{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/HF2_017186.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/HF2_017058.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/HF2_017172.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/HF2_017044.raw"],"Mzid":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/Export.mzid"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/HF2_017186.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/HF2_017172.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/HF2_017058.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD064008/HF2_017044.mgf"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["yohann.coute@cea.fr"],"submitter":["Hesse Anne-Marie"],"technology_type":["Mass Spectrometry","Gel-based experiment"],"disease":["Disease Free"],"software":[""],"submitter_keywords":["Rage / ck2 / phosphorylation"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD064008"],"tissue":["Epithelial Cell"],"sample_protocol":["FL cells were grown in a 10 cm plate (7.106 cells/plate) in presence or not of the specific CK2 inhibitor CX-4945. Forty-eight hours after RAGE-GFP constructs transfection, cells were lysed in 50 mM Tris-HCl, 150 mM NaCl, 1% Triton X-100, 1x Complete Protease inhibitor cocktail (Roche) for 30 min at 4 °C. After centrifugation (10 min, 8000 rpm, 4°C) and protein assay (Pierce™ BCA protein assay kit, Thermo Scientific), 1 mg total protein was immunoprecipitated with 3µg anti-tGFP (OriGene) coated to superparamagnetic nanoparticles conjugated with protein A and G (Master IP, Ademtech) during 30 min at room temperature in AutoMag solution (Ademtech). Immunoprecipitates were washed 30 sec, four times at room temperature with 50 mM Tris-HCl, 150 mM NaCl, 0.5% Triton X-100, 1x Complete Protease inhibitor cocktail (Roche). Beads were collected in 40 µl kinase buffer. After immunopurification, proteins were solubilized in Laemmli buffer and separated on a 4–12% NuPAGE gel (Invitrogen) before R-250 Coomassie blue staining. The gel bands were manually excised and digested using modified trypsin (sequencing grade, Promega). The dried extracted peptides were resuspended in 5% acetonitrile and 0.1% trifluoroacetic acid and analyzed by online nanoliquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) (Ultimate 3000 RSLCnano and the Q-Exactive HF, Thermo Fisher Scientific). Peptides were sampled on a 300μm 5mm PepMap C18 precolumn (Thermo Fisher Scientific) and separated on a 75μm 250mm C18 column (Reprosil-Pur 120 C18-AQ, 1.9 μm, Dr. Maisch HPLC GmbH). The nano-LC method consisted of a 60min multi-linear gradient at a flow rate of 300nl/min, ranging from 5 to 41% acetonitrile in 0.1% formic acid. For data dependent acquisition, the spray voltage was set at 2 kV and the heated capillary was adjusted to 270°C. Survey full-scan MS spectra (m/z = 300–2000) were acquired with a resolution of 120 000 after the accumulation of 3 x 106 ions (maximum filling time 100ms). The 20 most intense ions were fragmented by higher-energy collisional dissociation after the accumulation of 5 x 105 ions (maximum filling time: 200ms). For targeted proteomics, analyses were performed in PRM mode. The acquisition method combined two scan events corresponding to a full scan event and a time-scheduled PRM event targeting one of the 13 precursor ions selected in ±4.5 min elution time windows (based on DDA analysis, Supplementary table x). Survey full-scan MS spectra (m/z = 300–2000) were acquired with a resolution of 120 000 after the accumulation of 3 x 106 ions (maximum filling time 200ms). PRM spectra were acquired with a resolution of 30 000 after the accumulation of 1 x 106 ions (maximum filling time 400ms). MS and MS/MS data were acquired using the software Xcalibur (Thermo Scientific)."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["Data were processed automatically using Mascot Distiller software (version 2.7.1.0, Matrix Science). Peptides and proteins were identified using Mascot (version 2.8.3) through concomitant searches against Uniprot (Homo Sapiens taxonomy, Release 2025_01), a classical contaminants database (homemade), a database containing GFP-RAGE sequence and their corresponding reversed databases. Trypsin/P was chosen as the enzyme and two missed cleavages were allowed. Precursor and fragment mass error tolerances were set, respectively, to 10ppm and 20ppm. Peptide modifications allowed during the search were: cysteine carbamidomethylation (fixed), acetyl (protein N-terminal, variable), methionine oxidation (variable) and serine, threonine, tyrosine phosphorylation (variable). The Proline software (version 2.3.1) was used to merge DDA and PRM results. After combination, results were filtered: conservation of rank 1 peptide-spectrum match (PSM) with a minimal length of 6 and a minimal score of 25. Peptide-spectrum matching (PSM) score filtering is then optimized to reach a False Discovery Rate (FDR) of PSM identification below 1% by employing the target decoy approach. A minimum of one specific peptide per identified protein group was set. The DDA result was used to select the ions to follow in PRM mode. For quantification purpose, fragments area were extracted from PRM data with Xcalibur."],"omics_type":["Proteomics"],"labhead":["Yohann Couté"],"instrument_platform":[""],"labhead_affiliation":["Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)"],"publication":["42621156 Coste K, Hesse AM, Marceau G, Filhol O, Cochet C, Freton C, Blanchon L, Sapin V, Belville C. RAGE phosphorylation by CK2 in human epithelial cell model: Modulation of connexin 43 expression. iScience. 2026 29(8):117117 10.1016/j.isci.2026.117117"],"submitter_mail":["anne-marie.hesse@cea.fr"],"submitter_affiliation":["Laboratoire d'Etude de la Dynamique des Protéomes"],"submitter_country":["France"],"doi":["10.6019/PXD064008"],"pubmed_abstract":["The receptor for advanced glycation end products (RAGE) is a membrane protein involved in many diseases linked to epithelial dysfunction. Its activation mechanism remains unclear because RAGE lacks intrinsic kinase activity depending on other kinases for phosphorylation. Using an epithelial amniotic cell model (FL cells), researchers combined mass spectrometry, phosphorylation assays, microscale thermophoresis to show that RAGE intracellular domain binds to the α subunit of protein kinase CK2, leading to the phosphorylation of RAGE at serine 400. Ser400Ala mutation preserves CK2α binding but disrupts downstream signaling, altering phosphorylation of the transcription factors CREB (Ser133) and c-Jun (Ser63) after AGE ligands stimulation. <i>In silico</i> analyses identify binding sites for these two transcription factors in the connexin 43 promoter/UTR, a known RAGE target, associated with the overexpression of its mRNA. Overall, these findings highlight that phosphorylation at serine 400 is essential for RAGE signaling and transcriptional regulation in response to AGE ligands."],"pubmed_title":["RAGE phosphorylation by CK2 in human epithelial cell model: Modulation of connexin 43 expression."],"pubmed_authors":["Coste Karen K, Hesse Anne-Marie AM, Marceau Geoffroy G, Filhol Odile O, Cochet Claude C, Freton Céline C, Blanchon Loïc L, Sapin Vincent V, Belville Corinne C"],"additional_accession":[]},"is_claimable":false,"name":"A Specific RAGE Phosphorylation by CK2 in human Amniotic Epithelial cell model","description":"The receptor for advanced glycation end products (RAGE) is a multiligand, immunoglobulin-like transmembrane protein expressed in various cell types and implicated in a broad spectrum of diseases linked with epithelial dysfunctions. Despite significant progress in structural studies, the details of its activation mechanism remain poorly understood. Since RAGE lacks intrinsic kinase activity, its activation by phosphorylation depends on the action of intracellular kinases. In a model of epithelial amniotic cell line FL, mass spectrometry analyses combined with in vitro phosphorylation assays and Microscale thermophoresis reveal that the intracytoplasmic domain of RAGE interacts with the CK2 catalytic subunit of protein kinase CK2, leading to the phosphorylation of Serine 400. Structure-function analyses show that the Ser400Ala mutation does not alter the affinity of CK2α for RAGE but causes dysregulation of intracellular kinase signaling pathways, particularly affecting the phosphorylation of the transcription factors CREB (Serine 133) and c-Jun (Serine 63) in the presence of AGE ligands. In silico analyses identified binding sites for these two transcription factors in the Connexin-43 promoter/UTR, a RAGE target gene, and were associated with the overexpression of its mRNA. Our findings suggest that phosphorylation at Serine 400 plays a crucial role in the RAGE signaling in response to AGEs 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