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Steigenberger"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Gcn2","Translation","Zakα","Inflammation","Macrophage"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075112"],"sample_protocol":["Sample Preparation Proteins were denatured by adding 80 µL of SDC buffer containing 1% sodium deoxycholate (SDC; Sigma-Aldrich), 40 mM 2-chloroacetamide (CAA; Sigma-Aldrich), 10 mM tris(2-carboxyethyl)phosphine (TCEP; Thermo Fisher Scientific), and 100 mM Tris (pH 8.0). The mixture was incubated for 30 min at 37 °C. The samples were diluted 1:1 with water. Proteins were then digested overnight at 37 °C with 0.5 µg trypsin (Promega). Following digestion, peptides were acidified with trifluoroacetic acid (TFA; Merck) to a final concentration of 1%. Peptides were either desalted using SCX StageTips or directly loaded (200 ng total peptide) onto Evotips (Evotip Pure; Evosep).  LC–MS/MS Analysis Peptides were eluted from Evotips onto a 15 cm PepSep C18 column (15 cm × 150 µm, 1.5 µm; Bruker Daltonics) using an Evosep One HPLC system. The column was maintained at 50 °C, and peptides were separated using the 30 SPD method. Data were acquired on a timsTOF Pro mass spectrometer operated with timsControl software in data-independent acquisition (DIA) PASEF mode. The MS scan range was 100–1700 m/z with an ion mobility range of 1/K₀ = 0.70–1.30 Vs cm⁻². Equal ion accumulation and ramp times of 100 ms were used in the dual TIMS analyzer, yielding a spectral rate of 9.52 Hz. DIA-PASEF scans were acquired in the 350.2–1199.9 Da range with 42 DIA-PASEF windows assigned to one TIMS scan each. Precursor isolation windows were alternated, resulting in an overall cycle time of 2.21 s. The collision energy was linearly ramped from 45 eV at 1/K₀ = 1.30 Vs cm⁻² to 27 eV at 1/K₀ = 0.85 Vs cm⁻²."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Data Analysis Raw data were processed in Spectronaut 18.0 (Biognosys) using directDIA+ (library-free) mode. Spectra were searched against a predicted Mus musculus protein database from UniProt (SwissProt and TrEMBL; downloaded 2023). Cysteine carbamidomethylation was set as a fixed modification, and methionine oxidation and protein N-terminal acetylation were set as variable modifications. Protein quantification across samples was performed using label-free quantification (MaxLFQ) at the MS² level."],"omics_type":["Proteomics"],"labhead":["Rodrigo Dias Requião"],"instrument_platform":[""],"labhead_affiliation":["Unicamp"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"publication":["42600662 Requião RD, Lima-Silva LF, Estevão P, Costa WLG, Zani NC, Vasconcelos IC, Silva ÍEP, Xu TT, Prado HMDA, Steigenberger B, Bengtson MH, Murray PJ, Moraes-Vieira PM. The integrated stress response kinase GCN2 prevents ZAKα-Dependent inflammatory hyperactivation in macrophages. J Biol Chem. 2026 302(10):113452 10.1016/j.jbc.2026.113452"],"submitter_mail":["steigenberger@biochem.mpg.de"],"submitter_affiliation":["MPI of Biochemistry"],"submitter_country":["Germany"],"pubmed_abstract":["Macrophages orchestrate inflammation through rapid and extensive proteome remodeling, yet the translational programs governing macrophage activation remain poorly defined. Here, we show that classically activated macrophages (lipopolysaccharide + interferon-γ-treated) and alternatively activated macrophages (IL-4-treated) engage fundamentally distinct translational trajectories. Whereas alternatively activated macrophages sustain elevated protein synthesis, classically activated macrophages undergo a rapid but transient increase in translation that is subsequently restrained by the integrated stress response kinase General Control Nonderepressible 2 (GCN2). Using puromycin incorporation and quantitative proteomics, we demonstrate that GCN2-mediated phosphorylation of eukaryotic translation initiation factor 2α limits global translation and constrains the proinflammatory response. Genetic loss of GCN2 results in excessive translation and hyperinflammation driven by the ribosome-associated stress sensor ZAKα (Map3k20). Pharmacological inhibition of ZAKα in GCN2-deficient macrophages selectively normalizes tumor necrosis factor α secretion, establishing a functional regulatory axis in which GCN2 suppresses ZAKα-dependent inflammatory signaling. Together, these findings redefine translational control as a central checkpoint in macrophage activation, revealing how GCN2 mitigates ribosomal stress to prevent inflammatory hyperactivation, with potential therapeutic implications for tumor necrosis factor α -driven inflammatory diseases."],"pubmed_title":["The integrated stress response kinase GCN2 prevents ZAKα-Dependent inflammatory hyperactivation in macrophages."],"pubmed_authors":["Requião Rodrigo Dias RD, Lima-Silva Lincon Felipe LF, Estevão Paulo P, Costa Webster Leonardo Guimarães WLG, Zani Nicholas Camargo NC, Vasconcelos Israel Costa IC, Silva Ítalo Esposti Poly ÍEP, Xu Teng Teng TT, Prado Heloísa Monteiro do Amaral HMDA, Steigenberger Barbara B, Bengtson Mario Henrique MH, Murray Peter J PJ, Moraes-Vieira Pedro M PM"],"additional_accession":[]},"is_claimable":false,"name":"GCN2 Restrains ZAKα-Dependent TNFα Production in LPS+IFNγ Stimulated Macrophages","description":"Macrophages orchestrate inflammation through rapid and extensive proteome remodeling, yet the translational programs governing macrophage activation remain poorly defined. Here, we show that inflammatory M(LPS+IFNγ) and reparative M(IL-4) macrophages engage fundamentally distinct translational trajectories. Whereas M(IL-4) macrophages sustain elevated protein synthesis, M(LPS+IFNγ) macrophages undergo a rapid but transient increase in translation that is subsequently restrained by the integrated stress response kinase GCN2. Using puromycin incorporation, polysome profiling, and quantitative proteomics, we demonstrate that GCN2-mediated phosphorylation of eIF2α limits global translation and constrains pro-inflammatory output, particularly TNFα production. Genetic loss of GCN2 results in excessive translation and hyperinflammation driven by the ribosome-associated stress sensor ZAKα. Importantly, pharmacological inhibition of ZAKα in GCN2-deficient macrophages selectively normalizes TNFα secretion, establishing a functional regulatory axis in which GCN2 suppresses ZAKα-dependent inflammatory signaling. Together, these findings redefine translational control as a central checkpoint in macrophage activation, revealing how GCN2 mitigates ribosomal stress to prevent inflammatory hyperactivation, with potential therapeutic implications for TNFα-driven inflammatory diseases.","dates":{"publication":"2026-09-28","submission":"2026-03-02"},"accession":"PXD075112","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:260201","NEWT:35554","NCBITaxon:12939","NEWT:32046","NEWT:544496","NEWT:59529","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:10245","NEWT:55153","NEWT:89184","NEWT:10244","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:351581","NEWT:43186","NEWT:428146","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:661410","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:1401257","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:641809","NEWT:27933","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:111225","NEWT:7719","NEWT:7959","NEWT:2261","NEWT:868565","NEWT:94323","NEWT:31156","NEWT:3112","NEWT:79329","NEWT:4442","NEWT:31155","NEWT:192875","NEWT:1214915","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:284218","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:160621","NEWT:212790","NEWT:931281","NEWT:4432","NEWT:5762","NEWT:5763","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:2246","NEWT:2652724","NEWT:1912919","NEWT:5757","NEWT:68415","NCBITaxon:4563","NEWT:5755","NEWT:44688","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:347256","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:1367269","NEWT:145458","NEWT:633149","NEWT:1149786","NEWT:10239","NEWT:68895","NEWT:44685","NEWT:161934","NEWT:4897","NEWT:1148","NEWT:5744","NEWT:72901","NEWT:213863","NEWT:5508","NEWT:3329","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1235816","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:1772","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:11988","NEWT:284812","NEWT:8175","NEWT:400667","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:459758","NEWT:3702","NEWT:1245466","NEWT:243277","NEWT:1246791","NEWT:7067","NEWT:118694","NEWT:586722","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:274","NEWT:7070","NCBITaxon:287","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1303443","NEWT:9483","NEWT:333760","NEWT:34607","NEWT:56636","NEWT:1513458","NEWT:1233681","NEWT:2709072","NCBITaxon:40559","NEWT:506599","NEWT:2853422","NEWT:81077","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:65349","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NEWT:34613","NCBITaxon:4932","NEWT:109760","NEWT:29031","NEWT:943274","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:5936","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:2719099","NEWT:886559","NEWT:3750","NEWT:55521","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:1130798","NEWT:55529","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1116234","NEWT:561007","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:203696","NEWT:472","NEWT:352472","NEWT:97441","NEWT:1071661","NEWT:1202531","NEWT:1202532","NEWT:360094","NEWT:1408223","NEWT:470","NEWT:1408224","NEWT:41364","NEWT:5911","NEWT:1313","NEWT:1218097","NEWT:1080348","NCBITaxon:50557","NEWT:1314","NEWT:39251","NEWT:39491","NEWT:212142","NCBITaxon:5811","NEWT:29491","NEWT:101841","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:688333","NEWT:215402","NCBITaxon:548681","NEWT:318586","NCBITaxon:5820","NEWT:1547","NEWT:272634","NEWT:198107","NEWT:9031","NEWT:27292","NEWT:1872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