSF) as potential neuropathologically derived biomarkers. Following this hypothesis, mass spectrometry-based neuroproteomics has emerged as a powerful approach to profile neural proteomes derived from brain structures and CSF in order to map the extensive protein catalog of the human brain. This chapter provides a historical perspective on the Human Brain Proteome Project (HBPP), some recommendation to the experimental design in neuroproteomic projects, and a brief description of relevant technological and computational innovations that are emerging in the neurobiology field thanks to the proteomics community. Importantly, this chapter highlights recent discoveries from the biology- and disease-oriented branch of the HBPP (B/D-HBPP) focused on spatiotemporal proteomic characterizations of mouse models of neurodegenerative diseases, elucidation of proteostatic networks in different types of dementia, the characterization of unresolved clinical phenotypes, and the discovery of novel biomarker candidates in CSF.
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Affiliation(s)
- Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory,, Proteored-ISCIII, CIBERehd, Madrid, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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Han C, Li S, Yue Q, Li N, Yang H, Zhao Z. Polydopamine-capped AgNPs as a novel matrix overcoming the ion suppression of phosphatidylcholine for MALDI MS comprehensive imaging of glycerophospholipids and sphingolipids in impact-induced injured brain. Analyst 2019; 144:6304-6312. [DOI: 10.1039/c9an01361j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In this study, AgNPs@PDA was synthesized as a matrix for the analysis of lipids in both positive and negative ion modes.
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Affiliation(s)
- Chao Han
- Beijing National Laboratory for Molecular Sciences
- CAS Research/Education Center for Excellence in Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry Chinese Academy of Sciences
- Beijing Mass Spectrum Center
| | - Shumu Li
- Beijing National Laboratory for Molecular Sciences
- CAS Research/Education Center for Excellence in Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry Chinese Academy of Sciences
- Beijing Mass Spectrum Center
| | - Qingwei Yue
- Beijing National Laboratory for Molecular Sciences
- CAS Research/Education Center for Excellence in Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry Chinese Academy of Sciences
- Beijing Mass Spectrum Center
| | - Na Li
- Beijing National Laboratory for Molecular Sciences
- CAS Research/Education Center for Excellence in Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry Chinese Academy of Sciences
- Beijing Mass Spectrum Center
| | - Hui Yang
- Beijing National Laboratory for Molecular Sciences
- CAS Research/Education Center for Excellence in Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry Chinese Academy of Sciences
- Beijing Mass Spectrum Center
| | - Zhenwen Zhao
- Beijing National Laboratory for Molecular Sciences
- CAS Research/Education Center for Excellence in Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry Chinese Academy of Sciences
- Beijing Mass Spectrum Center
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