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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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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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Streijger F, Skinnider MA, Rogalski JC, Balshaw R, Shannon CP, Prudova A, Belanger L, Ritchie L, Tsang A, Christie S, Parent S, Mac-Thiong JM, Bailey C, Urquhart J, Ailon T, Paquette S, Boyd M, Street J, Fisher CG, Dvorak MF, Borchers CH, Foster LJ, Kwon BK. A Targeted Proteomics Analysis of Cerebrospinal Fluid after Acute Human Spinal Cord Injury. J Neurotrauma 2017; 34:2054-2068. [DOI: 10.1089/neu.2016.4879] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Femke Streijger
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael A. Skinnider
- Department of Biochemistry & Molecular Biology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Genome Sciences & Technologies Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jason C. Rogalski
- Department of Biochemistry & Molecular Biology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- BC Center for Disease Control, Vancouver, British Columbia, Canada
- PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | | | - Anna Prudova
- Department of Biochemistry & Molecular Biology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lise Belanger
- Vancouver Spine Program, Vancouver, British Columbia, Canada
| | - Leanna Ritchie
- Vancouver Spine Program, Vancouver, British Columbia, Canada
| | - Angela Tsang
- Vancouver Spine Program, Vancouver, British Columbia, Canada
| | - Sean Christie
- Division of Neurosurgery, Dalhousie University, Halifax Infirmary Halifax, Halifax, Nova Scotia, Canada
| | - Stefan Parent
- Department of Surgery, Hôpital du Sacré-Coeur de Montréal, Université de Montréal, Montréal, Quebec, Canada
- Chu Sainte-Justine, Department of Surgery, Université de Montréal, Montréal, Quebec, Canada
| | - Jean-Marc Mac-Thiong
- Department of Surgery, Hôpital du Sacré-Coeur de Montréal, Université de Montréal, Montréal, Quebec, Canada
- Chu Sainte-Justine, Department of Surgery, Université de Montréal, Montréal, Quebec, Canada
| | - Christopher Bailey
- Division of Orthopaedic Surgery, London Health Sciences Centre, University of Western Ontario, London, Ontario, Canada
| | - Jennifer Urquhart
- Division of Orthopaedic Surgery, London Health Sciences Centre, University of Western Ontario, London, Ontario, Canada
| | - Tamir Ailon
- Vancouver Spine Surgery Institute, Division of Neurosurgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott Paquette
- Vancouver Spine Surgery Institute, Division of Neurosurgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Boyd
- Vancouver Spine Surgery Institute, Division of Neurosurgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - John Street
- Department of Orthopaedics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charles G. Fisher
- Department of Orthopaedics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marcel F. Dvorak
- Department of Orthopaedics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian K. Kwon
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Orthopaedics, University of British Columbia, Vancouver, British Columbia, Canada
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Sengupta MB, Chakrabarti A, Saha S, Mukhopadhyay D. Clinical proteomics of enervated neurons. Clin Proteomics 2016; 13:10. [PMID: 27152104 PMCID: PMC4857373 DOI: 10.1186/s12014-016-9112-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/18/2016] [Indexed: 11/16/2022] Open
Abstract
The dynamic field of neurosciences entails ever increasing search for molecular mechanisms of disease states, especially in the domain of neurodegenerative disorders. The previous century heralded the techniques in proteomics when indexing of the human proteomes relating to various disease conditions became important. Early stage research in certain diseases or pathological conditions requires a more holistic approach of first discovering the proteins of interest for the condition. Despite its limitations, proteomics is one of the most powerful techniques available to us today to dissect the molecular scenario in a particular disease situation. In this review we will discuss about the current clinical research in neurodegenerative disorders that employ proteomics techniques. We will specifically focus on our understanding of Alzheimer’s disease, traumatic spinal cord injury and neuromyelitis optica. Discussions will include ongoing worldwide research in these areas, research in India and specifically our laboratory in these domains of neurodegenerative conditions.
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Affiliation(s)
- Mohor Biplab Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064 India
| | - Arunabha Chakrabarti
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064 India
| | - Suparna Saha
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064 India
| | - Debashis Mukhopadhyay
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064 India
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Molecular Architecture of Spinal Cord Injury Protein Interaction Network. PLoS One 2015; 10:e0135024. [PMID: 26241741 PMCID: PMC4524728 DOI: 10.1371/journal.pone.0135024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/16/2015] [Indexed: 12/17/2022] Open
Abstract
Spinal cord injury (SCI) is associated with complex pathophysiological processes that follow the primary traumatic event and determine the extent of secondary damage and functional recovery. Numerous reports have used global and hypothesis-driven approaches to identify protein changes that contribute to the overall pathology of SCI in an effort to identify potential therapeutic interventions. In this study, we use a semi-automatic annotation approach to detect terms referring to genes or proteins dysregulated in the SCI literature and develop a curated SCI interactome. Network analysis of the SCI interactome revealed the presence of a rich-club organization corresponding to a “powerhouse” of highly interacting hub-proteins. Studying the modular organization of the network have shown that rich-club proteins cluster into modules that are specifically enriched for biological processes that fall under the categories of cell death, inflammation, injury recognition and systems development. Pathway analysis of the interactome and the rich-club revealed high similarity indicating the role of the rich-club proteins as hubs of the most prominent pathways in disease pathophysiology and illustrating the centrality of pro-and anti-survival signal competition in the pathology of SCI. In addition, evaluation of centrality measures of single nodes within the rich-club have revealed that neuronal growth factor (NGF), caspase 3, and H-Ras are the most central nodes and potentially an interesting targets for therapy. Our integrative approach uncovers the molecular architecture of SCI interactome, and provide an essential resource for evaluating significant therapeutic candidates.
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