Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/SDRF_HDF_repregrammed_DCs_3_DIA.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_XCR1pos_L1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_XCR1pos_L2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_SCR_DP_L1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_SCR_DP_G1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_L2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_G1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_SC2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_L1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_XCR1neg_SC1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_G2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_XCR1neg_SC2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_SC1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_SCR_DP_G2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_SCR_DP_SC2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_SCR_DP_SC1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_SCR_DP_L2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_XCR1neg_L1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_XCR1pos_SC1_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_XCR1neg_L2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/250508_D9_142_DP_XCR1pos_SC2_120min_Exploris_FAIMS_DIA_CV-45-60.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD077362/20250511_094136__Reprogrammed_DCs_SN18_Exp.3_250511.sneprimaryOK200jenny.hansson@med.lu.seSudip GhoshMass SpectrometryData-independent acquisitionReprogrammingDendritic cellsMirnaData-independent acquisitionhttps://www.ebi.ac.uk/pride/archive/projects/PXD077362Dendritic CellHDFs were transduced with PIB on day -1 and transfected with a combination of miR-142 mimics (miR-142-3p, miR-142-3p-1, miR-142-3p-3 and miR-142-5p-1), or scrambled control. Cells were FACS-sorted on day 9 of reprogramming for CD45+ HLA-DR+ XCR1- and CD45+ HLA-DR+ XCR1+ populations. Cells were collected in ice-cold phosphate buffer saline Solution (PBS), centrifuged, and stored as dry pellets at -80 °C until further use. Pellets corresponding to 50,000 cells were solubilized in 50 mM ammonium bicarbonate (Sigma) with 0.1% RapiGest (Waters) to denature proteins and shaken on a thermomixer (Eppendorf) at 400 rpm for 15 minutes decreasing the temperature from 80°C to 56°C, at 400 rpm, followed by reduction of disulfide bonds with 0.1M dithiothreitol at 56°C, cysteine alkylation with 0.2 M iodoacetamide at room temperature, and digestion overnight at 37°C with sequencing grade modified trypsin (enzyme:protein ratio 1:50, Promega). Digested peptides were acidified with 10% trifluoroacetic acid (TFA) and RapiGest was precipitated by incubation at 37°C. Peptides were desalted with in-house C18 stage tips, dried by vacuum centrifugation, and resuspended in MS loading buffer prior to LC-MS analysis. LC-MS analyses were carried out on an Orbitrap Exploris 480 MS instrument with a reverse phase UltiMate 3000 UHPLC system via an EASY-Spray ion source equipped with FAIMS Pro (all Thermo Fisher Scientific). Peptide samples were analyzed by data-independent acquisition (DIA). Digested peptides were loaded onto a trap cartridge (Acclaim PepMap C18, 5 mm particle size, 0.3 mm inner diameter x 5 mm length, Thermo Fisher Scientific) and separated by EASY-Spray analytical column (2 mm particle size, 75 mm inner diameter x 500 mm length, Thermo Fisher Scientific). Each sample was injected once and eluted with a linear gradient ranging from 2-19% Solvent B (0.1%FA in 80% ACN) over 80 min, 19-41% B over 40 min, 41-90% B over 5 min and held at 90-95% B for 5 min at a constant flow rate of 300 nl/min at 45°C. FAIMS compensation voltages (CV) were set to -45 and -60. The spray voltage was set at 2.1 kV and the ion transfer tube temperature was set at 275°C. For DIA analysis, peptides were analyzed with one full scan (350–1,400 m/z, R = 120,000) at a normalized AGC target of 300%, followed by 28 DIA MS/MS scans (350–1,050 m/z) in HCD mode (isolation window 25 m/z, 1 m/z window overlap, normalized collision energy 27%), with fragments detected in the Orbitrap (R = 15,000). All data were acquired in positive polarity and MS/MS were acquired in centroid mode.PrideNot availableThe MS data were searched with ‘directDIA’ in Spectronaut (version 18, Biognosys AG) against the human SwissProt reference proteome and commonly used contaminants. Searches used carbamidomethylation as fixed modifications, and methionine oxidation as well as protein N-terminal acetylation as variable modifications. The Trypsin/P proteolytic cleavage rule was used, permitting a maximum of 2 missed cleavages and a minimum peptide length of 7 amino acids. ‘Cross run normalization’ was enabled with Normalization Strategy set to ‘local normalization’ based on rows with ‘Identified in All Runs (Complete)’. Data filtering was set to Q-value and the Q‐value thresholds were set to 0.01 at PSM, peptide, and protein levels. Protein quantification and statistical analysis were performed with MSStats (version 4.12.0). Contaminants were filtered and features were converted to MSStats format for downstream processing. Uninformative features were removed, and missing values were imputed with the ‘MBimpute’ function within MSStats. For statistical analysis, MSStats ‘group comparison’ was used for statistical analysis. Differentially expressed proteins were selected with an adjusted p-value of less than 0.05 and a fold change of more than 1.5 for each comparison.ProteomicsJenny HanssonProteomic Hematology Department of Experimental Medical Science, Lund Stem Cell Center, Lund UniversityPARTIALHomo Sapiens (human)sudip.ghosh@med.lu.seNot availableProteomic Hematology, Department of Experimental Medical Science, Lund Stem Cell Center, Lund UniversitySwedenfalseCanonical and isomiR products of miR-142 enhance dendritic cell reprogrammingMicroRNAs (miRNAs) regulate gene expression and generate isoforms (isomiRs) with distinct targeting properties, but their roles in cellular specification and reprogramming remain poorly understood. Here, we investigated miRNAs and isomiRs during direct reprogramming to conventional type 1 dendritic cells (cDC1s), identifying miR-124 and miR-142 as facilitators of the process. The canonical miR-124-3p strand induced a permissive chromatin landscape enriched for cooperative transcription factor motifs, thereby transiently increasing reprogramming efficiency. In contrast, miR-142 enhanced lineage fidelity by repressing fibroblast identity and activating cDC1-specific programs through cooperating isomiRs that drove XCR1 expression and increased type III interferon production. In addition, miR-142 mimics enhanced cancer cell reprogramming and anti-tumor immunity in vivo. Finally, we developed RNA-based cDC1 reprogramming using transcription factor mRNAs combined with miRNA mimics. Together, these findings uncover miRNA isoform diversity as a programmable regulatory layer in immune cell specification and establish RNA-driven reprogramming as a non-viral strategy for cancer immunotherapy.2026-07-162026-04-20PXD077362NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:43186NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:1912919NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:1367269NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1436733NEWT:460519NEWT:1247411NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:1034015NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:552NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:74649NEWT:52638NEWT:57075NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:1436183NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:5322NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:553470NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:981087NEWT:180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