Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-1.tandem.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-1.tandem.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-2.tandem.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-2.tandem.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-2.mzid_Sh-367-2.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-1.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-1.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-2.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-2.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-2.mzid_Sh-366-2.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-1.mzid_Sh-367-1.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-1.mzid_Sh-366-1.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-1.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-1.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-2.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-1.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-2.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Omar_20211228_SH366-Sh367_Phosphoproteome-ATR-inhibitor_Experiment_Condensed.sf3ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-367-1.datftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067042/Sh-366-2.datprimaryOK200arapidi@gmail.comGeorgij ArapidiData-dependent acquisitionMass SpectrometryBottom-up proteomicsCervical CancerPhosphoproteomicsEtoposideAtr inhibitorhttps://www.ebi.ac.uk/pride/archive/projects/PXD067042Malignant CellCell CultureHeLa cells were treated with 90 µM etoposide (VP16; Sigma-Aldrich, #E1383) for 30 min or were pretreated with 15 µM VE821 (ATR inhibitor; Sigma-Aldrich, #SML1415) for 6 h, followed by an additional treatment with 90 µM etoposide for 30 min. 107 cells were washed three times with PBS, lysed in buffer containing 4% SDS, 100 mM Tris-HCl (pH 8.0) with phosphatase inhibitor cocktails 1 and 2 (Sigma-Aldrich), and incubated at 60°C for 30 min. The cell lysates were subjected to sonication on ice (3 cycles: 10 sec on/off pulses with a 30% amplitude). Disulfide bonds were reduced with DTT (5 mM) for 30 min at room temperature (RT). Afterward, iodoacetamide was added to a final concentration of 10 mM. The samples were incubated at RT for 20 min in the dark, and the reaction was stopped by adding 5 mM DTT. After the precipitation of proteins using methanol/chloroform, the semi-dry protein pellet was dissolved in 50 µL of 8 M urea, 2 M thiourea, and 10 mM Tris-HCl (pH 8.0). Then, protein amounts were adjusted to 0.5 mg using the Quick Start Bradford protein assay (Bio-Rad), and samples were diluted with ammonium bicarbonate solution to reduce urea concentration to 2 M. Trypsin (Promega) was added at the ratio of 1:100 w/w, and the samples were incubated for 14 h at 37°C. The reaction was stopped by adding formic acid to the final concentration of 5%. The tryptic peptides were desalted using SDB-RPS membrane (SigmaAldrich) and vacuum-dried. Then, the phosphoenrichment procedure was performed according to the manufacturer's protocol. Before LC-MS/MS analysis, samples were redissolved in 5% acetonitrile with 0.1% trifluoroacetate solution and sonicated. Proteomic analysis was performed using a Q Exactive HF mass spectrometer. Samples were loaded onto 50-cm columns packed in-house with C18 3 μM Acclaim PepMap 100 (Thermo Fisher), with an Ultimate 3000 Nano LC System (Thermo Fisher) coupled to the MS (Q Exactive HF, Thermo Fisher). Peptides were loaded onto the column thermostatically controlled at 40°C in buffer A (0.2% Formic acid) and eluted with a linear (120 min) gradient of 4 to 55% buffer B (0.1% formic acid, 80% acetonitrile) in buffer A at a flow rate of 350 nl/min. Mass spectrometric data were stored during automatic switching between MS1 scans and up to 15 MS/MS scans (topN method). The target value for MS1 scanning was set to 3106 in the range 300–1200 m/z with a maximum ion injection time of 60 ms and a resolution of 60000. The precursor ions were isolated at a window width of 1.4 m/z and a fixed first mass of 100.0 m/z. Precursor ions were fragmented by high-energy dissociation in a C-trap with a normalized collision energy of 28 eV. MS/MS scans were saved with a resolution of 15000 at 400 m/z and at a value of 1105 for target ions in the range of 200–2000 m/z with a maximum ion injection time of 30 ms.PrideRaw LC-MS/MS data from Q Exactive HF mass spectrometer were converted to .mgf peak lists with MSConvert (ProteoWizard Software Foundation). For this procedure, we used the following parameters: “--mgf --filter peakPicking true”. For protein identification, the generated peak lists were searched with MASCOT (version 2.5.1, Matrix Science Ltd., UK) and X! Tandem (ALANINE, 2017.02.01, 2017.02.01, The Global Proteome Machine Organization) search engines against UniProt human protein knowledgebase with the concatenated reverse decoy dataset. The precursor and fragment mass tolerance were set at 20 ppm and 0.04 Da, respectively. Database-searching parameters included the following: tryptic digestion with one possible missed cleavage, static modification for carbamidomethyl (C), and dynamic/flexible modifications for oxidation (M) and phosphorylation (S, T, Y). For X! Tandem, we also selected parameters that allowed a quick check for protein N-terminal residue acetylation, peptide N-terminal glutamine ammonia loss, or peptide N-terminal glutamic acid water loss. Result files were submitted to Scaffold 5 software (version 5.1.0) for validation and meta-analysis. We used the local false discovery rate scoring algorithm with standard experiment-wide protein grouping. For the evaluation of peptide and protein hits, a false discovery rate of 5% was selected for both. False positive identifications were based on reverse database analysis. We also set protein annotation preferences in Scaffold to highlight Swiss-Prot accessions among others in protein groups.ProteomicsGeorgij ArapidiSystem Biology Lab. at Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological AgencyCOMPLETEHomo Sapiens (human)arapidi@gmail.com42152682 Petrova NV, Deriglazov DA, Kovina AP, Luzhin AV, Shender VO, Arapidi GP, Gavrikov AS, Mishin AS, Razin SV, Velichko AK. Treacle-dependent TOPBP1 condensation regulates the nucleolar DNA damage response. Nucleic Acids Res. 2026 54(9):gkag350 10.1093/nar/gkag350System Biology Lab. at Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological AgencyRussia10.6019/PXD067042Ribosomal DNA (rDNA) arrays are among the most highly transcribed repetitive regions of the genome and therefore require specialized mechanisms to maintain their stability. The nucleolar DNA damage response (n-DDR) safeguards rDNA integrity and is coordinated by the repair scaffold TOPBP1 and the fibrillar center (FC) protein Treacle. Here, we show that Treacle promotes phase separation of TOPBP1 within the FC to establish a spatially confined signaling platform that amplifies nucleolar DDR signaling and coordinates rDNA repair pathway engagement. Using an inducible TOPBP1 oligomerization system together with physiological models of rDNA damage, we demonstrate that phosphorylation of Treacle by CK2 and ATR/ATM enables its interaction with TOPBP1 and nucleates TOPBP1 condensation in the nucleolus. Functionally, Treacle-dependent condensation promotes robust ATR/ATM activation, γH2AX signaling, and recruitment of DNA repair factors. Disruption of this process does not impair the initial removal of rDNA double-strand breaks but shifts repair toward rapid DNA-PK-dependent nonhomologous end joining while attenuating ATR/ATM signaling and reducing engagement of homologous recombination-associated pathways. Treacle-knockout cells exhibit accelerated early rDNA repair but incomplete damage resolution at later stages. Together, our findings identify Treacle-dependent TOPBP1 condensation as a nucleolar signaling platform that promotes accurate maintenance of highly repetitive rDNA arrays.Treacle-dependent TOPBP1 condensation regulates the nucleolar DNA damage response.Petrova Nadezhda V NV, Deriglazov Dmitry A DA, Kovina Anastasia P AP, Luzhin Artem V AV, Shender Victoria O VO, Arapidi Georgij P GP, Gavrikov Alexey S AS, Mishin Alexander S AS, Razin Sergey V SV, Velichko Artem K AKfalseComparative phosphoproteomic analysis of HeLa cells in response to etoposide or to a combination of etoposide and the ATR inhibitor VE821To investigate the regulation of protein phosphorylation during the DNA damage response and the role of ATR kinase activity, we performed a comparative phosphoproteomic analysis of HeLa cells treated with etoposide alone or in combination with the ATR inhibitor VE821. Etoposide is a topoisomerase II inhibitor that induces DNA double-strand breaks, activating the DNA damage signaling cascade. We focused particularly on phosphorylation events associated with Treacle (TCOF1), a nucleolar protein implicated in the regulation of rDNA transcription and nucleolar DNA damage response. Quantitative mass spectrometry-based phosphoproteomics was used to identify and quantify global phosphorylation changes under both treatment conditions. This dataset enables the identification of ATR-dependent phosphorylation sites and may provide insights into the molecular mechanisms underlying nucleolar stress responses and the coordination of DNA repair processes.2026-05-252025-08-07PXD067042NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:475174NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:656064NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:38815NEWT:317447NEWT:4688NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:8165NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:317047NEWT:460523NEWT:235443NEWT:1757312NEWT:85694NEWT:108458NEWT:5936NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:166313NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:906914NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:9983NEWT:8655NEWT:5147NEWT:28108NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:40674NEWT:1194669NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:475932NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:99488NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:29829NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:300273NEWT:4232NEWT:416348NEWT:11298NEWT:4236NEWT:7742NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:72664NEWT:563041NEWT:36599NEWT:41949NEWT:249161NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:29835NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:35231NEWT:8644NEWT:1125630NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:637379NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:186801NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:194439NCBITaxon:12637NEWT:38727NEWT:218496NEWT:8618NEWT:70448NEWT:300251NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:54195NEWT:10136NEWT:38942NEWT:4762NEWT:6941NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:6938NCBITaxon:39054NEWT:1736309NEWT:4751NEWT:194963NEWT:15819NEWT:109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