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de.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F20.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F16.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F23.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F22.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F21.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F17.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F16.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F22.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F24.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F19.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F18.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F22.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F23.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F21.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F24.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F16.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET2_F8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET4_F20.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET3_F8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F17.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/20211224_KIM_TMT10_SET1_F.pdResultftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD065940/primary_cell_kim_TMT.pdStudyprimaryOK200hdh03@snu.ac.krDohyun HanMass SpectrometryBottom-up proteomicsNot availableDiesel exhaust particlesHuman nasal epitheliumTmthttps://www.ebi.ac.uk/pride/archive/projects/PXD065940EpitheliumPHNE obtained from 3 individual donors were homogenized with lysis buffer (4% SDS, 2mM TCEP, and 0.1M Tris-HCl pH 8.5). The protein concentration was determined using a reducing agent-compatible BCA assay kit (Thermo Fisher Scientific, Waltham, MA, USA). To remove contaminants, we performed acetone precipitation at -20℃ with 150μg of the lysate. The protein pellet was dissolved in 50ul of reduction buffer (4% SDS, 5mM TCEP, 20mM CAA, and 0.1M Tris-Cl, pH 8.5). Protein digestion was performed according to filter-aided sample preparation (FASP) method as described previously. After heating at 95℃ for 30 min, proteins were loaded into a 30-kDa Amicon Ultra-centrifugal filter unit (Millipore, Billerica, MA, USA). Buffer was exchanged to UA buffer (8 M urea in 0.1 M Tris-HCl, pH 8.5) twice by centrifugation and then to 50 mM HEPES pH 8.5 buffer three times. Proteins were digested at 37℃ overnight with trypsin/LysC [enzyme to substrate ratio (w/w) of 1:100]. The peptides were eluted with 50 mM HEPES pH 8.5 by centrifugation. The peptide concentrations were quantified based on tryptophan fluorescence.PrideFour sets of TMT experiments were processed using Proteome Discoverer (PD) version 2.5 (Thermo Fisher Scientific) based on SEQUEST-HT search engine. The acquired data was compared and searched against the UniProtKB HUMAN database (June 2021, 100,730 entries). The search parameters were as follows: complete trypsin digestion; precursor mass tolerance of 10 ppm and MS/MS tolerance of 20 ppm; false discovery rate (FDR) for all peptide-spectrum matches (PSMs) under 1%, and performed by Percolator software package (version 3.05) using delta Cn (0.05), strict FDR (0.01), relaxed FDR (0.05), and PEP (0.05) settings; fixed modifications were TMT tag (N-term and Lys, + 229.163 Da) and carbamidomethylation (Cys, + 57.021 Da); and variable modifications were oxidation (Met, + 15.995 Da) and deamidation (Asn and Gln, + 0.984 Da). Peptide groups were assigned to logical protein groups based on parsimony principle. The most confident centroid within 20 ppm of the expected mass of the reporter ions was used.ProteomicsDohyun HanPARTIALProteomics Core Facility, Biomedicial Research Institute, Seoul National University HospitalHomo Sapiens (human)41577101 Han D, Choi J, Park MK, Kim N, Han DH. Inflammatory responses and cilia reorganization induced by daily exposure to diesel exhaust particles in primary human nasal epithelium. Environ Res. 2026 294:123849 10.1016/j.envres.2026.123849hdh03@snu.ac.krProteomics Core Facility, Biomedical Research Institute, Seoul National University HospitalSouth KoreaDiesel exhaust particles (DEPs), a major component of airborne particulate matter (PM), are strongly associated with the development of both acute and chronic upper airway inflammatory diseases. We investigated the effects of prolonged daily exposure to low-dose DEPs on the development and maturation of primary human nasal epithelium (PHNE) to elucidate novel mechanisms that may underlie DEP-induced inflammatory responses or disease pathogenesis. PHNE cultured under air-liquid interface (ALI) conditions were exposed to 0.5 μg cm<sup>-2</sup> of DEPs for 5 h daily from ALI day 1 to day 23. PHNE cell pellets were subsequently collected on ALI days 6, 12, and 24 and analyzed using mass spectrometry-based isobaric labeling quantitative proteomics, and biochemistry assays. A total of 7993 proteins were identified, with approximately half exhibiting time-dependent differential expression patterns throughout the course of PHNE maturation. To determine the proteins differentially expressed in response to DEPs exposure, we conducted paired student's t-tests at each time point. Functional annotation clustering of these differentially expressed proteins revealed enrichment of gene ontology (GO) terms related to the inflammatory response on ALI day 6. By ALI day 24, several GO biological process (GO-BP) terms associated with cilia-such as cilium assembly, intraciliary transport, and cilium movement-were significantly enriched. Our findings suggest that repeated daily exposure to low-dose DEPs can trigger an inflammatory response during the early stages of PHNE maturation and further mainly affect ciliogenesis by disrupting cilia assembly and motility during the later stage of PHNE maturation.Inflammatory responses and cilia reorganization induced by daily exposure to diesel exhaust particles in primary human nasal epithelium.Han Dohyun D, Choi Jihyun J, Park Moo Kyun MK, Kim Nahyun N, Han Doo Hee DHfalseIn depth proteome analyais of primary human nasal epithelium induced by diesel exhaust particlesDiesel exhaust particles (DEPs), a major component of airborne particulate matter (PM), are strongly associated with the development of both acute and chronic upper airway inflammatory diseases. In this study, we investigated the effects of prolonged daily exposure to low-dose DEPs on the maturation of primary human nasal epithelium (PHNE). PHNE cultured under air-liquid interface (ALI) conditions were exposed to 0.5μg cm-² of DEPs for 5 hours daily from ALI day 1 to day 23. PHNE samples were subsequently collected on ALI days 6, 12, and 24 and analyzed using mass spectrometry-based label-free quantitative proteomics. A total of 7,993 proteins were identified, with approximately half exhibiting time-dependent differential expression patterns throughout the course of PHNE maturation. To determine the proteins differentially expressed in response to DEP exposure, we conducted paired Student’s t-tests at each time point. Functional annotation clustering of these differentially expressed proteins revealed enrichment of gene ontology (GO) terms related to the inflammatory response on ALI day 6. By ALI day 24, several GO biological process (GO-BP) terms associated with cilia—such as cilium assembly, intraciliary transport, and cilium movement—were significantly enriched. In conclusion, our findings suggest that repeated daily exposure to low-dose DEPs can trigger an immune response via IL-1α and IL-17 signaling pathways during the early stages of PHNE maturation and further affect ciliogenesis by disrupting cilia assembly and motility during later stage of PHNE maturation.2026-05-232025-07-09PXD065940NEWT:6945NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:1211601NEWT:876138NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:1351NEWT:1438992NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:3885NEWT:3888NEWT:1589NEWT:135622NEWT:6915NEWT:3649NEWT:101510NEWT:3880NEWT:272559NEWT:3641NEWT:383379NEWT:10029NEWT:1000589NEWT:85963NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:197NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:294128NEWT:11676NEWT:55571NEWT:100226NEWT:4530NEWT:4896NEWT:75058NEWT:13616NEWT:1094343NEWT:296543NEWT:1773NEWT:1895NEWT:1182590NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:990119NEWT:408172NEWT:408170NEWT:493760NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:460519NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:32644NEWT:499175NEWT:476272NEWT:3747NEWT:367830NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:28038NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:115104NEWT:1121114NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:13076NEWT:1249668NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:415540NEWT:675060NEWT:4081NEWT:554NEWT:98334NEWT:426428NEWT:7574NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:507601NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NCBITaxon:2NEWT:985076NEWT:1215323NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:216599NEWT:216595NEWT:243230NEWT:8355NEWT:9685NEWT:7029NEWT:1080772NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:260707NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:105231NEWT:1216981NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:5334NEWT:37334NEWT:382352NCBITaxon:10359NEWT:242619NEWT:632957NEWT:373995NEWT:5689NEWT:544404NEWT:9925NEWT:8839NEWT:4232NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:61674NEWT:1117957NEWT:9913NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:180066NEWT:135588NEWT:1843183NEWT:58002NEWT:326423NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:1678078NEWT:749906NEWT:418985NEWT:146479NEWT:1911079NEWT:264203NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:349741NEWT:9605NEWT:9606NEWT:157295NEWT:641501NEWT:7668NEWT:915099NEWT:74940NEWT:9721NEWT:137221NEWT:1450511NEWT:1143193NEWT:411901NEWT:9838NEWT:105884NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:58331NEWT:6326NEWT:6689NEWT:5476NEWT:1274432NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:521001NEWT:39947NEWT:1274420NEWT:578458415771010000-0002-0841-1598