Differential neuroproteomic and systems biology analysis of spinal cord injury (original) (raw)
Related papers
PLoS ONE, 2014
Recovery of sensory and motor functions following traumatic spinal cord injury (SCI) is dependent on injury severity. Here we identified 49 proteins from cerebrospinal fluid (CSF) of SCI patients, eight of which were differentially abundant among two severity groups of SCI. It was observed that the abundance profiles of these proteins change over a time period of days to months post SCI. Statistical analysis revealed that these proteins take part in several molecular pathways including DNA repair, protein phosphorylation, tRNA transcription, iron transport, mRNA metabolism, immune response and lipid and ATP catabolism. These pathways reflect a set of mechanisms that the system may adopt to cope up with the assault depending on the injury severity, thus leading to observed physiological responses. Apart from putting forward a picture of the molecular scenario at the injury site in a human study, this finding further delineates consequent pathways and molecules that may be altered by external intervention to restrict neural degeneration.
Journal of Neurotrauma, 2010
Traumatic spinal cord injury (SCI) causes marked neuropathological changes in the spinal cord, resulting in limited functional recovery. Currently, there are no effective treatments, and the mechanisms underlying these neuropathological changes are not completely understood. In this study, two-dimensional gel electrophoresis coupled with mass spectrometry was used to investigate injury-related changes in the abundance (SYPRO Ruby stain) and phosphorylation (Pro-Q Diamond stain) of proteins from the soluble fraction of the lesion epicenter at 24 h following SCI. Over 1500 SYPRO Ruby-stained spots and 100 Pro-Q Diamond-stained spots were examined. We identified 26 unique proteins within 38 gel spots that differentially changed in abundance, phosphorylation, or both in response to SCI. Protein redundancies among the gel spots were likely due to differences in proteolysis, post-translational modifications, and the existence of isoforms. The proteins affected were blood-related proteins, heat-shock proteins, glycolytic enzymes, antioxidants, and proteins that function in cell structure, cell signaling, DNA damage, and protein degradation. These protein changes post injury may suggest additional avenues of investigation into the underlying molecular mechanisms responsible for the pathophysiological consequences of SCI.
Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury
Molecular & Cellular Proteomics, 2021
Despite the emergence of promising therapeutic approaches in preclinical studies, the failure of large-scale clinical trials leaves clinicians without effective treatments for acute spinal cord injury (SCI). These trials are hindered by their reliance on detailed neurological examinations to establish outcomes, which inflate the time and resources required for completion. Moreover, therapeutic development takes place in animal models whose relevance to human injury remains unclear. Here, we address these challenges through targeted proteomic analyses of CSF and serum samples from 111 acute SCI patients and, in parallel, a large animal (porcine) model of SCI. We develop protein biomarkers of injury severity and recovery, including a prognostic model of neurological improvement at six months with an AUC of 0.91, and validate these in an independent cohort. Through cross-species proteomic analyses, we dissect evolutionarily conserved and divergent aspects of the SCI response, and establish the CSF abundance of glial fibrillary acidic protein (GFAP) as a biochemical outcome measure in both humans and pigs. Our work opens up new avenues to catalyze translation by facilitating the evaluation of novel SCI therapies, while also providing a resource from which to direct future preclinical efforts.
An optimal protocol to analyze the rat spinal cord proteome
Biomarker insights, 2009
Since the function of the spinal cord depends on the proteins found there, better defing the normal Spinal Cord Proteome is an important and challenging task. Although brain and cerebrospinal fluid samples from patients with different central nervous system (CNS) disorders have been studied, a thorough examination of specific spinal cord proteins and the changes induced by injury or associated to conditions such as neurodegeneration, spasticity and neuropathies has yet to be performed. In the present study, we aimed to describe total protein content in the spinal cord of healthy rats, employing different proteomics tools. Accordingly, we have developed a fast, easy, and reproducible sequential protocol for protein extraction from rat spinal cords. We employed conventional two dimensional electrophoresis (2DE) in different pH ranges (eg. 4-7, 3-11 NL) combined with identification by mass spectrometry (MALDI-TOF/TOF), as well as first dimension protein separation combined with Liquid ...
Spinal cord injury (SCI) represents a major debilitating health issue with a direct socioeconomic burden on the public and private sectors worldwide. Although several studies have been conducted to identify the molecular progression of injury sequel due from the lesion site, still the exact underlying mechanisms and pathways of injury development have not been fully elucidated. In this work, based on OMICs, 3D matrix-assisted laser desorption ion-ization (MALDI) imaging, cytokines arrays, confocal imaging we established for the first time that molecular and cellular processes occurring after SCI are altered between the lesion proximity, i.e. rostral and caudal segments nearby the lesion (R1-C1) whereas segments distant from R1-C1, i.e. R2-C2 and R3-C3 levels coexpressed factors implicated in neurogenesis. Delay in T regulators recruitment between R1 and C1 favor discrepancies between the two segments. This is also reinforced by presence of neurites outgrowth inhibitors in C1, absent in R1. Moreover, the presence of immunoglobulins (IgGs) in neu-rons at the lesion site at 3 days, validated by mass spec-trometry, may present additional factor that contributes to limited regeneration. Treatment in vivo with anti-CD20 one hour after SCI did not improve locomotor function and decrease IgG expression. These results open the door of a novel view of the SCI treatment by considering the C1 as the therapeutic target. Molecular & Cellular Proteomics 15: 10.1074/mcp.M115.057794, 2641–2670, 2016. Spinal cord injury (SCI) 1 belongs to the serious, currently incurable disorders of the central nervous system (CNS), that are often accompanied by a permanent disability (1). Most SCI are related to traumatic spinal cord damages induced by road trauma, falls, or sport injuries (diving). Among the hallmark features of SCI is the axonal disruption in the spinal cord, which is often caused by fractured intervertebral disc or vertebrate. This primary event is followed by a progressive cascade of secondary deleterious reactions spreading to the adjacent spared tissue leading to a worsening of the neuro-logical status (2, 3). Although axonal regeneration is initiated, it is hampered by a combination of local factors that include severe inflammation, lack of trophic support and development of an inhibitory scar-forming environment. In fact, the regen-erative capacity of the central nervous system is particularly challenged in SCI as multiple cues converge to act as a chemical and physical barrier for the repair process (4, 5). It is now acknowledged that inflammation is one of the major key player that determines abortive axonal repair in SCI. Thus, although the immune response is recognized as primordial to preserve tissue homeostasis, the spatio-temporal course of inflammation in SCI is not favorable to axonal regeneration. Acute inflammation develops hours to days following initial spinal cord trauma and is triggered by the axonal damage and
Combined Transcriptomics, Proteomics and Bioinformatics Identify Drug Targets in Spinal Cord Injury
International Journal of Molecular Sciences, 2018
Spinal cord injury (SCI) causes irreversible tissue damage and severe loss of neurological function. Currently, there are no approved treatments and very few therapeutic targets are under investigation. Here, we combined 4 high-throughput transcriptomics and proteomics datasets, 7 days and 8 weeks following clinically-relevant rat SCI to identify proteins with persistent differential expression post-injury. Out of thousands of differentially regulated entities our combined analysis identified 40 significantly upregulated versus 48 significantly downregulated molecules, which were persistently altered at the mRNA and protein level, 7 days and 8 weeks post-SCI. Bioinformatics analysis was then utilized to identify currently available drugs with activity against the filtered molecules and to isolate proteins with known or unknown function in SCI. Our findings revealed multiple overlooked therapeutic candidates with important bioactivity and established druggability but with unknown expression and function in SCI including the upregulated purine nucleoside phosphorylase (PNP), cathepsins A, H, Z (CTSA, CTSH, CTSZ) and proteasome protease PSMB10, as well as the downregulated ATP citrate lyase (ACLY), malic enzyme (ME1) and sodium-potassium ATPase (ATP1A3), amongst others. This work reveals previously unappreciated therapeutic candidates for SCI and available drugs, thus providing a valuable resource for further studies and potential repurposing of existing therapeutics for SCI.
Proteome analysis of up-regulated proteins in the rat spinal cord induced by transection injury
PROTEOMICS, 2006
Linear Immobiline DryStrips, 18 cm, ExcelGel SDS buffer strips, GelBond PAG film (2036260 mm), urea, CHAPS, Ndecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (SB3-10), acryl amide, Bis, pepstatin A and leupepsin, and CHCA were obtained from Sigma (St. Louis, Mo, USA). DTT was purchased from Promega (Madison, WI, USA). Thiourea was obtained from the Beijing Chemical Reagent Company (Beijing, PR China) and carrier ampholytes (pH 3-10) from the Academy of Military Medical Sciences (Beijing, PR China). Ammonium persulfate was purchased from Gibco BRL (Grand Island, NY, USA) and TEMED from Fluka. Sequencing-grade modified trypsin (porcine pancreas source) was obtained from Promega. TFA was from ACROS (NJ, USA); the primary antibodies of dynein (mouse monoclonal IgG), dynactin (goat polyclonal IgG), vimentin (rabbit polyclonal IgG), glypican (rabbit polyclonal IgG) and olfactory cyclic nucleotide-gated channel 2 (goat polyclonal IgG) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Other reagents were from local suppliers and were of analytical grade. An IPGphor IEF system, Multiphor II flatbed electrophoresis system, which includes an EPS 3501 XL power supply, Multiphor II electrophoresis unit, Multitemp III thermostatic circulator, Hoefer processor plus (automated gel stainer), and ImageMaster ® 2D Elite software were purchased from Amersham Pharmacia Biotech (Uppsala, Sweden). A Unicam UV-330 spectrometer (Cambridge, UK) was used to determine protein concentration. 2.2 Spinal cord injury model Eight young adult male Wistar rats (2.5 months of age) from the same litter were randomly divided into two groups. Under general phenobarbital anesthesia (40 mg/kg, intraperitoneally), one group of four rats was incised sterilely to
Spinal cord injury (SCI) represents a major debilitating health issue with a direct socioeconomic burden on the public and private sectors worldwide. Although several studies have been conducted to identify the molecular progression of injury sequel due from the lesion site, still the exact underlying mechanisms and pathways of injury development have not been fully elucidated. In this work, based on OMICs, 3D matrix-assisted laser desorption ionization (MALDI) imaging, cytokines arrays, confocal imaging we established for the first time that molecular and cellular processes occurring after SCI are altered between the lesion proximity, i.e. rostral and caudal segments nearby the lesion (R1-C1) whereas segments distant from R1-C1, i.e. R2-C2 and R3-C3 levels coexpressed factors implicated in neurogenesis. Delay in T regulators recruitment between R1 and C1 favor discrepancies between the two segments. This is also reinforced by presence of neurites outgrowth inhibitors in C1, absent in R1. Moreover, the presence of immunoglobulins (IgGs) in neurons at the lesion site at 3 days, validated by mass spectrometry, may present additional factor that contributes to limited regeneration. Treatment in vivo with anti-CD20 one hour after SCI did not improve locomotor function and decrease IgG expression. These results open the door of a novel view of the SCI treatment by considering the C1 as the therapeutic target.
2017
Spinal cord injury (SCI) is a severe, often life threatening, traumatic condition leading to serious neurological dysfunctions. The pathological hallmarks of SCI include inflammation, reactive gliosis, axonal demyelination, neuronal death, and cyst formation. Although much has been learned about the progression of SCI pathology affecting a large number of biochemical cascades and reactions, the roles of proteins involved in these processes are not well understood. Advances in proteomic technologies have made it possible to examine the spinal cord proteome from healthy and experimental animals and disclose a detailed overview on the spatial and temporal regionalization of these secondary processes. Data clearly demonstrated that neurotrophic molecules dominated in the segment above the central lesion, while the proteins associated with necrotic/apoptotic pathways abound the segment below the lesion. This knowledge is extremely important in finding optimal targets and pathways on whic...