Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/evidence.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/proteinGroups.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/peptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00415_Emmy_5297_SG_macr_KO_TNF_6h_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00371_Emmy_5297_SG_macr_WT_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00365_Emmy_5297_SG_macr_KO_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00409_Emmy_5297_SG_macr_WT_TNF_1h_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00369_Emmy_5297_SG_macr_WT_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00421_Emmy_5297_SG_macr_WT_TNF_6h_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00387_Emmy_5297_SG_macr_KO_LPS_6h_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00383_Emmy_5297_SG_macr_WT_LPS_1h_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00391_Emmy_5297_SG_macr_KO_LPS_6h_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00377_Emmy_5297_SG_macr_KO_LPS_1h_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00405_Emmy_5297_SG_macr_WT_TNF_1h_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00395_Emmy_5297_SG_macr_WT_LPS_6h_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00389_Emmy_5297_SG_macr_KO_LPS_6h_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00401_Emmy_5297_SG_macr_KO_TNF_1h_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00363_Emmy_5297_SG_macr_KO_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00417_Emmy_5297_SG_macr_WT_TNF_6h_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00413_Emmy_5297_SG_macr_KO_TNF_6h_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00367_Emmy_5297_SG_macr_KO_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00381_Emmy_5297_SG_macr_WT_LPS_1h_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00419_Emmy_5297_SG_macr_WT_TNF_6h_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00373_Emmy_5297_SG_macr_WT_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00375_Emmy_5297_SG_macr_KO_LPS_1h_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00393_Emmy_5297_SG_macr_WT_LPS_6h_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00399_Emmy_5297_SG_macr_KO_TNF_1h_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00379_Emmy_5297_SG_macr_KO_LPS_1h_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00403_Emmy_5297_SG_macr_KO_TNF_1h_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00385_Emmy_5297_SG_macr_WT_LPS_1h_biol_repl3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00407_Emmy_5297_SG_macr_WT_TNF_1h_biol_repl2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00411_Emmy_5297_SG_macr_KO_TNF_6h_biol_repl1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008726/H00397_Emmy_5297_SG_macr_WT_LPS_6h_biol_repl3.rawprimaryOK200003260kris.gevaert@vib-ugent.beEmmy Van QuickelbergheMass SpectrometryShotgun proteomicsNot availableLc-msmsBmdmA20http://www.ebi.ac.uk/pride/archive/projects/PXD008726Bone MarrowMacrophageBone marrow cells were isolated from tibia and femurs from A20myel-KO mice and control wild-type (WT) littermate mice, and flushed with RPMI medium 1640. Bone marrow derived macrophages (BMDMs) were generated by culturing bone marrow cells in RPMI medium supplemented with 10% fetal bovine serum, 25 units/ml penicillin, 25 µg/ml streptomycin, L-glutamine and 40 ng/ml mouse macrophage colony stimulating factor (MCSF). Every 48 h the medium was refreshed and on day 7, 3 x 106 BMDMs were seeded. The BMDMs were stimulated or not with 10 µg/ml lipopolysaccharide (LPS) or 1000 U/ml mouse tumor necrosis factor (TNF) for 1 or 6 h. Cells were washed twice with ice-cold Dulbecco’s phosphate buffered saline and scraped in 500 µl urea lysis buffer containing 20 mM HEPES pH 8.0, 9 M urea, 1 mM sodium orthovanadate, 2.5 mM sodium pyrophosphate and 1 mM β-glycerophosphate. Lysates were sonicated at 15 W output with 3 bursts of 15 s each and cleared by centrifugation for 15 min at 20,000 x g at room temperature, followed by reduction and alkylation of cysteines with respectively 5 mM dithiothreitol (DTT) for 30 min at 55°C and 10 mM iodoacetamide (IAA) for 15 min at room temperature in the dark. Proteins were digested with mass spectrometry grade Lysyl Endopeptidase (enzyme/substrate ratio of 1/250 w/w, Wako) for 3 h at 37°C. Samples were diluted with 20 mM HEPES pH 8.0 to a final concentration of 2 M urea and the proteins were further digested with sequencing-grade, modified trypsin (enzyme/substrate ratio of 1/100 w/w) overnight at 37°C. Digestion was terminated by adding trifluoroacetic acid (TFA) to a final concentration of 0.5%, peptide mixtures were desalted using Pierce C18 tips, dried and re-dissolved in 20 µl water/acetonitrile (ACN, 98/2 v/v) containing 0.1% TFA for subsequent LC-MS/MS analysis.PrideLabel freeiodoacetamide derivatized residueThe obtained peptide mixtures were introduced into an LC-MS/MS system, being an Ultimate 3000 RSLC nano LC in-line connected to a Q Exactive HF mass spectrometer (Thermo Fisher Scientific). The MS/MS spectra were searched with the MaxQuant software (version 1.5.4.1) against murine (Mus musculus) protein sequences in the SwissProt database (release of November 2015 containing 16,601 sequences), with a precursor mass tolerance set at 20 ppm for the first search and 4.5 ppm for the main search. Acetylation of protein N-termini and methionine oxidation were set as variable modifications and carbamidomethylation of cysteine as a fixed modification. Trypsin was selected as protease and cleavage was allowed when arginine or lysine was followed by proline. Two missed cleavages were allowed. The ‘matching between runs’ feature was activated. The false discovery rate (FDR) at the peptide spectrum match (PSM) and the protein level was set to 1% and the minimum peptide length was set to 7. For analysis of phosphorylation and ubiquitination sites, a separate search was performed with phosphorylation on serine, threonine and tyrosine included as variable modification. Data analysis was performed with the MSqRob software (version 0.6.3) that uses a peptide-based model to estimate the protein fold changes directly from peptide intensities. In total, 34,376 peptides were identified. The peptide intensities were log2 transformed and quantile normalized. Reversed sequences and potential contaminants were removed from the data. Peptides belonging to protein groups that contained one or more proteins that were also present in a smaller protein group, were discarded. Relative protein quantification was performed on 30,559 remaining peptides. The treatment effect was specified as fixed and contains all combinations of genotypes (WT and A20 KO) and stimulants (untreated, LPS and TNF). We accounted for the correlation structure in the peptide-level data by incorporating a random mouse effect (correlation due to the longitudinal design) and a random sample effect (peptides intensities from the same protein pool are more alike). We also corrected for peptide-specific effects by including a random effect for peptide sequence. A random peptide sequence effect enables a different shrinkage (regularization) of the sequence effect and the treatment effect. For each protein, we tested for differential abundance between genotypes (A20 KO vs WT BMDMs) at baseline, after 1 h of LPS treatment, after 6 h of LPS treatment, after 1 h of TNF treatment and after 6 h of TNF treatment.ProteomicsKris GevaertQ ExactivePARTIALVIB-UGent Center for Medical Biotechnology Department of Biochemistry, Ghent University Ghent, BelgiumMus Musculus (mouse)emmy.vanquickelberghe@vib-ugent.be29733654 Van Quickelberghe E, Martens A, Goeminne LJE, Clement L, van Loo G, Gevaert K. Identification of Immune-Responsive Gene 1 (IRG1) as a Target of A20. J Proteome Res. 2018 10.1021/acs.jproteome.8b00139BiologicalGhent UniversityBelgiumA20 is a negative regulator of NF-κB signaling; it controls inflammatory responses and ensures tissue homeostasis. A20 is thought to restrict NF-κB activation both by its ubiquitin-editing activity as well as by its nonenzymatic activities. Besides its role in NF-κB signaling, A20 also acts as a protective factor inhibiting apoptosis and necroptosis. Because of the ability of A20 to both ubiquitinate and deubiquitinate substrates, and its involvement in many cellular processes, we hypothesized that deletion of A20 might generally impact on protein levels, thereby disrupting cellular signaling. We performed a differential proteomics study on bone marrow-derived macrophages (BMDMs) from control and myeloid-specific A20 knockout mice, both in untreated conditions and after LPS or TNF treatment, and demonstrated A20-dependent changes in protein expression. Several inflammatory proteins were found up-regulated in the absence of A20, even without an inflammatory stimulus, but, depending on the treatment and the treatment time, more proteins were found regulated. Together these protein changes may affect normal signaling events, which may disturb tissue homeostasis and induce (autoimmune) inflammation, in agreement with A20s proposed identity as a susceptibility gene for inflammatory disease. We further verify that immune-responsive gene 1 (IRG1) is up-regulated in the absence of A20 and that its levels are transcriptionally regulated.Identification of Immune-Responsive Gene 1 (IRG1) as a Target of A20.Van Quickelberghe Emmy E, Martens Arne A, Goeminne Ludger J E LJE, Clement Lieven L, van Loo Geert G, Gevaert Kris KM-CSF, IL1BC, MeCN, Laboratory, CASP-1, A4, chronic obstructive pulmonary disease (COPD), Basodexan, 2-(indol-3-yl)ethanoic acid, Apaf-1, PPS1, House Mouse, dmTAF[[II]]230, Trifluoroacetate, Polypeptides, L-glutamine, macrophage, T22F8_160, ATGPR7, CH3-C#N, B1, Chronic irreversible airway obstruction, Urea, 1, L-2-aminoglutaramic acid, GRP8, 2, GRP7, Analysis, Sodium Ion, Il1bc, O-2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl-(1-2)-O-5-deoxy-3-C-formyl-alpha-L-lyxofuranosyl-(1-4)-N, (R*, C79325, TFIID TAF250, hac-1, Analyses, N'-bis(aminoiminomethyl)-, cel, OFC6, CG12919, weight-weight percentage, 32P2-labeled cpd, Q, Salt, chemical analysis., CAFL - Chronic airflow limitation, proteins, IL-1BC, DIF, AI047805, Strepto-Hefa, disease (COPD), ACN, D1, Acn, Red, TNFSF2, tumor necrosis factor, autolysin activity, podocyte, dif, LC-MS2, tnfa, dTAF[[II]]230, chronic obstructive lung disease [Ambiguous], Caspase-1 subunit p10, typical plasmatocyte, anon-53Fa, TNFA, TAF200, l(2)SH0173, Penicillin, VWS1, monocyte-derived macrophage, Spectrum Analysis, DmelCG7788, CHRONIC OBSTRUCTIVE AIRWAY DIS, (Indol-3-yl)acetate, Dm1, Regg1, sodium, Streptomycine Panpharma, Airflow Obstruction, natrium, CG6829, Estreptomicina Normon, Hydrogen Oxide, Monocyte-Derived Macrophages, dark/hac-1/dapaf-1, GLYCINE-RICH PROTEIN 8, Chronic Obstructive Airways Disease, Acid, Chronic obstructive lung disease, Caspase-14 subunit p10, Lanimostim, Swiss Mouse, proportionality, Spectrometry, rate, Caspase-14 subunit p19, (S)-2, beta Trypsin, w/w, Ran/M1, Indole-3-acetic acid, heteroauxin, F2G1.4, Taf250, OBSTRUCTIVE PULMONARY DISEASE (COPD), liquid chromatography-tandem mass spectroscopy, Cells, Drice, bacteriolytic toxin activity, Tnfa, Mouse, histiocyte, methyl cyanide, DRICE, TAF230, Cleland Reagent, 3.4.22.-, GLUTAMINE, TNF, DrIce, DrICE, Streptomycin Grünenthal, CAO - Chronic airflow obstruction, Pierce, Levoglutamide, 4-dimercapto-, mini-ICE, Strepto Fatol, Carbamide, CHRONIC OBSTRUCTIVE PULM DIS, Chronic obstructive pulmonary disease NOS, R*)-, and RNA binding 1, CG7826, Bone Marrow Cell, Chronic obstructive pulmonary disease finding, Ion Level, PULMONARY DISEASE (COPD), LC-MSMS, CG7835, Gene Products, Mus musculus domesticus, CG42273, Yellow, Carmol, MAM, agranular plasmatocyte, Cesium Trifluoroacetate, proportion, dTAF[[II]]250, Ly87, Acinus, cell, (2S)-2, RATTNF, PCE-2, Monosodium Salt, beta-Trypsin, Bone Marrow-Derived Macrophage, DmelCG12919, Bone Marrow, acinusL, Bone Marrow-Derived, Marrow Cell, CD284, dTAF250, darth, Caspase-1 subunit p20, ATGRP7, acinusS, ATGRP8, NEC, Chronic, peptidos, Antibiotics, Csfm, PIT, 4-(2-hydroxyethyl)-, Toll, PTHB1, 1H-indol-3-ylacetic acid, dark/dapaf-1/hac-1, decahydrate, mass percentage, 1-(14)C-labeled, chronic obstructive airways disease NOS, caspase 3, xtnf, dApaf-1, COAD, Proteins, Clelands Reagent, BG:DS00004.13, CE-2, anhydrous sodium pyrophosphate, COLD - Chronic obstructive lung disease, acetonitrile, buffer, Cell, chronic, mKIAA0670, dt1, dTAF230, polypeptide, APAF1, Monocyte-Derived, tetrasodium salt, Temperatures, medulla ossium, carbonyldiamide, Hac-1, C18, Glutamic acid 5-amide, TAF[[II]]250/230, VWS, Sodium, (COPD), chronic airway obstruction, chronic obstructive, CAL - Chronic airflow limitation, Mass Spectrum Analyses, U/ml, Macrophage, Sodium Ion Level, Cleland's, Achromobacter protease I, Taf[[II]]250, AU020952, Yellow Marrow, holin, DMDA1, Glutamic acid amide, medullary bone, Macrophages, GR-RBP7, GR-RBP8, 3-Indolylessigsaeure, Na, Natrium, Dark/Dapaf-1/HAC1, House Mice, IL-1 beta-converting enzyme, ethanenitrile, Interleukin-1 beta-converting enzyme, ME-IV, achromopeptidase, op, Cleland's Reagent, Gene Proteins, chronic obstructive lung disease (disorder), Bone Marrow-Derived Macrophages, granulocyte, quotient, liquid chromatography tandem mass spectrometry, phosphates, Sodium 23, chronic obstructive pulmonary disease, liquid chromatography tandem mass spectroscopy, Hac-1/Dark, T22F8.160, NCMe, determination, and rna binding 2, Chronic Airflow Obstructions, DmelCG6829, Mus domesticus, CG7788, crice, HEPES Monosodium Salt, CASP-14, Pi, lysis, Pl, L-(+)-glutamine, Alkylations, sodium diphosphate, peptide, sodio, Streptomycin Sulfate, L-Glutaminsaeure-5-amid, IAA, ClvPrd, peptido, BANF, CSF-1, medulla ossea, Monocyte-Derived Macrophage, chronic obstructive airways disease NOS (disorder), Min, Apaf1, Chronic Obstructive Pulmonary Disease (COPD), xtnf-alpha, ARK, DmelCG42273, Penicillin Antibiotics, Mass Spectrum Analysis, HEPES Monosodium, COLD (chronic obstructive lung disease), LCMSMS, reference sample, peptides, regg1, NEC in ICD9CM_2006, MCSF, E927b, 2610036I19Rik, 2610510L13Rik, PPS, min, arc, Swiss Mice, mAPC, achromobacter beta-lytic protease (blp), ark, T1, Chronic airflow limitation, Red Marrow, fSAP152, 1-Piperazineethanesulfonic acid, Sputolysin, ICE, GLYCINE RICH PROTEIN 7, trifluoro-, necrosis, dApaf1, house mouse, glycine-rich RNA-binding protein 8, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, ratio, CHRONIC, obstructive lung disease, ice, iCE, D-Apaf-1, drice, mouse, LC-MS/MS, Dmel_CG7826, shankbone, Lipopolysaccharide, TAFII-250, TAF250/230, C87615, Airflow Obstructions, ur, Spectroscopy, pulmonary disease (COPD), carbamide, Sodium-23, TAFII250, Lipoglycans, Cleland, Streptomycin Sulphate, drIce, drICE, low temperature, CHRONIC OBSTRUCTIVE, Mini-ICE, tnf-alpha, chronic obstructive pulmonary disease and allied conditions, lysyl endoprotease, Chronic airway disease, bacteriocin activity, NOS, IES, Dmel_CG7835, Acetic acid, TLR4, Rasl2-8, COPD NOS, CHRONIC OBSTRUCTIVE LUNG DIS, Mnb, MNB, Mus musculus, Chronic airway obstruction, cold, medulla of bone, mice, Xylella fastidiosa str. Temecula1, P45, Trifluoroacetic, 3-Butanediol, TNFalpha, hac1, BcDNA:RH51659, AW124434, MICE, CG17603, TAF[[II]], domesticus, L-glutamic acid gamma-amide, dapaf-1S, Chronic Airflow Obstruction, H2NC(O)NH2, apaf-1, shinbone, DMDA, lysin activity, dapaf-1L, phosphate, Cesium, phosphate ions, SR3-5, COPD - Chronic obstructive pulmonary disease, Acetamide, chronic obstructive airways disease, p45, Polypeptide, obstructive pulmonary disease (COPD), HEPES, Bone, COLD, chronic obstructive lung disease, 1728, TNF-alpha, d230, Dapaf-1/HAC-1, Monocyte Derived Macrophages, 5-diamino-5-oxopentanoic acid, DISEASE (COPD), Reagent, Gene, dTAFII250, circadian rhythm, Spectrum Analyses, ACINUS, (2S)-2-amino-4-carbamoylbutanoic acid, EfW1, TYPE, LC-MS-MS, Buffer, DAGA4, Dark/Hac-1/dApaf1, Karbamid, TNF-a, Cold, Hac1, Dark/Hac-1/dApaf-1, Pulmonary Disease, House, Strepto-Fatol, dmTAF1, Taf230, Marrow, Harnstoff, Mass, Strepto Hefa, Mice, SCG3, Level, Mass Spectroscopy, TAF250, Taf200, Cold Temperatures, D-Streptamine, TNF receptor binding, Swiss, Lps, LPS, diphosphoric acid, dapaf-1, Taf1p, Indoleacetic acid, dapaf, dark, Chronic Obstructive, Ect1, Xylella fastidiosa (strain Temecula1 / ATCC 700964), Estreptomicina CEPA, (indol-3-yl)acetic acid, lamellocyte, DARK, L-Glutamine, N-2-Hydroxyethylpiperazine-N'-2'-ethanesulfonic Acid, TAF, dArk, Dapaf-1, 2-iodo-, Controlled, COPD, macrophagocyte, disodium pyrophosphate, Tibias, Controlling, COAD - Chronic obstructive airways disease, DYRK1, TAF[[II]]250, ng/ml, Marrow Cells, 3H-labeled, Processed macrophage colony-stimulating factor 1, not elsewhere classified, ggr, l(3)84Ab, apaf1, Monocyte Derived, L-2-Aminoglutaramic acid, PULM DIS CHRONIC OBSTRUCTIVE, Peptide, LGMD2C, Chronic obstructive pulmonary disease finding (finding), tnfsf2, LC/MS/MS, Mus, p230, Protein, tumor necrosis factor receptor ligand, TFIID, Dyrk1, L-Glutamin, CES2A1, GLYCINE-RICH RNA-BINDING PROTEIN 7, Dark, tetrasodium pyrophosphate, Dark/Apaf-I, ACETONITRILE, cyanomethane, chronic obstructive airway disease, Temperature, Mass Spectrum, TAF[[II]]230, Streptomycin Sulfate (2:3) Salt, uree, Dops, urea, CC1, Tripcellim, N 2 Hydroxyethylpiperazine N' 2' ethanesulfonic Acid, Bone Marrow Derived Macrophages, TAF[II]250, Ran|M1, dApaf-1/DARK/HAC-1, UREA, Laboratory Mice, Interleukin-1 beta convertase, Protein Gene Products, Trypure, trisodium pyrophosphate, 11Na, DmelCG17603, concentration, Estreptomicina Clariana, SCARMD2, 3.4.22.36, Egr, cold (chronic obstructive lung disease), Peptid, Chronic Obstructive Lung Disease, assay, SCH, Laboratory Mouse, Tnfsf1a, dAPAF-1, TAF1TNFA1P2, A20., A-20, Tnfip3, INSDC_feature:gene, OTUD7C, responsive, RGD1563454, CAD, AI323667, RCB2745, A20 cellliquid chromatography tandem mass spectroscopy, SH2-Bb, IPP2A2, para Tyrosine, PLXN4, Lysine Hydrochloride, determination, PLXN3, Ass-1, L-arginine, DL-Arginine Acetate, cleavage, Irip, Monohydrate, L-Threonine, protein, PPS1, NAALAdase, phosphorylation, 2-Amino-3-hydroxypropionic acid, 5730420M11Rik, peptide, Polypeptides, NAALADase I, protein polypeptide chains, L-Isomer Methionine, FOLH, Lysine Acetate, Drug Tolerance, Methionine, ClvPrd, peptido, AA408052, L-Proline, fold, 2, C530001K22Rik, Software Engineering, 3.4.17.21, Analysis, Arg, protein aggregate, xtnf-alpha, Computer Program, WMS, Threonin, L Lysine, A20, SH2-B, somitogenic mesoderm, SET, (S)-2-amino-5-guanidinopentanoic acid, F, Ubiquitylation, LCMSMS, peptides, Membrane glutamate carboxypeptidase, Analyses, TAF-I, K, regg1, M, OFC6, Open, phosphatase 2A inhibitor I2PP2A, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, CG12919, (S)-2-Amino-5-guanidinovaleric acid, R, PPS, Computer Programs and Programming, epsilon-diaminocaproic acid, Arginine, proteins, Monohydrate DL-Arginine Acetate, present in organism, NAALAD1, Y, Folylpoly-gamma-glutamate carboxypeptidase, A20 cell, DmelCG4299, TNFA1P2, DIF, ASS, set, IGAAD, LYS, 2-amino-3-hydroxypropanoic acid, DmelCG10574, ppm, Lysin, Tyr, HSSEXGENE, sample, n, TNFSF2, ubiquitination, house mouse, Half Cystine, GPHYSD2, Racemethionine, 6.3, drug tolerance, Tnfsf1a., SGS, L-Arginin, ratio, LC-MS2, dif, phapii, tnfa, XAP-6, Zinc Cysteinate, unsegmented mesenchyme, immune system tolerance, acetylation, LC-MS/MS, mouse, 2-Amino-4-(methylthio)butyric acid, Arginine Hydrochloride, 2-Amino-3-(p-hydroxyphenyl)propionic acid, TNFA, StF-IT-1, arginine, VWS1, para-Tyrosine, SH2-B PH domain-containing signaling mediator 1, Source Softwares, Software Tools, Programs, ACMICD, Tyrosine, Program, Computer Applications, 3-Hydroxyalanine, PSM, Psm, Regg1, Computer Applications Software, tnf-alpha, Computer Applications Softwares, lysine, Immunologic Tolerance, Methionin, methionine, Softwares, Hmet, OTUD7C, presumptive somite mesoderm, Prostate-specific membrane antigen, fixed, tyrosine, TLR4, Rasl2-8, parent ion, L-Arginine, oligonucleotide random primer, Pteroylpoly-gamma-glutamate carboxypeptidase, Software Applications, Serine, HLA-DR-associated protein II, DI-2, Source Software, mice, I-2Dm, FGCP, proportionality, L-isomer, rate, L-Cysteine, MASS, CG4299, alpha, TNFalpha, inhibitor of granzyme A-activated DNase, BcDNA:RH51659, beta Trypsin, L isomer, organ system, I-2PP1, Pro-rich, Ran/M1, Applications, Self Tolerance, TAF-IBETA, precursor ion, Tolerance, liquid chromatography-tandem mass spectroscopy, PSMA, Tnfa, L Serine, TAF-Ibeta, L-Tyrosine, Mouse, Polypeptide, Tnfip3, L-Serine, i2pp2a, Liquimeth, RCB2745, Gruppe, Computer Software Applications, SH2 domain-containing protein 1B, TNF-alpha, 2-amino-4-(methylsulfanyl)butanoic acid, Cysteine Hydrochloride, conformation, False, TNF, unsegmented paraxial mesoderm, mouse <Mus musculus>, L Isomer, introduced into, FBN, Gene, Computer, precursor, protein-containing complex, somitomeric mesoderm, body system, GCPII, PHAPII, LC-MS-MS, L-(+)-arginine, TNF-a, polypeptide chain, template-activating factor I, (2S)-2-amino-5-(carbamimidamido)pentanoic acid, ECTOL1, LC-MSMS, Gene Products, L-Methionine, N-acetylated-alpha-linked acidic dipeptidase I, system, mKIAA1299, Lysine, Half-Cystine, Pedameth, Application, Open Source Softwares, SH2B, proportion, anatomical systems, Ly87, Software Application, L Cysteine, Lps, LPS, RATTNF, ipp2a2, beta-Trypsin, inserted, Open Source Software, Acetylations, 2pp2a, A-20, mGCP, L Threonine, DmelCG12919, Ect1, CG10574, Genotypes, Computer Software Application, OCTD, CD284, darth, RANDOM, 2PP2A, 2-amino-4-(methylthio)butanoic acid, Tools, 10^[-6], L Tyrosine, taf-ibeta, grupos, L Proline, dSET, dSet, L-Arg, peptidos, Tyrosin, metionina, PIT, relational structural quality, Toll, Applications Software, serine, Open Source, data, Computer Software, grupo, DL-Methionine, protein complex, xtnf, Proteins, igaad, Phosphorylations, ggr, backward, L-Isomer, DL Arginine Acetate, Peptide, Tool, GCP2, group, dt1, Glutamate carboxypeptidase II, polypeptide, tnfsf2, Serin, LC/MS/MS, Software Tool, Cell growth-inhibiting gene 27 protein, native protein, Immune Tolerance, natural protein, Genogroup, I-2PP2A, L-Isomer Arginine, tirosina, Mus, Acetate, Protein, Dm I-2, chemical analysis, I2PP2A, Hydrochloride, sequence, MFS1, VWS, L Arginine, segmental plate, connected anatomical system, Sh2bpsm1, Software, L-Lysine, Data Base, WMS2, Met, Random selection by shearing, 10^[-9], PH and SH2 domain-containing signaling mediator, (2S)-2-amino-5-guanidinopentanoic acid, Engineering, Tripcellim, Rest, Ran|M1, sample population, primary structure of sequence macromolecule, Folate hydrolase 1, Protein Gene Products, Computer Programs, Trypure, Gene Proteins, dSET/TAF-Ibeta, Genogroups, 2610030F17Rik, Applications Softwares, Data, SSKS, AI425885, alpha-amino-gamma-methylmercaptobutyric acid, quotient, Egr, liquid chromatography tandem mass spectrometry, Peptid, assay, threonine, variable, AA407739, 6-diaminohexanoic acid, Enisyl, groupe, Data Analyses, Tnfsf1a, reversed, Immunological Toleranceprojections, Inflammations, Activity, Laboratory, Mus domesticus, CASP-14, induction of necroptosis of activated-T cells, protein, type I programmed cell death, PPS1, House Mouse, Long Term, protein polypeptide chains, Extrinsic Pathway Apoptoses, Roles, Programmed, medulla ossea, Monocyte-Derived Macrophage, AA959943, Concepts, protein aggregate, xtnf-alpha, Effect, A20, High Mobility Protein 20, inflammatory response, reference sample, establishment of necroptosis, regg1, Moods, OFC6, CG12919, establishment of necroptosis of activated-T cells, PPS, Ubiquitin-related 1, Swiss Mice, proteins, A20 cell, Acts, Red Marrow, TNFA1P2, DIF, genetic, APF-1, Intrinsic Pathway Apoptosis, programmed necrotic cell death, Classic, signaling process, papilla, Role Concepts, Classical Apoptosis, induction of necroptosis by extracellular signals, Red, TNFSF2, Long-Term Effects, extracellular signal-induced necroptosis, single organism signaling, Acta-2, dif, cellular suicide, tnfa, anatomical protrusion, wide/broad, Caspase-Dependent Apoptosis, lamina, mouse, familial, TNFA, Longterm Effect, Actsk-1, flanges, VWS1, CEP52, Role Concept, signaling (initiator) caspase activity, induction of apoptosis, Intrinsic Pathway, Extrinsic Pathway Apoptosis, Regg1, Mini-ICE, shelf, tnf-alpha, Role, OTUD7C, Caspase-Dependent, regulator, activation, Ubiq, TLR4, Monocyte-Derived Macrophages, Rasl2-8, Ubiquitin, activation of necroptosis in response to extracellular signals, Mus musculus, absence, Factors, Caspase-14 subunit p10, medulla of bone, mice, shelves, Swiss Mouse, Human Ubiquitin, Caspase-14 subunit p19, Cell Death, TNFalpha, BcDNA:RH51659, RIPK1-mediated regulated necrosis, MICE, projection, ridge, domesticus, Intrinsic Pathway Apoptoses, execution phase of necroptotic process, Ran/M1, wide, TNF-induced necroptosis, induction of apoptosis by p53, Patient, spine, Extrinsic Pathway, Tnfa, Mouse, inherited genetic, Tnfip3, E430016J11Rik, RCB2745, Classical, Innate, Apoptoses, Bone, Proteomes, time, protein levels, 3.4.22.-, Inflammatory Response, biological signaling, TNF-alpha, Peptidomics, Monocyte Derived Macrophages, Effects, lamellae, TNF, caspase-dependent programmed cell death, Caspase Dependent Apoptosis, Gene, mini-ICE, ATP Dependent Proteolysis Factor 1, Ubiquitin carboxyl extension protein 80, broad, apoptotic programmed cell death, protein-containing complex, Ximpact, process of organ, activation of apoptosis, Human, protrusion, lamella, period, TNF-a, Client., polypeptide chain, House, Marrow, Gene Products, Mus musculus domesticus, HMG-20, activation of necroptosis of activated-T cells, Mood, Yellow, ubiquitin-like protein modifier, Type I, Mice, study, tissue maintenance, Ly87, Longterm, Swiss, Lps, LPS, RATTNF, absent from organism, A-20, Protective Factor, inflammation, Bone Marrow-Derived Macrophage, ridges, Long-Term, apoptosis activator activity, DmelCG12919, Ect1, Bone Marrow-Derived, CD284, 40S ribosomal protein S27a, darth, Innate Inflammatory Response, Classic Apoptosis, Clients, execution phase of apoptotic process, ubiquitin, activation of necroptosis, Long-Term Effect, PARP-dependent cell death, protein tagging activity, programmed cell death by apoptosis, laminae, constitutitional genetic, PIT, Toll, Controlled, Apoptosis, induction of necroptosis, Controlling, cell suicide, xtnf, protein complex, anatomical process, Affects, apoptotic cell death, Proteins, ggr, total expressed protein, Factor, Monocyte Derived, impact-a, necroptosis, Concept, dt1, tnfsf2, Monocyte-Derived, Ubiquitin A-52 residue ribosomal protein fusion product 1, necroptotic execution phase, native protein, medulla ossium, natural protein, Mus, Ubiquitin-related 2, activation of necroptosis by extracellular signals, Protective, Programmed Cell Death, Protein, Long Term Effects, programmed necrosis, VWS, parthanatos, ATP-Dependent Proteolysis Factor 1, flange, organ process, Macrophage, apoptosis signaling, covalent modifier, Yellow Marrow, apoptosis, medullary bone, Macrophages, Bone Marrow Derived Macrophages, House Mice, Ran|M1, signalling, Longterm Effects, Laboratory Mice, Classic Apoptoses, Protein Gene Products, processes, process, Gene Proteins, signalling process, 60S ribosomal protein L40, protein tag, DEL, apoptotic program, Innate Inflammatory Responses, Bone Marrow-Derived Macrophages, commitment to apoptosis, Egr, processus, Ubiquitin-related, hereditary, General activity, Laboratory Mouse, RWDD5, Tnfsf1aprojections, Inflammations, Activity, Laboratory, Mus domesticus, CASP-14, induction of necroptosis of activated-T cells, protein, type I programmed cell death, PPS1, House Mouse, Long Term, protein polypeptide chains, Extrinsic Pathway Apoptoses, Roles, anatomical structure inflammation, Programmed, medulla ossea, Monocyte-Derived Macrophage, AA959943, Concepts, protein aggregate, xtnf-alpha, Effect, A20, average, High Mobility Protein 20, inflammatory response, establishment of necroptosis, reference sample, regg1, Moods, OFC6, CG12919, establishment of necroptosis of activated-T cells, PPS, Ubiquitin-related 1, Swiss Mice, proteins, A20 cell, Acts, Red Marrow, TNFA1P2, DIF, APF-1, Intrinsic Pathway Apoptosis, programmed necrotic cell death, inflammatory disease, Classic, signaling process, papilla, Role Concepts, Classical Apoptosis, induction of necroptosis by extracellular signals, Red, TNFSF2, Long-Term Effects, extracellular signal-induced necroptosis, single organism signaling, Acta-2, dif, cellular suicide, tnfa, anatomical protrusion, Caspase-Dependent Apoptosis, lamina, mouse, TNFA, Longterm Effect, Actsk-1, flanges, VWS1, Normalcy, CEP52, Role Concept, signaling (initiator) caspase activity, induction of apoptosis, Intrinsic Pathway, Extrinsic Pathway Apoptosis, Regg1, Mini-ICE, shelf, tnf-alpha, Role, OTUD7C, Individual, Caspase-Dependent, regulator, activation, Ubiq, TLR4, Monocyte-Derived Macrophages, Rasl2-8, Ubiquitin, activation of necroptosis in response to extracellular signals, Mus musculus, absence, Factors, Caspase-14 subunit p10, medulla of bone, mice, shelves, Swiss Mouse, Human Ubiquitin, Caspase-14 subunit p19, INSDC_feature:gene, Cell Death, TNFalpha, BcDNA:RH51659, AI323667, RIPK1-mediated regulated necrosis, MICE, projection, ridge, domesticus, Intrinsic Pathway Apoptoses, execution phase of necroptotic process, Ran/M1, TNF-induced necroptosis, Health, induction of apoptosis by p53, spine, Extrinsic Pathway, Tnfa, Mouse, Tnfip3, inflammation of anatomical structure, E430016J11Rik, RCB2745, Classical, Innate, Apoptoses, Bone, time, protein levels, 3.4.22.-, Inflammatory Response, biological signaling, TNF-alpha, Peptidomics, Monocyte Derived Macrophages, Effects, lamellae, TNF, caspase-dependent programmed cell death, Caspase Dependent Apoptosis, Gene, mini-ICE, ATP Dependent Proteolysis Factor 1, Ubiquitin carboxyl extension protein 80, apoptotic programmed cell death, protein-containing complex, Ximpact, Normalcies, process of organ, activation of apoptosis, Human, protrusion, lamella, period, TNF-a, RGD1563454, polypeptide chain, House, Marrow, Gene Products, Mus musculus domesticus, HMG-20, activation of necroptosis of activated-T cells, Mood, Yellow, ubiquitin-like protein modifier, Type I, Mice, Normalities, study, tissue maintenance, Ly87, Longterm, Swiss, Lps, LPS, RATTNF, absent from organism, A-20, Protective Factor, inflammation, Bone Marrow-Derived Macrophage, ridges, Long-Term, apoptosis activator activity, DmelCG12919, Ect1, Bone Marrow-Derived, CD284, 40S ribosomal protein S27a, darth, Innate Inflammatory Response, Classic Apoptosis, execution phase of apoptotic process, ubiquitin, activation of necroptosis, Long-Term Effect, PARP-dependent cell death, protein tagging activity, programmed cell death by apoptosis, laminae, PIT, Toll, Controlled, Apoptosis, Individual Health, induction of necroptosis, Controlling, cell suicide, xtnf, protein complex, anatomical process, Affects, apoptotic cell death, Proteins, ggr, Factor, Monocyte Derived, impact-a, necroptosis, Concept, dt1, tnfsf2, Monocyte-Derived, Ubiquitin A-52 residue ribosomal protein fusion product 1, CAD, necroptotic execution phase, native protein, medulla ossium, natural protein, Mus, Ubiquitin-related 2, activation of necroptosis by extracellular signals, Protective, Programmed Cell Death, Protein, Long Term Effects, programmed necrosis, VWS, parthanatos, ATP-Dependent Proteolysis Factor 1, flange, organ process, Macrophage, apoptosis signaling, covalent modifier, Yellow Marrow, susceptibility, inflammatory disorder, apoptosis, Normality, medullary bone, Macrophages, A20., Bone Marrow Derived Macrophages, House Mice, Ran|M1, signalling, Longterm Effects, Laboratory Mice, Classic Apoptoses, Protein Gene Products, processes, process, Gene Proteins, signalling process, 60S ribosomal protein L40, protein tag, DEL, apoptotic program, Innate Inflammatory Responses, Bone Marrow-Derived Macrophages, commitment to apoptosis, Egr, processus, Ubiquitin-related, responsive, General activity, Laboratory Mouse, RWDD5, Tnfsf1aTNFA1P2, Peptidomics., Mus, mice, mouse, Mouse, A-20, Tnfip3, house mouse, OTUD7C, RCB2745, A20 cell, A20326trueMouse WT vs. A20 KO BMDM differential proteomicsA20 is a negative regulator of NF-κB signaling, crucial to control inflammatory responses and ensure tissue homeostasis. A20 is thought to restrict NF-κB activation both by its ubiquitin-editing activity as by non-enzymatic activities. Besides its role in NF-κB signaling, A20 also acts as a protective factor inhibiting apoptosis and necroptosis. Because of the ability of A20 to both ubiquitinate and deubiquitinate substrates and its involvement in many cellular processes, we hypothesized that deletion of A20 might generally impact on protein levels, thereby disrupting cellular processes. We performed a differential proteomics study of bone marrow derived macrophages (BMDMs) from control and myeloid-specific A20 knockout mice, both in untreated conditions and after LPS and TNF treatment, and demonstrate proteome-wide changes in protein expression upon A20 deletion. Several inflammatory proteins are up-regulated in the absence of A20, even without an inflammatory stimulus. Depending on the treatment and the time, more proteins are regulated. Together these changes may affect multiple signaling pathways disturbing tissue homeostasis and inducing (autoimmune) inflammation, as suggested by genetic studies in patients.2018-05-152018-01-19PXD0087264466449917558258038804333029535851114512067811080612461962461972842188090320637522995811363350906836351524260275838538791187947398007186801NCBITaxon:128057230711143011872635555714683514526236491508472746707364113546138855821803582329031388869152167786889539978447518704351123294126246942229692812397713310343043654813583334607925198183659219813143205965581947621493632957263737192222693812478186613283882813955843451358672217554372949140816918045416193413903634530586112041623264460711210411706127443210859561496367469412831666943694559729452811320810039237514633087936944784475174206542208964317447127044597413797911194669400667145458793299352932010198126469041066114575512165994048339251216597216595160621213312831282128033952321832172920435315227794428112454349825741948147871720309498019752555536231439841356742951053948824261914548140479NCBITaxon:21575515343989903712285775975320596876231935163098005888455818178081736309431796989361604885661409859566416242515059071187021187053204963063863235554320466322261866331299456586068845351216129567171360441001602358700264203694569410167634102107612773511316582150480227933428146100293578617463313252911187002157641809699745774449156666754760445246767561917265181301941119294396336641136336721751117645102398709NCBITaxon:40559325823590927883965264982174982163472565691569387224982116544872056971666905108944835525663661410NCBITaxon:4932871556891758543102459808108944475741710005894526808732287535311561263730069303911415542193255521872687238724872987271235987555295476242231414654773055180066556484198822445299767446982510216998231174673897641041051155744689444474153NCBITaxon:50557960167767446851000364960065349118226370824854801299114578458359741276473194439137086326547876569835566369838192011164034624136810893161001428099612NCBITaxon:548681NCBITaxon:582054641430774794640986099586522836373791966272905876689605960615729513722187594467087562270861711013354833090349741298293878343061512793654319474703342494729859610896158865597464998703920211107287827215407821190857075298352061894804189853502471587796273002515630411902528674636046147964696443759391462472746128746011345062534526591972219638191552638588596NCBITaxon:615750521105172375059576131302409263419610526419407722774694163481123869497515NCBITaxon:235231703612506174767927459615384005257313136862697968666299034694171344346360347515363296440421018110867310185109760635586331496161286287246200966927294351338968583551865368595968912801726071018568729411009118696141633316780781186941436183NCBITaxon:6191118698840231719475932118691443906NCBITaxon:102982100071257118387279694836419080218787870384766455347095145122578656870861822607046183260705260707NCBITaxon:780NCBITaxon:1502451516658457702921158612184520928574707856100713370565295076192126385454195NCBITaxon:30555044573915383379913998192875NCBITaxon:10239NCBITaxon:71428291268063130957044830064175158592381055524159084128108228233446900815025754122810451930174830085210977970671356225833136185509924NCBITaxon:56938268830640527796179469958334240906151015151034809NCBITaxon:631240674482428130767070876138370828167728503515819901195195337024924053608881756261583558333760212671928532177357267119350184645177299808616787917743737111049056371215348112153239576769014726647091317047571256274579031133355085962859634792491308126387121203511082332648373153214693NCBITaxon:9615383233185862607991412622002981314131349376083334111497019281239655833321018413856959111006581237561275045426662551519788749200375036009412934971530094114903524725175014012573983649908515151438992NCBITaxon:11552374539883747445446415259311792866432359839062887051580119459932716011497861603293338922853422999810894535936457428412754121536024271831627713512251179948875058NCBITaxon:1040724271550277916797181673871349130627415895521010306502780291595412629158515849327159570210022633889128768913558867551293094514647920312421641332803828035192843436909398580894621080348179392118259028788929502745609906901749342725632273218903829286757221247190400727NCBITaxon:57965374571143112335235621140206411981087135547714245072295337969835552222129167141262161154293157546139622421392139077020114319338293550833292307411292211484896160106772526499975744727580240550717629968335366581214053576229412816078395763206672400540296543282311843183224659620575549922957575759284593936053307972551811354970667143673315974953502611595564442143213818492231124060721054211109697622611117957529818184319229438119496340161433479866265281046603815181044214547448500796267825356709747731751351240565050NCBITaxon:1313607699389424688795588012014887519795962141140822414082232645614219728909101412285316435186763185431520767737677764940894144242327742NCBITaxon:17732140922088931157781154756208895929793244704207559101177499067499073129899136645112273231663170187367451011610358991513284262658721036098334139269611307981336795358893164071034015303337330158191306413992530654788883910337212336819940445864498115357652611114716122491113131663430531201755499351299385057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