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PXD003375/sci1_10d_r1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci1-3d-c2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sc2_ctrl_r3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci3_3d_r2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci1_10d_c1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sc3_ctrl_r3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sc1-ctrl-r2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci2_7d_r3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci1_10d_r2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci2_3d_lesion.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci3_10d_r1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sc2_ctrl_r2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci3_10d_lesion.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci1-3d-c3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci1_10d_r3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci2_10d_c3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci1_7d_c1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci3_3d_r1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sc3_ctrl_r2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci1-7d-c2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci2_3d_r3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/sci2_7d_r2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/SEARCH.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/abundance_ibaq_SCI_CM.spsftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/perseus_SCI_CM.spsftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/Perseus.rarftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003375/annotated_spectra.zipprimaryOK200003970michel.salzet@univ-lille1.frMaxence WisztorskiMass SpectrometryShotgun proteomicsNot availableSpinal cord lesionProteomicsMass spectrometry imagingMicroglial cellshttp://www.ebi.ac.uk/pride/archive/projects/PXD003375Nerve CordThe SCI was induced using the modified balloon compression technique in adult male Wistar rats, according to our previously published study. Manual bladder expression, 2 times a day, was required for 3-10 days after the injury. In the control group, a 2-French Fogarty catheter was inserted at the same level of spinal cord, but the balloon was not inflated and no lesion was performed. Experimental SCI rats (n=3 for each survival time) at 3, 7 and 10 days and sham-operated-control rats (n=3) were sacrificed by isoflurane anesthesia followed by decapitation. The spinal cord was pressure expressed by injecting sterile saline (10ml) throughout the vertebrate canal, along the caudo-rostral axis. Each spinal cord was macroscopically observed to check that lesion was well centered at the Th8-Th9 level on the longitudinal axis. Entire spinal cord was divided into transversally sectioned slides (approximately 1cm thick each) obtained from the lesion site (Th7-Th11) and from the segments rostral (C1-Th6) and caudal (Th12-L6) to the site of injury. Slides were then chopped into 0.5cm thick sections (2 sections per segment) and deposited into a 12-well culture plate containing 1ml DMEM without FCS. After 24 hours incubation in a humidified atmosphere with 5% CO2 at 37°C, 1ml of SCI-derived conditioned media (CM-SCI) were collected (rostral, lesion, caudal segments) and centrifuged 30 minutes at 15.000 rpm at 4°C. The same procedure was performed for obtaining CM from control spinal cord tissue. Samples were stored at -80°C.A volume of 150µL of tissue supernatants were denatured with 2M urea in 10mM HEPES pH 8 by ultrasonication on ice. Protein reduction is realized by incubation with 10mM DTT for 40 minutes at 56°C followed by alkylation with 55mM IAA for 40 minutes in the dark. IAA was quenched with 100mM thiourea. Protein digestion was performed with 30µg/mL LysC/Trypsin mix, overnight, at 37°C. Digestion was stopped with 0.5% TFA. The solution was dried in a SpeedVac to reduce the volume. Peptides were desalted using C18 ziptips (Millipore). Elution peptides were dried in a SpeedVac and resuspended in 0.1% FA before injecting into nanoLC. Samples were separated by online reversed-phase chromatography using a Thermo Scientific Proxeon Easy-nLC 1000 system equipped with a Proxeon trap column (100 μm ID x 2 cm, Thermo Scientific) and a C18 packed-tip column (100μm ID x 15cm, NikkyoTechnos Co. Ltd). Peptides were separated using an increasing amount of AcN (5%-35% over 100 minutes) at a flow rate of 300nL/min. The LC eluent was electrosprayed directly from the analytical column and a voltage of 1.7 kV was applied via the liquid junction of the nanospray source. The chromatography system was coupled to a Thermo Scientific Qexactive mass spectrometer programmed to acquire in a data-dependent mode Top 10 most intense ion method. The survey scans were acquired at a resolution of 70,000 with a mass range of m/z 400 to 2,000.PrideMaxQuant:LFQ intensityacetylated residueAll the MS data were processed with MaxQuant16 using the Andromeda17 search engine. Proteins were identified by searching MS and MS/MS data against Decoy version of the complete proteome for Rattusnorvegicus of the UniProt database (Release June 2014, 33,675 entries) combined with 262 commonly detected contaminants. Trypsin specificity was used for the digestion mode with N-terminal acetylation and methionine oxidation selected as the variable. Carbamidomethylation of cysteines was set as a fixed modification, with up to two missed cleavages. For MS spectra, an initial mass accuracy of 6 ppm was selected and the MS/MS tolerance was set to 20 ppm for HCD data. For identification, the FDR at the peptide spectrum matches (PSMs) and protein level was set to 1%. Relative label-free quantification of proteins was performed using the MaxLFQ algorithm19 integrated into MaxQuant with the default parameters. Analysis of the proteins identified was performed using Perseus software (http://www.perseus-framework.org/) (version 1.5.0.31). The file containing the information from identification was used with hits to the reverse database and proteins only identified with modified peptides and potential contaminants were removed. Then, the LFQ intensity was logarithmized (log2[x]). Categorical annotation of rows was used to defined different groups after grouping replicates: i) Time (control, 3, 7 and 10 days), ii) Segment (R3, R2, R1, L, C1, C2 and C3). Multiple samples tests were performed using ANOVA test with a FDR of 5% and preserving grouping in randomization. Normalization was achieved using a Z-score with a matrix access by rows. For the statistical analysis, only proteins presenting as significant by the ANOVA test were used for statistical analysis. Hierarchical clustering depending on time or segment was first performed using the Euclidean parameter for distance calculation and average option for linkage in row and column trees using a maximum of 300 clusters. For visualization of the variation of proteins expression depending to the condition, the profile plot tool was used with a reference profile and an automatic selection of the 10 or 15 correlated profiles. To quantify fold changes of proteins across samples, we used MaxLFQ. To visualize these fold changes in the context of individual protein abundances in the proteome, we projected them onto the summed peptide intensities normalized by the number of theoretically observable peptides. Specifically, to compare relative protein abundances between and within samples, protein lengths normalized to log 2 protein intensities (termed “iBAQ” value in MaxQuant) were added to the MaxLFQ differences.ProteomicsMichel SalzetQ ExactivePARTIALUniv. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000 Lille, FranceRattus Norvegicus (rat)27250205 Devaux S, Cizkova D, Quanico J, Franck J, Nataf S, Pays L, Hauberg-Lotte L, Maass P, Kobarg JH, Kobeissy F, Meriaux C, Wisztorski M, Slovinska L, Blasko J, Cigankova V, Fournier I, Salzet M. Proteomic analysis of the spatio-temporal based molecular kinetics of acute spinal cord injury identifies a time- and segment-specific window for effective tissue repair. Mol Cell Proteomics. 2016 Jun 1. pii: mcp.M115.057794maxence.wisztorski@univ-lille1.frBiologicalBiomedicalUniversity of LilleFranceSpinal 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.Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair.Devaux Stephanie S, Cizkova Dasa D, Quanico Jusal J, Franck Julien J, Nataf Serge S, Pays Laurent L, Hauberg-Lotte Lena L, Maass Peter P, Kobarg Jan H JH, Kobeissy Firas F, Mériaux Céline C, Wisztorski Maxence M, Slovinska Lucia L, Blasko Juraj J, Cigankova Viera V, Fournier Isabelle I, Salzet Michel MRat, isofluranum, PLIP, IL1BC, Terminalis, ion, Laboratory, CASP-1, Physical, Basodexan, 2-(indol-3-yl)ethanoic acid, Apaf-1, Norway Rats, Type 2A-interacting protein, thomson., trauma, Polypeptides, rat, Th9, protein polypeptide chains, salicylhydroxamate, serial element, Cultural, B1, 1, Urea, 2, Il1bc, adult, WMS, 1-trifluoro-, HTATIP, nup154, ethnicity, fissura cerebro-cerebellaris, Divorced, C79325, hac-1, C2, Tissue, Salt, Conus Medullaris, proteins, Divorces, SURGICAL AND MEDICAL PROCEDURES, IL-1BC, AI047805, Conus, Conus Terminali, Coccygeal Cords, cPLA2, column, vertebra 2, infertility, ACN, D1, Acn, ATH9, TIP, SGS, Spinal Cords, Degradations, subdivided, Caspase-1 subunit p10, Injury and Wounds, anon-53Fa, l(2)SH0173, Physical Traumas, Medullaris, C2 vertebra, fissura cerebrocerebellaris, Procedure, tip, ANAC091, not genetically inherited, Aerrane, DmelCG7788, ACMICD, Putative MAPK-activating protein PM10, Cultural Background, (Indol-3-yl)acetate, Cultures, Dm1, vesica urinaria, Detrusor Muscles, simple tissue, Sacral Cord, TIP60, CG6829, cerebrocerebellar fissure, forked, dark/hac-1/dapaf-1, divided, maleate, Protein Digestions, axis [C II], septate, rats, beta Trypsin, experimental procedures, Atmospheres, Indole-3-acetic acid, heteroauxin, Drice, Research-Related Injuries, DRICE, tlp, TIP41, Detrusor Urinae, Research Related Injuries, region or site annotation, DrIce, DrICE, T helper cells type 9, introduced into, stalk, Carbamide, protein-containing complex, Injuries and Wounds, body system, ESA1, CG7826, mass-to-charge ratio, Wounds, Rats, 1-chloro-2, CG7835, CG42273, system, TRX H9, sterile, Carmol, Backgrounds, Thoracic Cord, positional, Injury, anatomical systems, Acinus, Forane, interventionDescription, axis (CII), Monosodium Salt, PCE-2, beta-Trypsin, inserted, Cultural Relativisms, ions, culm, Solution, acinusL, DmelCG4579, ms(2)zk, SpC, SHAM, Caspase-1 subunit p20, acinusS, breakpoint, Customs, peptidos, Wistar Rat, Chromatographies, 4-(2-hydroxyethyl)-, PTHB1, Terminali, Reproductive, 1H-indol-3-ylacetic acid, dark/dapaf-1/hac-1, 2-chloro-2-(difluoromethoxy)-1, grupo, caspase 3, dApaf-1, BcDNA:LD21772, THIOREDOXIN TYPE H 9, medulla spinalis, CE-2, Cultural Backgrounds, backward, Digestions, mKIAA0670, polypeptide, APAF1, native protein, Proteolyses, traumatic injury, Wounds and Injury, Conus Medullari, carbonyldiamide, Hac-1, anatomical junction, C18, Trauma, Laboratory Rats, Infertile (finding), MFS1, infertility disorder, MIXL, Intervention, boundary, AU020952, Thoracic Cords, cervical vertebra 2, Separations, wound, 3-Indolylessigsaeure, CG4579, Spinalis, Dark/Dapaf-1/HAC1, IL-1 beta-converting enzyme, Conus Terminalis, Interleukin-1 beta-converting enzyme, ME-IV, male human body, plan specification, binding_or_interaction_site, air-filled, Sterility, Ethane, Isoflurane, Relativisms, Norway, Relativism, Cultural Relativism, Lumbar, Lumbar Cord, reversed, Hac-1/Dark, Nup32D, Medullari, second cervical vertebra, Wound, adult stage, DmelCG6829, 2-trifluoroethyl difluoromethyl ether, CG7788, Norway Rat, crice, HEPES Monosodium Salt, protein, clefted, injury, binding site, Alkylations, axis vertebra, peptide, Background, caudal, IAA, peptido, BANF, dJ69E11.3, Min, Norway rat, Apaf1, Wistar, (2Z)-but-2-enedioate, protein aggregate, ARK, Research-Related, MIX, DmelCG42273, male, spinal cord structure, portion of tissue, HEPES Monosodium, Spinali, reference sample, peptides, Coccygeal, E927b, 2610036I19Rik, 2610510L13Rik, arc, min, mAPC, Forene, ark, Protein Degradation, T1, Laboratory Rat, fSAP152, 1-Piperazineethanesulfonic acid, ICE, Urinary, dApaf1, GPHYSD2, Decapitations, junction, sterility, ice, iCE, D-Apaf-1, drice, ZC2HC5, Sacral Cords, Dmel_CG7826, Th, Rattus, segment, infertile, HTATIP1, Thermo Scientific, ur, carbamide, Mus norvegicus, Medulla, Ionen, drIce, drICE, Digestion, Myelon, tissue portion, Physical Trauma, IES, Adults, region, Dmel_CG7835, Mnb, MNB, MILD1, adults, positional polypeptide feature, P45, DMEM, Lumbar Cords, isoflurano, hac1, MASS, AW124434, isoflurane, Detrusor Muscle, 2-chloro-2-difluoromethoxy-1, organ system, dapaf-1S, nanospray, H2NC(O)NH2, apaf-1, dapaf-1L, p45, Research-Related Injury, Polypeptide, HEPES, bladder, fertility disorders, 1728, Gruppe, T(H)-9 cell, Beliefs, Catheter, Coccygeal Cord, norvegicus, Dapaf-1/HAC-1, experimental, Infertile, 1-trifluoroethane, Degradation, FBN, ACINUS, Intervention or Procedure, Dark/Hac-1/dApaf1, Karbamid, method, Hac1, Wistar Rats, Dark/Hac-1/dApaf-1, polypeptide chain, ECTOL1, Arabidopsis NAC domain containing protein 91, method used in an experiment, Harnstoff, zk, cerebro-cerebellar fissure, Separated, brown rat, study, vesica, l(2)10432, methods, Rattus norvegicus, experimental section, iones, dapaf-1, Interventional, Indoleacetic acid, dapaf, dark, Protein Degradations, Myelons, OCTD, (indol-3-yl)acetic acid, DARK, grupos, time of survival, Traumas, Reproductive Sterility, Sacral, site, N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, liquid, l(2)01501, culture, dArk, Dapaf-1, thioredoxin H-type 9, Controlled, D-MEM, Intervention Strategies, Controlling, DYRK1, data, Males, axis, protein complex, Cords, tailed, apaf1, Protein Digestion, Peptide, Cord, group, Belief, cervical axis, survival, Sterile, Bladder Detrusor Muscles, natural protein, Protein, Dyrk1, Vertebrate, CES2A1, Dark, connected anatomical system, Dark/Apaf-I, WMS2, Separation, urocyst, nup32D, Bladder, uree, INSDC_feature:misc_binding, urea, CC1, Rest, Tripcellim, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, dApaf-1/DARK/HAC-1, Injuries, UREA, Interleukin-1 beta convertase, spinal medulla, Trypure, Pressures, Ion, SSKS, 3.4.22.36, Spinal, TCV-interacting protein, Peptid, Medulla Spinalis, SCH, groupe, Thoracic, Medulla Spinali, dAPAF-1, Bladder Detrusor MuscleTraumatic Myelopathy, portion of tissue, Spinal Cord Transection, Spinal Cord Trauma, simple tissue., Effects, Longterm, Tissue, Longterm Effect, segment, Long-Term, temporal, Long Term, Longterm Effects, Acute onset, period, Post-Traumatic Myelopathy, serial element, Long Term Effects, proteomic analysis, tissue portion, Spinal Cord Injuries, Long-Term Effect, SCI, Spinal Cord Laceration, Effect, time, Long-Term Effects, incidence, Spinal Cord ContusionIPP2A2, determination, Ass-1, selection process, protein, Long Term, 5730420M11Rik, peptide, Polypeptides, L-Isomer Methionine, protein polypeptide chains, Methionine, Drug Tolerance, serial element, ClvPrd, peptido, diseases, AA408052, fold, diseases and disorders, Software Engineering, protein aggregate, Gpi-1, Effect, WMS, Computer Program, average, SET, human disease, peptides, reference sample, TAF-I, Nlk, M, phosphatase 2A inhibitor I2PP2A, Open, Computer Programs and Programming, proteins, number of, free, DmelCG4299, ASS, set, IGAAD, column, DmelCG10574, ppm, Homo sapiens disease, GPHYSD2, Racemethionine, Long-Term Effects, drug tolerance, SGS, NK/GPI, phapii, Gpi, visualization, immune system tolerance, T5E21.12, acetylation, 2-Amino-4-(methylthio)butyric acid, Longterm Effect, StF-IT-1, Search, segment, extra or missing physical or functional parts, Normalcy, Source Softwares, Software Tools, ACMICD, Programs, Program, Computer Applications, HCD, mOC-X, Computer Applications Software, Computer Applications Softwares, Immunologic Tolerance, Methionin, methionine, NK|GPI, Hmet, Softwares, T5E21_12, ORG, Org, Software Applications, HLA-DR-associated protein II, DI-2, Source Software, I-2Dm, Gpi1-r, Gpi1-s, CG4299, MASS, inhibitor of granzyme A-activated DNase, Gpi1-t, beta Trypsin, I-2PP1, data encoding as image, disease, Applications, Health, TAF-IBETA, Self Tolerance, Tolerance, TAF-Ibeta, Polypeptide, Liquimeth, i2pp2a, Proteomes, time, Bglap-rs1, Gpi1s, Computer Software Applications, other disease, 2-amino-4-(methylsulfanyl)butanoic acid, AI461847, Effects, number, L Isomer, FBN, Gene, Computer, protein-containing complex, PHAPII, period, template-activating factor I, polypeptide chain, ECTOL1, Gene Products, L-Methionine, disease or disorder, Pgi, Pedameth, Application, Normalities, Open Source Softwares, Search Engines, Longterm, Gpi-1r, Software Application, Gpi-1s, ipp2a2, Phi, beta-Trypsin, Gpi-1t, Acetylations, Open Source Software, 2pp2a, Long-Term, CG10574, Computer Software Application, OCTD, non-neoplastic, 2-amino-4-(methylthio)butanoic acid, 2PP2A, 10^[-6], Tools, taf-ibeta, has or lacks parts of type, dSET, dSet, disorder, peptidos, Long-Term Effect, metionina, statistical analysis, Controlled, Applications Software, Open Source, data, Controlling, Computer Software, DL-Methionine, protein complex, Proteins, igaad, disorders, total expressed protein, Random, medical condition, MF, Tree, L-Isomer, Amf, Peptide, Engine, Tool, mereological quality, polypeptide, Software Tool, Immune Tolerance, native protein, natural protein, I-2PP2A, Protein, Dm I-2, chemical analysis, Long Term Effects, I2PP2A, condition, MFS1, Software, Data Base, Met, WMS2, NK, Normality, Protein., Engineering, Tripcellim, Randomization, Allocation, Longterm Effects, Protein Gene Products, Computer Programs, Gene Proteins, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, Applications Softwares, SSKS, cardinality, alpha-amino-gamma-methylmercaptobutyric acid, Peptid, assay, variable, AA407739, Immunological Toleranceprojections, Traumatic Myelopathy, Research Related Injuries, Spinal Cord Transection, results., single-organism developmental process, Immunoglobulin, region or site annotation, Effects, AA960661, lamellae, Wound, Globulin, Nerve, Physical, number, Immune Globulin, CK-20, Imaging, Spectrum Analyses, Normalcies, injury, Injuries and Wounds, process of organ, presence, Long Term, binding site, trauma, protrusion, period, lamella, lymphocyte antigen 44, caudal, Wounds, B-lymphocyte antigen CD20, B1, Mass, LEU-16, Analysis, Effect, Research-Related, Mass Spectroscopy, Normalities, Mass Spectrum Analysis, CD20, average, Neurite, positional, S7, Injury, Analyses, Longterm, absent from organism, Bp35, B-cell surface antigen CD20, present in organism, W, ridges, Long-Term, Cd20, Immune, h, Traumas, papilla, site, remote from, Neuron, Long-Term Effect, nervous system cell generation, Spinal Cord Laceration, laminae, Nerve Cell, Leukocyte surface antigen Leu-16, Long-Term Effects, B-cell differentiation antigen Ly-44, leukocyte surface antigen Leu-16, Individual Health, Spinal Cord Trauma, anatomical protrusion, KRT21, Injury and Wounds, anatomical process, lamina, Longterm Effect, flanges, Endogenous, Physical Traumas, tailed, function, Normalcy, Immune Globulins, Spectrum Analysis, Cell, Spectroscopy, development, count in organism, Cytokine, traumatic injury, Wounds and Injury, B-lymphocyte surface antigen B1, Trauma, Long Term Effects, shelf, Spinal Cord Injuries, Physical Trauma, Individual, CK20, region, flange, Mass Spectrum Analyses, MS4A2, organ process, MS4A1, Membrane-spanning 4-domains subfamily A member 1, distant from, Mass Spectrum, Regenerations, absence, Ly-44, Nerve Cells, positional polypeptide feature, K20, IgG, Normality, INSDC_feature:misc_binding, shelves, Neurogeneses, wound, Spectrometry, projection, ridge, Injuries, Longterm Effects, processes, process, Post-Traumatic Myelopathy, Health, MALDI, Endogenous Regeneration, binding_or_interaction_site, spine, Lymphocyte antigen 44, Ms4a2, Cells, Research-Related Injuries, Regeneration, processus, Globulins, Research-Related Injury, quantitative, SCI, neural cell differentiation, time, Spinal Cord Contusion, presence or absence in organism, CVID5projections, Traumatic Myelopathy, Research Related Injuries, Spinal Cord Transection, results., single-organism developmental process, Immunoglobulin, region or site annotation, Effects, AA960661, lamellae, Wound, Globulin, Nerve, Physical, number, Immune Globulin, CK-20, Imaging, Spectrum Analyses, Normalcies, injury, Injuries and Wounds, process of organ, presence, Long Term, binding site, trauma, protrusion, period, lamella, lymphocyte antigen 44, caudal, Wounds, B-lymphocyte antigen CD20, B1, Mass, LEU-16, Analysis, Effect, Research-Related, Mass Spectroscopy, Normalities, Mass Spectrum Analysis, CD20, average, Neurite, positional, S7, Injury, Analyses, Longterm, absent from organism, Bp35, B-cell surface antigen CD20, present in organism, W, ridges, Long-Term, Cd20, Immune, h, Traumas, papilla, site, remote from, Neuron, Long-Term Effect, nervous system cell generation, Spinal Cord Laceration, laminae, Nerve Cell, Leukocyte surface antigen Leu-16, Long-Term Effects, B-cell differentiation antigen Ly-44, leukocyte surface antigen Leu-16, Individual Health, Spinal Cord Trauma, anatomical protrusion, KRT21, Injury and Wounds, anatomical process, lamina, Longterm Effect, flanges, Endogenous, Physical Traumas, tailed, function, Normalcy, Immune Globulins, Spectrum Analysis, Cell, Spectroscopy, development, count in organism, Cytokine, traumatic injury, Wounds and Injury, B-lymphocyte surface antigen B1, Trauma, Long Term Effects, shelf, Spinal Cord Injuries, Physical Trauma, Individual, CK20, region, flange, Mass Spectrum Analyses, MS4A2, organ process, MS4A1, Membrane-spanning 4-domains subfamily A member 1, distant from, Mass Spectrum, Regenerations, absence, Ly-44, Nerve Cells, positional polypeptide feature, K20, IgG, Normality, INSDC_feature:misc_binding, shelves, Neurogeneses, wound, Spectrometry, projection, ridge, Injuries, Longterm Effects, processes, process, Post-Traumatic Myelopathy, Health, MALDI, Endogenous Regeneration, binding_or_interaction_site, spine, Lymphocyte antigen 44, Ms4a2, Cells, Research-Related Injuries, Regeneration, processus, Globulins, Research-Related Injury, quantitative, SCI, neural cell differentiation, time, Spinal Cord Contusion, presence or absence in organism, CVID5Traumatic Myelopathy, portion of tissue, Spinal Cord Transection, Spinal Cord Trauma, simple tissue., Effects, Longterm, Tissue, Longterm Effect, segment, Long-Term, Long Term, Longterm Effects, Acute onset, period, Post-Traumatic Myelopathy, serial element, Long Term Effects, proteomic analysis, tissue portion, Spinal Cord Injuries, Long-Term Effect, SCI, Spinal Cord Laceration, Effect, time, Long-Term Effects, Spinal Cord Contusion397trueProteomic analysis of the spatiotemporal based molecular kinetics of acute spinal cord injury identifies a time- and segment-specific window for effective tissue repair.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 MALDI imaging, cytokines arrays, confocal imaging we established for the first time that molecular and cellular processes occurring after spinal cord injury (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 co-expressed 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 IgG expression. These results open the door of a novel view of the SCI treatment by considering the C1 as the therapeutic target.2016-06-082015-12-18PXD00337528065516460991804982953585111451462133352442249215684354407110946194202452787284218809036809327042933084581058113633363515242601198343006636362758385696363NCBITaxon:1280688885618961114301187263514725557114526314526236493461364031952065126957366649239161974670738538836411354615821582310665903416889539053113636476272112329442229118099555832323122586365458333460792519365914320597129386558195851149315242592637371250232NCBITaxon:127211195774818661488584310430024513586722568076175543735925408169180454266834295319453058612668352010891498225058149636744521585545281132081479564100392375146369420494332089643795042089634459741379791387127283844006672032754532602935293671567593880364784346438677160521659940483216597216595455032309813152826930421659156271616968339162432183217292042779447623764543121810017203094980197525556978159509329629439843948840479NCBITaxon:21575253381315273551531051067439899037122857759515205968762262311210884555588845587077918178081736309431796758144571698936160488409859NCBITaxon:3716210478267940150590714836432042106132049138169363035554320466326333119945654567453511025411103217459216129288671264201288676410026420369456941016763410210761277351524867131658239254727933428146135843014172987609174633457744491675476048932128735675684030135062191726518130194111929439367110411310239320255598632582788396591047594120347495109716049016529982790513355252731336636681024298036691758543980110243260866310245980875741755518320196447145268012675777641457966313670190832331156114155355104219325552113834397634981812359871069955529NCBITaxon:4751850298335476113615741465477180066556484337677602072144137929976798251021699823897641400820840741400821137351155711089725482444474153NCBITaxon:5055789969844675251000364653493341471474935480194675129911435974127647313708115466632654787656589363983532215958936698381920111067757727103481120837098523487802655541488414222863809664794640986099586157187176685991963371572951372211711012929211752711076878349741986020280913485855025392499148840633424951869123423515233598589859886559132497464998703920211107294331171139363527215987419085037117082711708282874341821144522350241451139692931902197822474636046147123747226940210195375939723287581721874202532566481219071NCBITaxon:573905079452659600131972211915853101774208588596321387NCBITaxon:6157505210283079895155864110519899723750599897576131720002631887634196102641088878176179212190659407121906772275885815689964975151950582873756269072445066NCBITaxon:250682023717NCBITaxon:170361220199985705060506172407476792745062724915961533355433355418400524643213686150596487844612286662941786661347515363291018194301086731018510184NCBITaxon:176357303963558633149246437286287151458670580430801321650852718481865368595105135553482260710185687294296110091416333NCBITaxon:619184023210007348824123363630710470058127187878645159812894555663577553470951451225786425011449447260704NCBITaxon:1335626260705260707573061658457367734054163677483167233150561007133705654195NCBITaxon:3055504457913998781681190119287512987222829126806315327341478281055524NCBITaxon:9606135858469008171929111167815021979153283051930283672859300852900561742NCBITaxon:56938268830640179469913899591510118499526225435258759131515901448242838111394422584416041937047592721204414370860423281677285035158199011951953259084126738637013702492405360883858162248839432293653186156227748817562615835583715371633376057267119350199808611935021678791085791371137127240719065037147591713291212266262981288057125627457572701329090309031133355037281424337385794792491007875282411082NCBITaxon:961572433594633185862607991612432141262200298147802492670NCBITaxon:12637192812492125283038568385695911692661006581373530963223756127504542666255151978813566381647520375064422366950236009412934979054632245552536352472140125751511519976499085151514389923745461703747445446415226473243235937605920222887051580595536100199955508815793271602938515781149786338924794362938211620894535936479437509173NCBITaxon:685441275422511775299159010901341673871589552101296610306129671423687158515845158491575923765939341410384327159100226376733889147923590461423444234546700128768959119833296610914944670414647929365761642803411602216413315992803828035369091089176881498946218121410803481793924640287889295027113133295282829445686174934681911265269972273218903821028621076012471904007271597369978281143114020641198108713554774365814245072295337969820423212422312916321803369822347087145372091645733215358157546266940265619401371654675992877702020603281143193382935508332912922114864374572526499972830357390871830872672710379085507176299707678926837041557372921405315628876513882941281607839563924314262654898227377561159253905962073220865958827355516936053307972551811354914321371597495350261159556143213840607258781414473352150949334919496340161433472800593604631646104660762903381518454744850035670974772656691180771951240174841855601335755547920427415805360769946881037620148874162763870532972610059412003758289093164354282683142568500712303839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