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Coppini A, Falconieri A, Mualem O, Nasrin SR, Roudon M, Saper G, Hess H, Kakugo A, Raffa V, Shefi O. Can repetitive mechanical motion cause structural damage to axons? Front Mol Neurosci 2024; 17:1371738. [PMID: 38912175 PMCID: PMC11191579 DOI: 10.3389/fnmol.2024.1371738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024] Open
Abstract
Biological structures have evolved to very efficiently generate, transmit, and withstand mechanical forces. These biological examples have inspired mechanical engineers for centuries and led to the development of critical insights and concepts. However, progress in mechanical engineering also raises new questions about biological structures. The past decades have seen the increasing study of failure of engineered structures due to repetitive loading, and its origin in processes such as materials fatigue. Repetitive loading is also experienced by some neurons, for example in the peripheral nervous system. This perspective, after briefly introducing the engineering concept of mechanical fatigue, aims to discuss the potential effects based on our knowledge of cellular responses to mechanical stresses. A particular focus of our discussion are the effects of mechanical stress on axons and their cytoskeletal structures. Furthermore, we highlight the difficulty of imaging these structures and the promise of new microscopy techniques. The identification of repair mechanisms and paradigms underlying long-term stability is an exciting and emerging topic in biology as well as a potential source of inspiration for engineers.
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Affiliation(s)
| | | | - Oz Mualem
- Faculty of Engineering, Bar Ilan Institute of Nanotechnologies and Advanced Materials, Gonda Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Syeda Rubaiya Nasrin
- Graduate School of Science, Division of Physics and Astronomy, Kyoto University, Kyoto, Japan
| | - Marine Roudon
- Department of Biomedical Engineering, Columbia University, New York, NY, United States
| | - Gadiel Saper
- Department of Biomedical Engineering, Columbia University, New York, NY, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, NY, United States
| | - Akira Kakugo
- Graduate School of Science, Division of Physics and Astronomy, Kyoto University, Kyoto, Japan
| | | | - Orit Shefi
- Faculty of Engineering, Bar Ilan Institute of Nanotechnologies and Advanced Materials, Gonda Brain Research Center, Bar Ilan University, Ramat Gan, Israel
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2
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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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3
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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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Huang C, You Z, He Y, Li J, Liu Y, Peng C, Liu Z, Liu X, Sun J. Combined transcriptomics and proteomics forecast analysis for potential biomarker in the acute phase of temporal lobe epilepsy. Front Neurosci 2023; 17:1145805. [PMID: 37065920 PMCID: PMC10097945 DOI: 10.3389/fnins.2023.1145805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
BackgroundTemporal lobe epilepsy (TLE) is a common chronic episodic illness of the nervous system. However, the precise mechanisms of dysfunction and diagnostic biomarkers in the acute phase of TLE are uncertain and hard to diagnose. Thus, we intended to qualify potential biomarkers in the acute phase of TLE for clinical diagnostics and therapeutic purposes.MethodsAn intra-hippocampal injection of kainic acid was used to induce an epileptic model in mice. First, with a TMT/iTRAQ quantitative labeling proteomics approach, we screened for differentially expressed proteins (DEPs) in the acute phase of TLE. Then, differentially expressed genes (DEGs) in the acute phase of TLE were identified by linear modeling on microarray data (limma) and weighted gene co-expression network analysis (WGCNA) using the publicly available microarray dataset GSE88992. Co-expressed genes (proteins) in the acute phase of TLE were identified by overlap analysis of DEPs and DEGs. The least absolute shrinkage and selection operator (LASSO) regression and support vector machine recursive feature elimination (SVM-RFE) algorithms were used to screen Hub genes in the acute phase of TLE, and logistic regression algorithms were applied to develop a novel diagnostic model for the acute phase of TLE, and the sensitivity of the diagnostic model was validated using receiver operating characteristic (ROC) curves.ResultsWe screened a total of 10 co-expressed genes (proteins) from TLE-associated DEGs and DEPs utilizing proteomic and transcriptome analysis. LASSO and SVM-RFE algorithms for machine learning were applied to identify three Hub genes: Ctla2a, Hapln2, and Pecam1. A logistic regression algorithm was applied to establish and validate a novel diagnostic model for the acute phase of TLE based on three Hub genes in the publicly accessible datasets GSE88992, GSE49030, and GSE79129.ConclusionOur study establishes a reliable model for screening and diagnosing the acute phase of TLE that provides a theoretical basis for adding diagnostic biomarkers for TLE acute phase genes.
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Affiliation(s)
- Cong Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhipeng You
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yijie He
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiran Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yang Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chunyan Peng
- Department of Orthopedics, Xinyu People’s Hospital, Xinyu, China
| | - Zhixiong Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xingan Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiahang Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Jiahang Sun,
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Xu XJ, Liu BY, Dong JQ, Ge QQ, Lu SH, Yang MS, Zhuang Y, Zhang B, Niu F. Tandem Mass Tag-based proteomics analysis reveals the vital role of inflammation in traumatic brain injury in a mouse model. Neural Regen Res 2023. [PMID: 35799536 PMCID: PMC9241417 DOI: 10.4103/1673-5374.343886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Sîrbulescu RF, Ilieş I, Amelung L, Zupanc GKH. Proteomic characterization of spontaneously regrowing spinal cord following injury in the teleost fish Apteronotus leptorhynchus, a regeneration-competent vertebrate. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2022; 208:671-706. [PMID: 36445471 DOI: 10.1007/s00359-022-01591-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/30/2022]
Abstract
In adult mammals, spontaneous repair after spinal cord injury (SCI) is severely limited. By contrast, teleost fish successfully regenerate injured axons and produce new neurons from adult neural stem cells after SCI. The molecular mechanisms underlying this high regenerative capacity are largely unknown. The present study addresses this gap by examining the temporal dynamics of proteome changes in response to SCI in the brown ghost knifefish (Apteronotus leptorhynchus). Two-dimensional difference gel electrophoresis (2D DIGE) was combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and tandem mass spectrometry (MS/MS) to collect data during early (1 day), mid (10 days), and late (30 days) phases of regeneration following caudal amputation SCI. Forty-two unique proteins with significant differences in abundance between injured and intact control samples were identified. Correlation analysis uncovered six clusters of spots with similar expression patterns over time and strong conditional dependences, typically within functional families or between isoforms. Significantly regulated proteins were associated with axon development and regeneration; proliferation and morphogenesis; neuronal differentiation and re-establishment of neural connections; promotion of neuroprotection, redox homeostasis, and membrane repair; and metabolism or energy supply. Notably, at all three time points examined, significant regulation of proteins involved in inflammatory responses was absent.
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Affiliation(s)
- Ruxandra F Sîrbulescu
- School of Engineering and Science, Jacobs University Bremen, 28725, Bremen, Germany
- Laboratory of Neurobiology, Department of Biology, Northeastern University, Boston, MA, 02115, USA
- Vaccine and Immunotherapy Center, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Iulian Ilieş
- School of Humanities and Social Sciences, Jacobs University Bremen, 28725, Bremen, Germany
- Laboratory of Neurobiology, Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Lisa Amelung
- Laboratory of Neurobiology, Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Günther K H Zupanc
- School of Engineering and Science, Jacobs University Bremen, 28725, Bremen, Germany.
- Laboratory of Neurobiology, Department of Biology, Northeastern University, Boston, MA, 02115, USA.
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7
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Bindila L, Eid T, Mills JD, Hildebrand MS, Brennan GP, Masino SA, Whittemore V, Perucca P, Reid CA, Patel M, Wang KK, van Vliet EA. A companion to the preclinical common data elements for proteomics, lipidomics, and metabolomics data in rodent epilepsy models. A report of the TASK3-WG4 omics working group of the ILAE/AES joint translational TASK force. Epilepsia Open 2022. [PMID: 36259125 DOI: 10.1002/epi4.12662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/19/2022] [Indexed: 11/07/2022] Open
Abstract
The International League Against Epilepsy/American Epilepsy Society (ILAE/AES) Joint Translational Task Force established the TASK3 working groups to create common data elements (CDEs) for various preclinical epilepsy research disciplines. This is the second in a two-part series of omics papers, with the other including genomics, transcriptomics, and epigenomics. The aim of the CDEs was to improve the standardization of experimental designs across a range of epilepsy research-related methods. We have generated CDE tables with key parameters and case report forms (CRFs) containing the essential contents of the study protocols for proteomics, lipidomics, and metabolomics of samples from rodent models and people with epilepsy. We discuss the important elements that need to be considered for the proteomics, lipidomics, and metabolomics methodologies, providing a rationale for the parameters that should be documented.
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Affiliation(s)
- Laura Bindila
- Clinical Lipidomics Unit, Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Tore Eid
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - James D Mills
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, the Netherlands
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - Gary P Brennan
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Susan A Masino
- Neuroscience Program and Psychology Department, Life Sciences Center, Trinity College, Hartford, Connecticut, USA
| | - Vicky Whittemore
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Piero Perucca
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Austin Health, Heidelberg, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Christopher A Reid
- Epilepsy Research Centre, Department of Medicine (Austin Health), The University of Melbourne, Heidelberg, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Manisha Patel
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kevin K Wang
- Program for Neurotrauma, Neuroproteomics & Biomarker Research (NNBR), Department of Emergency Medicine, Psychiatry and Neuroscience, University of Florida, Gainesville, Florida, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, Gainesville, Florida, USA
| | - Erwin A van Vliet
- Amsterdam UMC location University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, the Netherlands
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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Abstract
Research into TBI biomarkers has accelerated rapidly in the past decade owing to the heterogeneous nature of TBI pathologies and management, which pose challenges to TBI evaluation, management, and prognosis. TBI biomarker proteins resulting from axonal, neuronal, or glial cell injuries are widely used and have been extensively studied. However, they might not pass the blood-brain barrier with sufficient amounts to be detected in peripheral blood specimens, and further might not be detectable in the cerebrospinal fluid owing to flow limitations triggered by the injury itself. Despite the advances in TBI research, there is an unmet clinical need to develop and identify novel TBI biomarkers that entirely correlate with TBI pathologies on the molecular level, including mild TBI, and further enable physicians to predict patient outcomes and allow researchers to test neuroprotective agents to limit the extents of injury. Although the extracellular vesicles have been identified and studied long ago, they have recently been revisited and repurposed as potential TBI biomarkers that overcome the many limitations of the traditional blood and CSF assays. Animal and human experiments demonstrated the accuracy of several types of exosomes and miRNAs in detecting mild, moderate, and severe TBI. In this paper, we provide a comprehensive review of the traditional TBI biomarkers that are helpful in clinical practice. Also, we highlight the emerging roles of exosomes and miRNA being the promising candidates under investigation of current research.
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Generation and Release of Neurogranin, Vimentin, and MBP Proteolytic Peptides, Following Traumatic Brain Injury. Mol Neurobiol 2021; 59:731-747. [PMID: 34762230 DOI: 10.1007/s12035-021-02600-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/12/2021] [Indexed: 10/19/2022]
Abstract
Traumatic brain injury (TBI) is a major neurological disorder without FDA-approved therapies. In this study, we have examined the concept that TBI might trigger global brain proteolysis in the acute post-injury phase. Thus, we conducted a systemic proteolytic peptidomics analysis using acute cerebrospinal fluid (CSF) samples from TBI patients and normal control samples. We employed ultrafiltration-based low molecular weight (LMW; < 10 kDa) peptide enrichment, coupled with nano-reversed-phase liquid chromatography/tandem mass spectrometry analysis, followed with orthogonal quantitative immunoblotting-based protein degradation analysis. We indeed identified novel patterns of injury-dependent proteolytic peptides derived from neuronal components (pre- and post-synaptic terminal, dendrites, axons), extracellular matrix, oligodendrocytes, microglial cells, and astrocytes. Among these, post-synaptic protein neurogranin was identified for the first time converted to neurogranin peptides including neurogranin peptide (aa 16-64) that is phosphorylated at Ser-36/48 (P-NG-fragment) in acute human TBI CSF samples vs. normal control with a receiver operating characteristic area under the curve of 0.957. We also identified detailed processing of astroglia protein (vimentin) and oligodendrocyte protein (MBP and Golli-MBP) to protein breakdown products (BDPs) and/or LMW proteolytic peptides after TBI. In addition, using MS/MS selected reaction monitoring method, two C-terminally released MBP peptides TQDENPVVHFF and TQDENPVVHF were found to be elevated in acute and subacute TBI CSF samples as compared to their normal control counterparts. These findings imply that future therapeutic strategies might be placed on the suppression of brain proteolysis as a target. The endogenous proteolytic peptides discovered in human TBI biofluid could represent useful diagnostic and monitoring tools for TBI.
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10
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Lin S, Mei X. Role of NLRP3 Inflammasomes in Neuroinflammation Diseases. Eur Neurol 2020; 83:576-580. [PMID: 33202405 DOI: 10.1159/000509798] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/27/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Inflammasomes are large intracellular multi-protein signaling complexes that are formed in the cytosolic compartment as an inflammatory immune response to endogenous danger signals. The formation of the inflammasome enables activation of an inflammatory protease caspase-1 and pyroptosis initiation with the subsequent cleaving of the pro-inflammatory cytokines interleukin (IL)-1β and proIL-18 to produce active forms. The inflammasome complex consists of a nod-like receptor, the adapter apoptosis-associated speck-like protein, and caspase-1. Dysregulation of NLRP3 inflammasome activation is involved in neuroinflammation disease pathogenesis, although its role in SCI development and progression remains controversial due to the inconsistent findings described. SUMMARY In this review, we summarize the current knowledge on the contribution of the NLRP3 inflammasome on potential neuroinflammation diseases therapy.
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Affiliation(s)
- Sen Lin
- Department of Orthopedic, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Xifan Mei
- Department of Orthopedic, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China,
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Liu S, Kang Y, Zhang C, Lou Y, Li X, Lu L, Qi Z, Jian H, Zhou H. Isobaric Tagging for Relative and Absolute Protein Quantification (iTRAQ)-Based Quantitative Proteomics Analysis of Differentially Expressed Proteins 1 Week After Spinal Cord Injury in a Rat Model. Med Sci Monit 2020; 26:e924266. [PMID: 33144554 PMCID: PMC7650090 DOI: 10.12659/msm.924266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background Spinal cord injury (SCI) is a devastating trauma of the central nervous system (CNS), with high levels of morbidity, disability, and mortality. One week after SCI may be a critical time for treatment. Changes in protein expression have crucial functions in nervous system diseases, although the effects of changes occurring 1 week after SCI on patient outcomes are unclear. Material/Methods Protein expression was examined in a rat contusive SCI model 1 week after SCI. Differentially expressed proteins (DEPs) were identified by isobaric tagging for relative and absolute protein quantification (iTRAQ)-coupled liquid chromatography tandem-mass spectrometry (LC-MS/MS) proteomics analysis. Gene Ontology (GO) analysis was performed to identify the biological processes, molecular functions, and cellular component terms of the identified DEPs, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was used to identify key enriched pathways. Protein–protein interaction (PPI) networks were analyzed to identify the top 10 high-degree core proteins. Results Of the 295 DEPs identified, 204 (69.15%) were upregulated and 91 (30.85%) were downregulated 1 week after injury. The main cellular components, molecular functions, biological processes, and pathways identified may be crucial mechanisms involved in SCI. The top 10 high-degree core proteins were complement component C3 (C3), alpha-2-HS-glycoprotein (Ahsg), T-kininogen 1 (Kng1), Serpinc1 protein (Serpinc1), apolipoprotein A-I (Apoa1), serum albumin (Alb), disulfide-isomerase protein (P4hb), transport protein Sec61 subunit alpha isoform 1 (Sec61a1), serotransferrin (Tf), and 60S ribosomal protein L15 (Rpl15). Conclusions The proteins identified in this study may provide potential targets for diagnosis and treatment 1 week after SCI.
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Affiliation(s)
- Shen Liu
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China (mainland)
| | - Yi Kang
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China (mainland)
| | - Chi Zhang
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China (mainland)
| | - Yongfu Lou
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China (mainland)
| | - Xueying Li
- Key Laboratory of Immuno Microenvironment and Disease of the Educational Ministry of China, Department of Immunology, Tianjin Medical University, Tianjin, China (mainland)
| | - Lu Lu
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China (mainland)
| | - Zhangyang Qi
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China (mainland)
| | - Huan Jian
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China (mainland)
| | - Hengxing Zhou
- Department of Orthopaedics, Tianjin Medical University General Hospital, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin, China (mainland)
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Shakkour Z, Habashy KJ, Berro M, Takkoush S, Abdelhady S, Koleilat N, Eid AH, Zibara K, Obeid M, Shear D, Mondello S, Wang KK, Kobeissy F. Drug Repurposing in Neurological Disorders: Implications for Neurotherapy in Traumatic Brain Injury. Neuroscientist 2020; 27:620-649. [PMID: 33089741 DOI: 10.1177/1073858420961078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Traumatic brain injury (TBI) remains a significant leading cause of death and disability among adults and children globally. To date, there are no Food and Drug Administration-approved drugs that can substantially attenuate the sequelae of TBI. The innumerable challenges faced by the conventional de novo discovery of new pharmacological agents led to the emergence of alternative paradigm, which is drug repurposing. Repurposing of existing drugs with well-characterized mechanisms of action and human safety profiles is believed to be a promising strategy for novel drug use. Compared to the conventional discovery pathways, drug repurposing is less costly, relatively rapid, and poses minimal risk of the adverse outcomes to study on participants. In recent years, drug repurposing has covered a wide range of neurodegenerative diseases and neurological disorders including brain injury. This review highlights the advances in drug repurposing and presents some of the promising candidate drugs for potential TBI treatment along with their possible mechanisms of neuroprotection. Edaravone, glyburide, ceftriaxone, levetiracetam, and progesterone have been selected due to their potential role as putative TBI neurotherapeutic agents. These drugs are Food and Drug Administration-approved for purposes other than brain injuries; however, preclinical and clinical studies have shown their efficacy in ameliorating the various detrimental outcomes of TBI.
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Affiliation(s)
- Zaynab Shakkour
- Department of Biochemistry & Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | | | - Moussa Berro
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Samira Takkoush
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Samar Abdelhady
- Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Nadia Koleilat
- Division of Child Neurology, Department of Pediatric and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ali H Eid
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Kazem Zibara
- PRASE and Biology Department, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Makram Obeid
- Division of Child Neurology, Department of Pediatric and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon.,Department of Anatomy, Cell Biology and Physiological Sciences, American University of Beirut, Beirut, Lebanon
| | - Deborah Shear
- Brain Trauma Neuroprotection/Neurorestoration, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Sicilia, Italy
| | - Kevin K Wang
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Departments of Emergency Medicine, Psychiatry, Neuroscience and Chemistry, University of Florida, Gainesville, FL, USA
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Departments of Emergency Medicine, Psychiatry, Neuroscience and Chemistry, University of Florida, Gainesville, FL, USA
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13
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Wang H, Chen J, Gao C, Chen W, Chen G, Zhang M, Luo C, Wang T, Chen X, Tao L. TMT-based proteomics analysis to screen potential biomarkers of acute-phase TBI in rats. Life Sci 2020; 264:118631. [PMID: 33131748 DOI: 10.1016/j.lfs.2020.118631] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/09/2020] [Accepted: 10/17/2020] [Indexed: 01/19/2023]
Abstract
AIMS Traumatic brain injury (TBI) is a common nervous system injury. However, the detailed mechanisms about functional dysregulation and dignostic biomarkers post-TBI are still unclear. So we aimed to identify potential differentially expressed proteins and genes in TBI for clinical diagnosis and therapeutic purposes. MAIN METHODS Rat TBI model was established by the weight-drop method. First, through TMT-proteomics, we screened for the change in the proteins expression profile acute phase post-TBI. The DAVID and Reactome databases were used to analyze and visualize the dysregulation proteins. Then, using publicly available microarray datasets GSE45997, differentially expressed genes (DGEs) were identified for the 24 h post-TBI stage. Also, the proteomic data were compared with microarray data to analyze the similarity. KEY FINDINGS We found significant proteomics and transcriptomic changes in post-TBI samples. 989, 881, 832, 1057 proteins were quantitated at 1 h, 6 h, 24 h, and 3 d post-injury correspondingly. Concerning proteomics findings, oxygen transport, acute-phase response, and negative regulation of endopeptidase activity were influenced throughout the acute phrase of TBI. Also, pathways related to scavenging of heme from plasma, binding, and uptake of ligands by scavenger receptors were highly enriched in all time-points of TBI samples. SIGNIFICANCE We noticed that the interaction-networks trend to get complicated with more node connections following the progression of TBI. We inferred that Hk-1, PRKAR2A, and MBP could be novel candidate biomarkers related to time-injury in acute-phase TBI. Also, Ceruloplasmin and Complement C3 were found to be important proteins and genes are involved in the TBI.
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Affiliation(s)
- Haochen Wang
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China.
| | - Jie Chen
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Cheng Gao
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Wei Chen
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Guang Chen
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Mingyang Zhang
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Chengliang Luo
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Tao Wang
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China
| | - Xiping Chen
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China.
| | - Luyang Tao
- Department of Forensic Medicine, Medical School of Soochow University, Suzhou 215123, China.
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14
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Martin-Rojas T, Sastre-Oliva T, Esclarín-Ruz A, Gil-Dones F, Mourino-Alvarez L, Corbacho-Alonso N, Moreno-Luna R, Hernandez-Fernandez G, Lopez JA, Oliviero A, Barderas MG. Effects of Growth Hormone Treatment and Rehabilitation in Incomplete Chronic Traumatic Spinal Cord Injury: Insight from Proteome Analysis. J Pers Med 2020; 10:jpm10040183. [PMID: 33096745 PMCID: PMC7720149 DOI: 10.3390/jpm10040183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022] Open
Abstract
Despite promising advances in the medical management of spinal cord injury (SCI), there is still no available effective therapy to repair the neurological damage in patients who experience this life-transforming condition. Recently, we performed a phase II/III placebo-controlled randomized trial of safety and efficacy of growth hormone (GH) treatment in incomplete chronic traumatic spinal cord injury. The main findings were that the combined treatment of GH plus rehabilitation treatment is feasible and safe, and that GH but not placebo slightly improves the SCI individual motor score. Moreover, we found that an intensive and long-lasting rehabilitation program per se increases the functional outcome of SCI individuals. To understand the possible mechanisms of the improvement due to GH treatment (motor score) and due to rehabilitation (functional outcome), we used a proteomic approach. Here, we used a multiple proteomic strategy to search for recovery biomarkers in blood plasma with the potential to predict response to somatropin treatment and to delayed intensive rehabilitation. Forty-six patients were recruited and followed for a minimum period of 1 year. Patients were classified into two groups based on their treatment: recombinant somatropin (0.4 mg) or placebo. Both groups received rehabilitation treatment. Our strategy allowed us to perform one of the deepest plasma proteomic analyses thus far, which revealed two proteomic signatures with predictive value: (i) response to recombinant somatropin treatment and (ii) response to rehabilitation. The proteins implicated in these signatures are related to homeostasis, inflammation, and coagulation functions. These findings open novel possibilities to assess and therapeutically manage patients with SCI, which could have a positive impact on their clinical response.
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Affiliation(s)
- Tatiana Martin-Rojas
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45071 Toledo, Spain; (T.M.-R.); (T.S.-O.); (F.G.-D.); (L.M.-A.); (N.C.-A.); (R.M.-L.); (G.H.-F.)
| | - Tamara Sastre-Oliva
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45071 Toledo, Spain; (T.M.-R.); (T.S.-O.); (F.G.-D.); (L.M.-A.); (N.C.-A.); (R.M.-L.); (G.H.-F.)
| | - Ana Esclarín-Ruz
- Department of Physical Medicine and Rehabilitation, Hospital Nacional de Parapléjicos, SESCAM, 45071 Toledo, Spain;
| | - Felix Gil-Dones
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45071 Toledo, Spain; (T.M.-R.); (T.S.-O.); (F.G.-D.); (L.M.-A.); (N.C.-A.); (R.M.-L.); (G.H.-F.)
- Department of Genetic, Facultad de Ciencias Biológicas, UCM, 28040 Madrid, Spain
| | - Laura Mourino-Alvarez
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45071 Toledo, Spain; (T.M.-R.); (T.S.-O.); (F.G.-D.); (L.M.-A.); (N.C.-A.); (R.M.-L.); (G.H.-F.)
| | - Nerea Corbacho-Alonso
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45071 Toledo, Spain; (T.M.-R.); (T.S.-O.); (F.G.-D.); (L.M.-A.); (N.C.-A.); (R.M.-L.); (G.H.-F.)
| | - Rafael Moreno-Luna
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45071 Toledo, Spain; (T.M.-R.); (T.S.-O.); (F.G.-D.); (L.M.-A.); (N.C.-A.); (R.M.-L.); (G.H.-F.)
- Department of Neuroinflammation, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45004 Toledo, Spain
| | - German Hernandez-Fernandez
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45071 Toledo, Spain; (T.M.-R.); (T.S.-O.); (F.G.-D.); (L.M.-A.); (N.C.-A.); (R.M.-L.); (G.H.-F.)
| | | | - Antonio Oliviero
- FENNSI Group, Hospital Nacional de Parapléjicos, SESCAM, 45071 Toledo, Spain
- Correspondence: (A.O.); (M.G.B.); Fax: +34-925-247-745 (M.G.B.)
| | - María G. Barderas
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos (HNP), SESCAM, 45071 Toledo, Spain; (T.M.-R.); (T.S.-O.); (F.G.-D.); (L.M.-A.); (N.C.-A.); (R.M.-L.); (G.H.-F.)
- Correspondence: (A.O.); (M.G.B.); Fax: +34-925-247-745 (M.G.B.)
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15
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Protein Degradome of Spinal Cord Injury: Biomarkers and Potential Therapeutic Targets. Mol Neurobiol 2020; 57:2702-2726. [PMID: 32328876 DOI: 10.1007/s12035-020-01916-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/31/2020] [Indexed: 12/13/2022]
Abstract
Degradomics is a proteomics sub-discipline whose goal is to identify and characterize protease-substrate repertoires. With the aim of deciphering and characterizing key signature breakdown products, degradomics emerged to define encryptic biomarker neoproteins specific to certain disease processes. Remarkable improvements in structural and analytical experimental methodologies as evident in research investigating cellular behavior in neuroscience and cancer have allowed the identification of specific degradomes, increasing our knowledge about proteases and their regulators and substrates along with their implications in health and disease. A physiologic balance between protein synthesis and degradation is sought with the activation of proteolytic enzymes such as calpains, caspases, cathepsins, and matrix metalloproteinases. Proteolysis is essential for development, growth, and regeneration; however, inappropriate and uncontrolled activation of the proteolytic system renders the diseased tissue susceptible to further neurotoxic processes. In this article, we aim to review the protease-substrate repertoires as well as emerging therapeutic interventions in spinal cord injury at the degradomic level. Several protease substrates and their breakdown products, essential for the neuronal structural integrity and functional capacity, have been characterized in neurotrauma including cytoskeletal proteins, neuronal extracellular matrix glycoproteins, cell junction proteins, and ion channels. Therefore, targeting exaggerated protease activity provides a potentially effective therapeutic approach in the management of protease-mediated neurotoxicity in reducing the extent of damage secondary to spinal cord injury.
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16
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Chen M, Song H, Cui J, Johnson CE, Hubler GK, DePalma RG, Gu Z, Xia W. Proteomic Profiling of Mouse Brains Exposed to Blast-Induced Mild Traumatic Brain Injury Reveals Changes in Axonal Proteins and Phosphorylated Tau. J Alzheimers Dis 2019; 66:751-773. [PMID: 30347620 DOI: 10.3233/jad-180726] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease (AD), the most prevalent form of dementia, is characterized by two pathological hallmarks: Tau-containing neurofibrillary tangles and amyloid-β protein (Aβ)-containing neuritic plaques. The goal of this study is to understand mild traumatic brain injury (mTBI)-related brain proteomic changes and tau-related biochemical adaptations that may contribute to AD-like neurodegeneration. We found that both phosphorylated tau (p-tau) and the ratio of p-tau/tau were significantly increased in brains of mice collected at 3 and 24 h after exposure to 82-kPa low-intensity open-field blast. Neurological deficits were observed in animals at 24 h and 7 days after the blast using Simple Neuroassessment of Asymmetric imPairment (SNAP) test, and axon/dendrite degeneration was revealed at 7 days by silver staining. Liquid chromatography-mass spectrometry (LC-MS/MS) was used to analyze brain tissue labeled with isobaric mass tags for relative protein quantification. The results from the proteomics and bioinformatic analysis illustrated the alterations of axonal and synaptic proteins in related pathways, including but not being limited to substantia nigra development, cortical cytoskeleton organization, and synaptic vesicle exocytosis, suggesting a potential axonal damage caused by blast-induced mTBI. Among altered proteins found in brains suffering blast, microtubule-associated protein 1B, stathmin, neurofilaments, actin binding proteins, myelin basic protein, calcium/calmodulin-dependent protein kinase, and synaptotagmin I were representative ones involved in altered pathways elicited by mTBI. Therefore, TBI induces elevated phospho-tau, a pathological feature found in brains of AD, and altered a number of neurophysiological processes, supporting the notion that blast-induced mTBI as a risk factor contributes to AD pathogenesis. LC/MS-based profiling has presented candidate target/pathways that could be explored for future therapeutic development.
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Affiliation(s)
- Mei Chen
- Geriatric Research Education and Clinical Center, Office of Research and Development, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, USA.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hailong Song
- Department of Pathology & Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, USA.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jiankun Cui
- Department of Pathology & Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, USA.,Truman VA Hospital Research Service, Columbia, MO, USA
| | - Catherine E Johnson
- Department of Mining and Nuclear Engineering, Missouri University of Science and Technology, Rolla, MO, USA
| | - Graham K Hubler
- Sidney Kimmel Institute for Nuclear Renaissance, Department of Physics and Astronomy, University of Missouri, Columbia, MO USA
| | - Ralph G DePalma
- Office of Research and Development, Department of Veterans Affairs, Washington, DC, USA Department of Surgery, Uniformed University of the Health Science, Bethesda, MD, USA
| | - Zezong Gu
- Department of Pathology & Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, USA.,Truman VA Hospital Research Service, Columbia, MO, USA
| | - Weiming Xia
- Geriatric Research Education and Clinical Center, Office of Research and Development, Edith Nourse Rogers Memorial Veterans Hospital, Bedford, MA, USA.,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
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17
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Song H, Chen M, Chen C, Cui J, Johnson CE, Cheng J, Wang X, Swerdlow RH, DePalma RG, Xia W, Gu Z. Proteomic Analysis and Biochemical Correlates of Mitochondrial Dysfunction after Low-Intensity Primary Blast Exposure. J Neurotrauma 2019; 36:1591-1605. [PMID: 30484371 PMCID: PMC6909772 DOI: 10.1089/neu.2018.6114] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Service members during military actions or combat training are frequently exposed to primary blasts by weaponry. Most studies have investigated moderate or severe brain injuries from blasts generating overpressures >100 kPa, whereas understanding the pathophysiology of low-intensity blast (LIB)-induced mild traumatic brain injury (mTBI) leading to neurological deficits remains elusive. Our recent studies, using an open-field LIB-induced mTBI mouse model with a peak overpressure at 46.6 kPa, demonstrated behavioral impairments and brain nanoscale damages, notably mitochondrial and axonal ultrastructural changes. In this study, we used tandem mass tagged (TMT) quantitative proteomics and bioinformatics analysis to seek insights into the molecular mechanisms underlying ultrastructural pathology. Changes in global- and phospho-proteomes were determined at 3 and 24 h and at 7 and 30 days post injury (DPI), in order to investigate the biochemical and molecular correlates of mitochondrial dysfunction. Results showed striking dynamic changes in a total of 2216 proteins and 459 phosphorylated proteins at vary time points after blast. Disruption of key canonical pathways included evidence of mitochondrial dysfunction, oxidative stress, axonal/cytoskeletal/synaptic dysregulation, and neurodegeneration. Bioinformatic analysis identified blast-induced trends in networks related to cellular growth/development/movement/assembly and cell-to-cell signaling interactions. With observations of proteomic changes, we found LIB-induced oxidative stress associated with mitochondrial dysfunction mainly at 7 and 30 DPI. These dysfunctions included impaired fission-fusion dynamics, diminished mitophagy, decreased oxidative phosphorylation, and compensated respiration-relevant enzyme activities. Insights on the early pathogenesis of primary LIB-induced brain damage provide a template for further characterization of its chronic effects, identification of potential biomarkers, and targets for intervention.
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Affiliation(s)
- Hailong Song
- Department of Pathology & Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri
| | - Mei Chen
- Bedford VA Medical Center, Bedford, Massachusetts
| | - Chen Chen
- Department of Computer Sciences, University of Missouri, Columbia, Missouri
| | - Jiankun Cui
- Department of Pathology & Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri
- Truman VA Hospital Research Service, Columbia, Missouri
| | - Catherine E. Johnson
- Department of Mining and Nuclear Engineering, Missouri University of Science and Technology, Rolla, Missouri
| | - Jianlin Cheng
- Department of Computer Sciences, University of Missouri, Columbia, Missouri
| | - Xiaowan Wang
- Department of Neurology, University of Kansas Alzheimer's Disease Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Russell H. Swerdlow
- Department of Neurology, University of Kansas Alzheimer's Disease Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Ralph G. DePalma
- Office of Research and Development, Department of Veterans Affairs, Washington, DC
- Norman Rich Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Weiming Xia
- Bedford VA Medical Center, Bedford, Massachusetts
| | - Zezong Gu
- Department of Pathology & Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri
- Truman VA Hospital Research Service, Columbia, Missouri
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18
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Proteomic Investigations of Autism Spectrum Disorder: Past Findings, Current Challenges, and Future Prospects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:235-252. [DOI: 10.1007/978-3-030-05542-4_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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19
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Vaysse PM, Heeren RMA, Porta T, Balluff B. Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations. Analyst 2018. [PMID: 28642940 DOI: 10.1039/c7an00565b] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.
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Affiliation(s)
- Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Tiffany Porta
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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20
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Veillon L, Fakih C, Abou-El-Hassan H, Kobeissy F, Mechref Y. Glycosylation Changes in Brain Cancer. ACS Chem Neurosci 2018; 9:51-72. [PMID: 28982002 DOI: 10.1021/acschemneuro.7b00271] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Protein glycosylation is a posttranslational modification that affects more than half of all known proteins. Glycans covalently bound to biomolecules modulate their functions by both direct interactions, such as the recognition of glycan structures by binding partners, and indirect mechanisms that contribute to the control of protein conformation, stability, and turnover. The focus of this Review is the discussion of aberrant glycosylation related to brain cancer. Altered sialylation and fucosylation of N- and O-glycans play a role in the development and progression of brain cancer. Additionally, aberrant O-glycan expression has been implicated in brain cancer. This Review also addresses the clinical potential and applications of aberrant glycosylation for the detection and treatment of brain cancer. The viable roles glycans may play in the development of brain cancer therapeutics are addressed as well as cancer-glycoproteomics and personalized medicine. Glycoprotein alterations are considered as a hallmark of cancer while high expression in body fluids represents an opportunity for cancer assessment.
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Affiliation(s)
- Lucas Veillon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock Texas 79409, United States
| | - Christina Fakih
- Department
of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hadi Abou-El-Hassan
- Department
of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Firas Kobeissy
- Department
of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Yehia Mechref
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock Texas 79409, United States
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21
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Ercole A, Magnoni S, Vegliante G, Pastorelli R, Surmacki J, Bohndiek SE, Zanier ER. Current and Emerging Technologies for Probing Molecular Signatures of Traumatic Brain Injury. Front Neurol 2017; 8:450. [PMID: 28912750 PMCID: PMC5582086 DOI: 10.3389/fneur.2017.00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/14/2017] [Indexed: 01/10/2023] Open
Abstract
Traumatic brain injury (TBI) is understood as an interplay between the initial injury, subsequent secondary injuries, and a complex host response all of which are highly heterogeneous. An understanding of the underlying biology suggests a number of windows where mechanistically inspired interventions could be targeted. Unfortunately, biologically plausible therapies have to-date failed to translate into clinical practice. While a number of stereotypical pathways are now understood to be involved, current clinical characterization is too crude for it to be possible to characterize the biological phenotype in a truly mechanistically meaningful way. In this review, we examine current and emerging technologies for fuller biochemical characterization by the simultaneous measurement of multiple, diverse biomarkers. We describe how clinically available techniques such as cerebral microdialysis can be leveraged to give mechanistic insights into TBI pathobiology and how multiplex proteomic and metabolomic techniques can give a more complete description of the underlying biology. We also describe spatially resolved label-free multiplex techniques capable of probing structural differences in chemical signatures. Finally, we touch on the bioinformatics challenges that result from the acquisition of such large amounts of chemical data in the search for a more mechanistically complete description of the TBI phenotype.
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Affiliation(s)
- Ari Ercole
- Division of Anaesthesia, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Sandra Magnoni
- Department of Anesthesiology and Intensive Care, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Gloria Vegliante
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Roberta Pastorelli
- Unit of Gene and Protein Biomarkers, Laboratory of Mass Spectrometry, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Jakub Surmacki
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Elizabeth Bohndiek
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Elisa R. Zanier
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
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