{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/protein.raw.intensity.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_5.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_6.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_9.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_8.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD063380/0320TMTP3_2.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["libei2021@fmmu.edu.cn"],"submitter":["Wenzhe Wang"],"technology_type":["Mass Spectrometry","Top-down proteomics"],"disease":["Periodontitis"],"software":[""],"submitter_keywords":["γδt17 cells","extracellular vesicles","Mucosal immunity","arthritis","Mucosal immunity; arthritis; γδt17 cells; extracellular vesicles; c3.","c3."],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063380"],"tissue":["Cell Suspension Culture","Macrophage"],"sample_protocol":["TMT-plexed quantitative proteomic analysis Proteomic analysis of Ctrl-EVs and Ba-EVs was performed by nano-liquid chromatography-tandem mass spectrometry (Nano-LC-MS/MS, Lc-Bio Technologies Co., Ltd). Protein in EVs were extracted using radio immunoprecipitation assay buffer (RIPA) supplemented with protease inhibitors and phosphatase inhibitors. Protein concentration was accurately quantified using the BCA kit. Protein was enzymolyzed into peptides at a 50:1 protein-to-trypsin ratio (w/w). A proper amount of peptide was taken from each sample and then redissolved to 30 μl with 100 mM TEAB after vacuum drying. TMT labels dissolved in anhydrous acetonitrile were reacted with peptides (label:peptide = 5: 1) for 1-2 h at room temperature, followed by equal pooling of labeled peptides and primary fractionation using an Agilent ZORBAX 300Extend-C18 column (3.5 μm, 4.6×150 mm) on an UltiMate 3000 system (Thermo Fisher Scientific) with 0.3 ml/min gradient elution. The elution peaks were monitored at 214 nm and fractions were collected every min. Fractions were pooled based on chromatograms, lyophilized, and reconstituted in 0.1% FA for secondary separation on a self-packed C18 column via EASY-nLC 1200 (Thermo Fisher Scientific). The separated peptides were ionized via a nano-ESI and analyzed using an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific) operating in data dependent acquisition (DDA) mode. The ion source voltage was set at 2.2 kV. Primary mass spectrometry scans were performed over a range of 350–1,500 m/z with a resolution of 120,000, and the normalized AGC target was set to 300%. For secondary mass spectrometry, higher-energy collisional dissociation (HCD) was used as the fragmentation mode, with an energy setting of 36%. The resolution for MS/MS scans was 45,000, and a dynamic exclusion time of 60 s was applied. The acquired TMT-labeled MS/MS spectra were processed with MaxQuant software (v2.1.4.0) for peptide identification and quantification. Subsequent statistical analyses were conducted in R (v4.0.0). Hierarchical clustering was carried out with the pheatmap package. Functional annotation was performed through hypergeometric enrichment analysis of KEGG pathways and Gene Ontology terms. Additional characterization included subcellular localization predictions using WoLF PSORT and transcription factor annotation based on AnimalTFDB/PlantTFDB databases. Data visualization was accomplished using the OmicStudio cloud platform."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["The acquired TMT-labeled MS/MS spectra were processed with MaxQuant software (v2.1.4.0) for peptide identification and quantification. Subsequent statistical analyses were conducted in R (v4.0.0). Hierarchical clustering was carried out with the pheatmap package. Functional annotation was performed through hypergeometric enrichment analysis of KEGG pathways and Gene Ontology terms. Additional characterization included subcellular localization predictions using WoLF PSORT and transcription factor annotation based on AnimalTFDB/PlantTFDB databases. Data visualization was accomplished using the OmicStudio cloud platform."],"omics_type":["Proteomics"],"labhead":["Bei Li"],"instrument_platform":[""],"labhead_affiliation":["State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, School of Stomatology, The Fourth Military Medical University, Xi’an, Shaanxi 710032, China."],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["576501855@qq.com"],"publication":["Not available"],"submitter_affiliation":["Hospital of Stomatology"],"submitter_country":["China"],"additional_accession":[]},"is_claimable":false,"name":"Oral γδT17 cells induced by macrophages-derived extracellular vesicles in peridontitis exacerbate rheumatoid arthritis","description":"Periodontitis (PD) is one of the most common human inflammatory diseases, yet the immunological mechanism linking oral and systemic immune responses are not well defined. Here, we show that the accumulation of interleukin-17 (IL-17)-producing γδT (γδT17) cells occurs not only in the oral cavity, but also in the peripheral lymph nodes and spleens in experimental periodontitis in mice. Strikingly, oral γδT17 cells derived from experimental periodontitis migrated to the inflamed joint and led to an exacerbation of rheumatoid arthritis (RA) in a collagen-induced arthritis model in mice. Mechansitically, we demonstrated that the dysbiosis in periodontitis led to an increase in production of complement component 3 (C3)-enriched extracellular vesicles (EVs) derived from macrophages. These C3-enriched EVs were taken up by γδT cells and stimulated intracellular C3a receptor to drive IL-17A production in γδT cells. Our findings revealed an previously unrecognized immunological mechanism linking periodontitis to RA through the accumulation and migration of oral γδT17 cells.","dates":{"publication":"2026-04-08","submission":"2025-04-28"},"accession":"PXD063380","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:1211601","NEWT:876138","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:260707","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:105231","NEWT:1216981","NCBITaxon:6073","NEWT:884204","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:38783","NEWT:8727","NEWT:4006","NEWT:8726","NEWT:6426","NEWT:6669","NEWT:10090","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","N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