JPOST Repositoryapplication/xmlhttps://storage.jpostdb.org/JPST000569/files/cTEC_LFQ.xlsxhttps://storage.jpostdb.org/JPST000569/files/beta5tKO_cTEC_2nd.rawhttps://storage.jpostdb.org/JPST000569/files/WT_cTEC_2nd.rawhttps://storage.jpostdb.org/JPST000569/files/WT_cTEC_1st.rawhttps://storage.jpostdb.org/JPST000569/files/beta5tKO_cTEC_1st.rawprimary200OKProteomicsHidetaka KosakoMus Musculus (mouse)https://repository.jpostdb.org/entry/JPST000569Tokushima UniversityjPOSTThe thymic function to produce self-protective and self-tolerant T cells is chiefly mediated by cortical thymic epithelial cells (cTECs) and medullary TECs (mTECs). Recent studies including single-cell transcriptomic analyses have highlighted a rich diversity in functional mTEC subpopulations. Because of their limited cellularity, however, the biochemical characterization of TECs, including the proteomic profiling of cTECs and mTECs, has remained unestablished. Utilizing genetically modified mice that carry enlarged but functional thymuses, here we show a combination of proteomic and transcriptomic profiles for cTECs and mTECs, which identified signature molecules that characterize a developmental and functional contrast between cTECs and mTECs. Our results reveal a highly specific impact of the thymoproteasome on proteasome subunit composition in cTECs and provide an integrated trans-omics platform for further exploration of thymus biology.Trans-omics Impact of Thymoproteasome in Cortical Thymic Epithelial Cells.Ohigashi Izumi I, Tanaka Yu Y, Kondo Kenta K, Fujimori Sayumi S, Kondo Hiroyuki H, Palin Amy C AC, Hoffmann Victoria V, Kozai Mina M, Matsushita Yosuke Y, Uda Shinsuke S, Motosugi Ryo R, Hamazaki Jun J, Kubota Hiroyuki H, Murata Shigeo S, Tanaka Keiji K, Katagiri Toyomasa T, Kosako Hidetaka H, Takahama Yousuke YcTEC, cTEC.big, 3.4.22.-, d230, Epithelial Cell, Laboratory, Mus domesticus, Thymus, thymus organ, dTAFII250, mini-ICE, CASP-14, Glandular Epithelial, Glandular, EfW1, Ximpact, House Mouse, Thymus Glands, dmTAF[[II]]230, large, Multicatalytic Proteinase, Squamous Epithelial Cells, dmTAF1, House, Taf230, Multicatalytic Endopeptidase Complex, CG9063, Mus musculus domesticus, Mice, Squamous Epithelial, Epithelial, TAF250, imprinted and ancient gene protein, Taf200, Glands, dTAF[[II]]250, thymus gland, TFIID TAF250, cel, Macropain, cell, Swiss, Complex, THYMUS, Taf1p, Swiss Mice, Adenomatous Epithelial, mTEC, BcDNA:GH03694, Proteasome Endopeptidase, 20S Proteasome, dTAF250, Multicatalytic Endopeptidase, Epithelial Cells, Transitional Epithelial Cells, Multicatalytic, great, Macroxyproteinase, 26S proteasome, Thymus., TAF, Squamous Epithelial Cell, Glandular Epithelial Cell, DmelCG9063, Transitional Epithelial Cell, Transitional, tolerant, Squamous Cells, dTAF[[II]]230, TAF[[II]]250, Proteinase, Endopeptidase Complex, CASP14, mouse, TAF200, Adenomatous, l(3)84Ab, function, BG:DS00004.13, Squamous, TAFII-250, TAF250/230, Transitional Epithelial, Cell, results, impact-a, Proteasome, dTAF230, Ingensin, TAFII250, Cuboidal Glandular Epithelial Cells, Gland, Mus, p230, Mini-ICE, TAF[[II]]250/230, TFIID, IMPACT, imprinted and ancient gene protein homolog, Columnar Glandular Epithelial Cells, Thymus <eudicots>, Adenomatous Epithelial Cell, Taf[[II]]250, proteasome, Mus musculus, Adenomatous Epithelial Cells, Squamous Cell, TAF[[II]]230, Caspase-14 subunit p10, Prosome, mice, BcDNAGH03694, Swiss Mouse, expanded, Glandular Epithelial Cells, House Mice, 20S, TAF[II]250, Caspase-14 subunit p19, CG17603, MICE, TAF[[II]], 3L6, Laboratory Mice, domesticus, DmelCG17603, Taf250, rich, enlarged, SR3-5, Cells, Mouse, E430016J11Rik, multicatalytic endopeptidase, Laboratory Mouse, RWDD5, TAF230, proteasome endopeptidase complex, TAF1imprinted and ancient gene protein, Transitional Epithelial Cell, Transitional, Adenomatous Epithelial Cell, Squamous Cells, Adenomatous Epithelial Cells, Squamous Cell, Epithelial Cell, Glandular Epithelial Cell., Glandular Epithelial Cells, Adenomatous, Adenomatous Epithelial, Glandular Epithelial, Squamous, Glandular, Ximpact, Transitional Epithelial, impact-a, Cell, Squamous Epithelial Cells, Cuboidal Glandular Epithelial Cells, Epithelial Cells, Transitional Epithelial Cells, Cells, IMPACT, imprinted and ancient gene protein homolog, Columnar Glandular Epithelial Cells, E430016J11Rik, Squamous Epithelial Cell, Squamous Epithelial, RWDD5, EpithelialMethane, liquid chromatography tandem mass spectroscopy, Nup32D, IPP2A2, Bru, PLIP, Raw, determination, Laboratory, hypersomnia with periodic respiration, TFA, Mus domesticus, Dm NinaC, NINA C, CG5125, CASP-14, protein, House Mouse, heavy chain disease, Type 2A-interacting protein, trichloro-, Long Term, 5730420M11Rik, Polypeptides, Techniques, peptido, dorsal marginal zone, dJ69E11.3, Method, sleep apneas, SEC, mixed central and obstructive sleep apnea, protein aggregate, Injectables, Effect, WMS, MIX, HTATIP, wood alcohol, nup154, C79691, Svc, SET, LCMSMS, peptides, TAF-I, sleep, sec, hypopnea, hypoplasia, Swiss Mice, purification, T6G21.3, free, DmelCG4299, Lccp, isolation and purification, IGAAD, set, Nina C, cPLA2, Methodological Studies, DmelCG10574, sample, TF, hypopneas, Sodium Methoxide, house mouse, GPHYSD2, TIP, Long-Term Effects, CT16120, SGS, LC-MS2, phapii, Stars, Alcohol, ZC2HC5, Trypsin/K, CASP14, mouse, LC-MS/MS, Longterm Effect, StF-IT-1, Th, Search, HTATIP1, mixed central and obstructive, mixed sleep apnea, Procedure, tip, ANAC091, not genetically inherited, mice C57BL/6xCBA/CaJ hybrid, ACMICD, DmelCG5125, Putative MAPK-activating protein PM10, HCD, Mini-ICE, Henson's node, TIP60, sleep hypopnea, Carbinol, carbinol, DRONINAC, parent ion, Mus musculus, MILD1, HLA-DR-associated protein II, Caspase-14 subunit p10, DI-2, mice, I-2Dm, Swiss Mouse, Caspase-14 subunit p19, MASCOT, LNKN-1, Methodological, MASS, CG4299, MICE, beta Trypsin, Methodological Study, domesticus, Trichloromethane, apnea syndromes, I-2PP1, Wood, breathing, TAF-IBETA, precursor ion, spirit of wood, liquid chromatography-tandem mass spectroscopy, label, DMZ, Mouse, TAF-Ibeta, mixed sleep Apneas, Polypeptide, tlp, STARS, TIP41, i2pp2a, Methyl Alcohol, sleep-disordered, 3.4.22.-, apnea syndrome, Procedures, Effects, AW549739, mouse <Mus musculus>, FBN, Gene, mini-ICE, Methyl, CH3OH, precursor, Methylalkohol, thomson, protein-containing complex, sleep apnea, ESA1, PHAPII, LC-MS-MS, mass-to-charge ratio, sleep hypopneas, method, reduced, House, Ms1, isolation, ECTOL1, Injection, Arabidopsis NAC domain containing protein 91, method used in an experiment, LC-MSMS, Gene Products, Studies, Mus musculus domesticus, zk, Wood Alcohol, Del(8)44H, tiny, NINAC, Mice, apneas, Technique, CG54125, T6K12_14, Search Engines, l(2)10432, NinaC, MS1, ninac, Longterm, Swiss, nodus primitivus, Selb, ipp2a2, beta-Trypsin, 2pp2a, Long-Term, CG10574, CG 5125, OCTD, Study, Injectable, mKIAA0989, DmelCG4579, ms(2)zk, 2PP2A, wood naphtha, taf-ibeta, stem node, male sterility 1, apnea, dSET, dSet, peptidos, Long-Term Effect, l(2)01501, D8Wsu49e, 2.2, small, protein complex, BcDNA:LD21772, Proteins, igaad, Methyl alcohol, Peptide, Engine, group, Mus muscaris, CD142, LC/MS/MS, secret agent, native protein, Mus, I-2PP2A, Protein, chemical analysis, Long Term Effects, Dm I-2, I2PP2A, CT42491, MFS1, Sodium, MIXL, MeOH, WMS2, Data Base, T6K12.14, nup32D, PRSS, Col4a-1, underdeveloped, mixed, ensemble, nodal stem, MALE STERILITY 1 PROTEIN, Striated muscle activator of Rho-dependent signaling, Tripcellim, CG4579, House Mice, CDA08, sample population, Longterm Effects, Laboratory Mice, Protein Gene Products, plan specification, Gene Proteins, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, wood spirit, SSKS, TCV-interacting protein, liquid chromatography tandem mass spectrometry, Peptid, assay, AA407739, Laboratory Mouse, Peptide., MethoxidefalseLFQ_K5D1-cTEC_K5D1-beta5tKO-cTECCortical TECs from K5D1 and K5D1-β5tKO mice were lysed, reduced, alkylated, and subjected to methanol/chloroform precipitation. Proteins were digested with trypsin/Lys-C mix. The digests were desalted using GL-Tip SDB, and the eluates were evaporated in a SpeedVac concentrator and dissolved in 0.1% TFA. LC-MS/MS analysis of the resultant peptides (400 ng each) was performed on an EASY-nLC 1200 UHPLC connected to a Q Exactive Plus mass spectrometer. The mass spectrometer was operated in a data-dependent acquisition mode with a top 10 MS/MS method. MS1 spectra were measured with a resolution of 70,000, an AGC target of 1×106 and a mass range from 350 to 1,500 m/z. HCD MS/MS spectra were acquired at a resolution of 17,500, an AGC target of 5×104, an isolation window of 2.0 m/z, a maximum injection time of 60 msec and a normalized collision energy of 27. Dynamic exclusion was set to 10 sec. Raw data were directly analyzed against the Swiss-Prot database restricted to Mus musculus using Proteome Discoverer version 2.2 with Mascot search engine version 2.5 for identification and label-free precursor ion quantification. Peptides and proteins were filtered at a FDR of 1% using the percolator node and the protein FDR validator node, respectively. Normalization was performed such that the total sum of abundance values for each sample over all peptides was the same.Tue Oct 08 00:00:00 BST 2019PXD0131331009031775054