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Following differentiation, the cells were treated with or without dexamethasone for 6 hours. After treatment, the cells were lysed using IP lysis buffer. From each condition, 2 mg of lysate was used for immunoprecipitation to enrich GR proteins. This was performed using an anti-GR antibody (Cell Signaling Technology, #12041) according to the protocol provided with the Co-Immunoprecipitation Kit (Thermo Fisher Scientific, #26149). Subsequently, the immunoprecipitated beads were washed and then treated with urea lysis buffer (9 M urea, 20 mM HEPES pH 8.0, 1 mM sodium orthovanadate, 2.5 mM sodium pyrophosphate, 1 mM beta-glycerophosphate) to denature the enriched proteins. Disulfides were reduced with 4 mM DTT at room temperature for 1h and then alkylated with 10 mM IAA for 15 min in the dark.  then samples were diluted 4x with 20 mM HEPES pH 8. Samples were digested overnight at room temp with either TPCK-treated trypsin at 1:37(enzyme: substrate) or sequencing grade GluC at 1:100 (Promega). After digestion, the samples were acidified with 1% TFA and purified by solid phase extraction on 50 mg C18 Sep Paks. The eluates were dried in a speedvac. Half of each IP sample was enriched for phosphopeptides using IMAC iron (III)-NTA cartridges (Agilent) with the Agilent Bravo liquid handler following the manufacturer’s protocol. IMAC control peptides (Cell Signaling Technology cat #59524) were spiked into each sample to monitor enrichment reproducibility. Enriched peptides were eluted in 50% acetonitrile (ACN)/ 2.5% NH3, dried, then desalted on C18 tips.    LCMS Analysis One fifth of each peptide fraction was injected on-column in duplicate for LCMS analysis on a Thermo Fusion Lumos Orbitrap mass spectrometer. The LC used a 100 um x 50 cm column packed with 1.8 um C18 beads. Samples that did not undergo IMAC enrichment were analyzed by data-independent analysis (DIA) using 23.4 m/z windows and a three second cycle time. LC separation was performed with a 45min analytical gradient from 2-30% acetonitrile. MS1 scans were collected from 35-1200m/z  at 120K resolution. Precursors were fragmented with HCD fragmentation at 27% normalized collision energy. MS2 scans were collected from 200-2000m/z  in the orbitrap at 30K resolution, with a max injection time of 54ms and an AGC of 1E6.  IMAC-enriched peptides were analyzed with a DDA method operating on a three second cycle time.  The LC gradient ramped from 5 to 41% ACN in 150 min with a total run time of 180 min. MS1 scans were collected with Orbitrap (OT) resolving power at 120K, scanning from 350-1500 m/z. Charge states from 2-7 were allowed and dynamic exclusion was set to 30s. Precursors were isolated with a 1.6 m/z window prior to HCD fragmentation at 27% NCE Fragments were detected in the OT at 30K resolving power using a maximum injection time of 54ms and an AGC target of 50,000."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["MS Data Analysis  MS raw files were searched against the Swissprot mouse database downloaded 08 November 2023. DDA searches were carried out using the Comet search algorithm 76 implemented in GFY Core software from Harvard, and DIA searches were performed in Spectronaut.  Peptides were required to have at least one tryptic end (cleavage at K or R but not KP or RP) with up to five missed cleavages allowed. The precursor ion tolerance was 20ppm and the fragment mass tolerance was 0.02 Da. Carbamidomethylcysteine was a static modification, while oxidized Met and phosphorylation of Ser, Thr, or Tyr was a variable modification. Both peptide and protein identifications were controlled at a 1% FDR cutoff using the target-decoy search approach. Phosphopeptide site localization was scored using AscorePro (cite) software, and peptides with a score >=13 were considered confidently localized. Phosphopeptide quantification was performed by extracting MS1 peak areas using Skyline software.  Phosphopeptide peak areas were adjusted for protein-level changes by subtracting the log2-fold changes for each treatment comparison."],"omics_type":["Proteomics"],"labhead":["Ana Carrizosa Anderson"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["The Gene Lay Institute of Immunology and Inflammation Harvard Medical School and Brigham and Women's Hospital"],"species":["Mus Musculus (mouse)"],"publication":["10.1016/J.IMMUNI.2026.05.016"],"submitter_mail":["yhan8@bwh.harvard.edu"],"submitter_affiliation":["Brigham and Women's Hospital"],"submitter_country":["United States"],"additional_accession":[]},"is_claimable":false,"name":"Interleukin-23 promotes a pro-inflammatory Th17 cell state by stabilizing RORγt and suppressing glucocorticoid receptor activity","description":"Interleukin-23 receptor (IL-23R) signaling is critical for the generation of pro-inflammatory CD4+ IL-17-producing T cells (Th17) that can drive autoimmune tissue inflammation, but the underlying mechanisms are not clear. We integrated phosphoproteomic and transcriptomic data downstream of IL-23R and IL-12R, which share a common subunit, to identify mechanisms engaged specifically by IL-23. We identified chromodomain helicase DNA-binding protein 1 (CHD1), an epigenetic regulator, and the glucocorticoid receptor (GR), a transcription factor (TF), as mediators of IL-23R signaling. IL-23R activation promoted CHD1 interaction with TF STAT3 and co-binding at the TF RORγt locus to enforce a pro-inflammatory Th17 state. Conversely, IL-23R signaling altered phosphorylation of the GR, thereby preventing its activation and nuclear translocation, ultimately impairing GR-driven inhibition of pro-inflammatory Th17 gene programs. Our findings uncover two mechanisms by which IL-23 promotes a pro-inflammatory Th17 cell state, offering potential therapeutic targets for treating Th17-driven autoimmune tissue inflammation and restoring 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