Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report.stats.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report.pg_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report-first-pass.gg_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report-first-pass.stats.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report.gg_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report.unique_genes_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report-first-pass.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report-first-pass.pg_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report-first-pass.unique_genes_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report-first-pass.pr_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report.pr_matrix.tsvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/Annotation.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report.log.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/report.pdfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_8_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_4_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_5_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_7_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_13_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_6_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_6_6_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_11_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_10_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_12_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_9_9_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_2_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_1_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_3_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_11_11_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_13_13_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_14_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_3_3_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_10_10_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_2_2_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_7_7_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_12_12_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_4_4_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_8_8_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_1_1_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_5_5_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_14_14_AM.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD063764/240503_PCa_Organoids_9_AM.rawprimaryOK200w.mansour@uke.deAyham MoustafaMass SpectrometryBottom-up proteomicsProstate CancerOrganoidsProteomicsHormon therapyProstate cancerhttps://www.ebi.ac.uk/pride/archive/projects/PXD063764Prostate Cancer CellThe PDOs of three PCa patients (pat1, pat2, and pat3) were cultivated as described before (MO`s Paper) and treated with either olaparib or abiraterone as a single treatment or combined. The protein extraction was performed after incubating the PDOs pellets in 100 mM triethyl ammonium bicarbonate and 1% w/v sodium deoxycholate buffer. Samples were boiled at 95 °C for 5 minutes to denature proteins and then sonicated to shear DNA and RNA molecules. The protein concentration was determined using the Pierce bicinchoninic acid assay (BCA) Protein assay kit (Thermo Fisher), and samples were diluted to 20 μg of protein in 50 µL buffer. Dithiothreitol (DTT) in a concentration of 10 mM was added to the samples for 30 min at 56 °C to reduce disulfide-bonded cysteine residues. The alkylation of the reduced cysteine residues was performed in the presence of 20 mM iodoacetamide for 30 min at 37 °C in the dark. For each 10 µg protein, 1 µL carboxylate modified magnetic beads (GE Healthcare Sera-Mag™, Chicago, USA) at 1:1 (hydrophilic/hydrophobic) ratio in methanol/LC-MS grade water were used. The concentration of acetonitrile (ACN) in all samples was raised to 70% acetonitrile (ACN) following the single-pot, solid-phase enhanced sample preparation (SP3)-protocol workflow. After shaking the samples at 1400 rpm for 18 min at room temperature, the tubes were placed on a magnetic rack to separate the beads from the solution. The beads-free supernatant was discarded, and the magnetic beads were washed two times with 100% ACN and two times with 70% Ethanol on the magnetic rack. The ammonium bicarbonate in a concentration of 50 mM was added before the protein digestion by trypsin (sequencing grade, Promega) at a 1:100 (enzyme:protein) ratio at 37 °C overnight on a shaker at 1400 rpm. To let the generated tryptic peptides bind to the beads, 95% ACN was added while the samples were shaken at 1400 rpm for 10 min at room temperature. The beads-free supernatant was removed after placing the tubes on the magnetic rack. The beads carrying the digested peptides were washed two times with 100% ACN. Elution was performed with 2% DMSO in 1% formic acid. The supernatant was dried in a vacuum centrifuge and stored at -80°C until further use. The tryptic peptides of each sample were resuspended in 0.1% formic acid to a final concentration of 1 μg/μl. A volume of 1 μl was injected into a nano-UHPLC (Dionex Ultimate 3000 UHPLC system, Thermo Fisher) via an autosampler. Chromatographic separation of peptides was done using a two-buffer system (buffer A: 0.1% FA in H2O, buffer B: 0.1% FA in ACN). For online desalting and purification, a peptide trap (100 µm x 20 mm, 100 Å pore size, 5 µm particle size, C18, Nano Viper, Thermo Fisher) was attached to the UHPLC, followed by a 25 cm C18 reversed-phase column (75 µm x 250 mm, 130 Å pore size, 1.7 µm particle size, peptide BEH C18, nanoEase, Waters). Peptides were separated using an 80 min method with linearly increasing ACN concentration from 2% to 30% ACN over 60 minutes. MS/MS measurements were performed on a quadrupole-ion-trap-orbitrap MS (Orbitrap Fusion, Thermo Fisher). Eluting peptides were ionized using a nano-electrospray ionization source (nano-ESI) with a spray voltage of 1,800 V and analyzed in data-independent acquisition (DIA) mode. For each MS1 scan, ions were accumulated for a maximum of 120 milliseconds or until a charge density of 2 x 105 ions (AGC Target) was reached. Fourier-transformation-based mass analysis of the data from the orbitrap mass analyzer was performed, covering a mass range of m/z 400 – 1,300 with a resolution of 120,000 at m/z = 200. Peptides with charge states between 2+ - 5+ above an intensity threshold of 1,000 were isolated within a m/z 1.6 isolation window in Top Speed mode for 3 seconds from each precursor scan and fragmented with a normalized collision energy of 30% using higher energy collisional dissociation (HCD). MS2 scanning was performed using an ion trap mass analyzer at a rapid scan rate, covering a mass range starting at m/z 120 and accumulated for 60 ms or to an AGC target of 1 x 105. Already fragmented peptides were excluded for 30 s.PrideDIA MS raw files of all samples were searched with the DIA-NN 1.8.1 software1 against a reviewed human Swissprot database obtained in June 2021, containing 20,386 entries. Carbamidomethylation of cysteine residues was set as a fixed modification. The oxidation of methionine and pyro-glutamate formation at glutamine residues at the peptide N-terminus, as well as acetylation of the protein N-terminus, were allowed as variable modifications. A maximum number of two missing tryptic cleavages was set. Peptides between 7 and 30 amino acids were considered. For the analysis of LC/MS data, Perseus software2 (Max Plank Institute for Biochemistry, version 2.0.3.0) was used in statistical analysis. Protein abundances were imported into the software and then were log2 transformed. To overcome the injection-related discrepancies in total protein amounts, protein abundances were median normalized by column. The gene Enrichment analysis was achieved with Enrichr3-5 (Molecular Signatures Database (MSigDB) hallmark gene set library). The R software environment (version 2023.12.1+402) was used to generate the bubble charts of the enriched terms. Bar charts of the relative abundances of RAD51 and PCA plots were visualized in GraphPad Prism 8.0.2. The heat map was visualized by Perseus software2. R-software environment (version 4.4.2). Unless otherwise noted, biological duplicates of samples were used in all measurements for proteomics.ProteomicsProf. Dr. Wael MansourPARTIALTargeting DNA repair in systemic and radiation cancer therapy II.Medical Oncology Dept, Radiotherapy and Radiooncology Dept Research team leader: DSB repair in tumors Mildred Scheel Nachwuchszentrum HaTriCS4Homo Sapiens (human)42414479 Elsesy ME, Moustafa A, Oh-Hohenhorst SJ, Müller C, Alawi M, Mair T, Siebels B, Hu Z, Hahn J, Burdak-Rothkamm S, Tilki D, Schlüter H, Petersen C, Maurer T, von Amsberg G, Bokemeyer C, Rothkamm K, Mansour WY. Functional and omics-based rationale for the induction of BRCAness by androgen receptor pathway inhibitors to sensitize prostate cancer to PARP inhibition, regardless of HRR status. Br J Cancer. 2026 10.1038/s41416-026-03518-7a.moustafa@uke.deDepartment of Radiotherapy and Radiooncology & Section for Mass spectrometry proteomics_ University Medical Center Hamburg Eppendorf, Hamburg, GermanyGermanyfalseFunctional and omics-based rationale for the induction of BRCAness by androgen receptor pathway inhibitors to sensitize prostate cancer to PARP inhibition, regardless of HRR statusTwo PARP inhibitors (PARPi) olaparib and talazoparib have been approved in combination with novel-hormonal-therapies (NHTs) for the treatment of metastatic castration resistant prostate cancer (mCRPC) – in Europe independent of the HRR status. However, the underlying mechanism of action in HRR negative patients is still not fully understood. In the current study, we revealed that combining PARPi (olaparib or talazoparib) with NHTs (abiraterone, enzalutamide, or apalutamide) significantly reduced cell survival in HS LNCaP and CR DU145 and 22RV1 PCa cell lines. While PDOs did not respond to olaparib alone, talazoparib mono-treatment reduced survival >2-fold in one LN-metastatic PDO and marginally (1.1-fold) in the other two. NHTs using abiraterone, enzalutamide or apalutamide all significantly reduced survival in the two LN-metastatic PDOs but were ineffective in the bone-metastatic PDOs. Importantly, the combination of any of the PARPi with any of the NHTs demonstrated significantly greater cytotoxic effects across all PDOs. None of these PDOs displayed a profile typically linked to BRCAness, as identified by the HRDetect score. Sequential (NHT followed by PARPi) and simultaneous treatment strategies yielded comparable results. Transcriptomic and immunoblotting analyses revealed that NHTs downregulate the homologous recombination repair gene RAD51, inducing a "BRCAness-like" phenotype characterized by reduced RAD51 foci formation at DNA double-strand break (DSB) sites, and sensitizing tumor cells to PARPi. Consistently, among the LN-metastatic TSCs, 67% exhibited a substantial reduction in DSB repair capacity when treated with the combined regime compared to monotherapies. Further, proteomic analyses indicate that olaparib may suppress metastasis by inhibiting key pro-metastatic pathways, including epithelial-mesenchymal transition and angiogenesis. Collectively, we provide a mechanistic rationale for integrating NHTs with PARPi, regardless of treatment sequence, in treating mPCa patients. NHT induces a BRCAness-like phenotype, rendering cells sensitive to PARPi. Additionally, we establish the potential of PARPi to suppress metastasis in mPCa during the treatment course.2026-07-102025-05-08PXD063764NEWT:3555NEWT:71647NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:96731NEWT:383379NEWT:10029NEWT:913645NEWT:44491NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:108061NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:931281NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:5759NEWT:1736231NEWT:5518NEWT:1392NEWT:498217NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:633149NEWT:10239NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1390NEWT:11557NEWT:1094343NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:935293NEWT:375146NEWT:118698NEWT:263NEWT:118696NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:408172NEWT:408170NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:1436733NEWT:460519NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:1513458NCBITaxon:40559NEWT:84588NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:644223NEWT:235443NEWT:108458NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:352472NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:39491NCBITaxon:5811NEWT:29491NEWT:2014887NEWT:33952NEWT:261756NEWT:571256NEWT:40483NEWT:272634NEWT:9031NEWT:1872122NEWT:7091NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:4093NEWT:4096NEWT:185579NEWT:941442NEWT:13076NEWT:7108NEWT:40479NEWT:4076NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:1268063NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:407821NCBITaxon:2NEWT:985076NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:28532NEWT:353152NEWT:8496NEWT:27448NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:104395NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:80863NEWT:105231NEWT:52638NEWT:57075NEWT:4097NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NEWT:632957NEWT:9925NEWT:89462NCBITaxon:9606NEWT:8839NEWT:90690NEWT:4232NEWT:2758385NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:312017NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:284593NEWT:100392NEWT:5315NEWT:9913NEWT:265872NEWT:105841NEWT:337330NEWT:2666255NEWT:2285NEWT:999810NCBITaxon:5693NEWT:1392998NEWT:380394NEWT:981087NEWT:180066NEWT:226900NEWT:231490NEWT:430615NEWT:563041NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1416333NEWT:1678078NEWT:749906NEWT:418985NEWT:1817808NEWT:749907NEWT:145263NEWT:694569NEWT:27606NEWT:9739NEWT:59202NEWT:9975NEWT:51953NEWT:3197NEWT:860688NEWT:13443NEWT:36329NEWT:62615NCBITaxon:3044782NEWT:160235NEWT:72407NEWT:349741NEWT:157295NEWT:2096NEWT:192222NEWT:9721NEWT:137221NEWT:9963NEWT:1617910NEWT:565050NEWT:2785785NEWT:411901NEWT:105884NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:58331NEWT:6689NEWT:298315NEWT:70448NEWT:698936NEWT:9940NEWT:3168NEWT:521001NEWT:192011NEWT:1813887NEWT:118702NEWT:118700NEWT:224911NEWT:118705NCBITaxon:11552NEWT:6945NEWT:184922NEWT:6703NEWT:2104NEWT:2NEWT:157546NEWT:474186NEWT:38942NEWT:307972NEWT:1496NEWT:2102NEWT:45474NEWT:1590841NEWT:4513NEWT:1247NEWT:70667NEWT:6938NEWT:376741NCBITaxon:10407NEWT:1736309NEWT:4751NEWT:10360NEWT:47664NEWT:317548NEWT:15819NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:1239NEWT:36745NEWT:272563NEWT:82688NEWT:3885NEWT:3888NEWT:5821NEWT:44139NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:2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