{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/comparison_analysis_between_WT_VS_MUT.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/data_processing_before_comparion_analysis.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/BLM_G4_WT_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/BLM_G4_MUT_3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/BLM_G4_WT_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/BLM_G4_MUT_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/BLM_G4_MUT_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075345/BLM_G4_WT_2.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["kbwang@cpu.edu.cn"],"submitter":["Yingying Wang"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"disease":["Colon Cancer"],"software":["Not available"],"submitter_keywords":["Blm-g4","Pulldown","Ip-ms","Ht-29 cell"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075345"],"tissue":["Malignant Cell","Cell Culture"],"sample_protocol":["HT-29 cells were lysed by using RIPA buffer. The equivalent obtained protein supernatents were respectively incubated with biotin-labelled BLM-G4-WT or BLM-G4-MUT overnight, then incubated with streptavidin agarose beads for 4 h. Wash the beads for the subsequent LC-MS/MS analysis."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Samples include BLM-G4-WT and BLM-G4-MUT group, with each group containing 3 biological repeats.  1. Remove proteins identified with # Protein Unique Peptides < 3 in both the experimental and control groups. 2. Perform missing value imputation using the impute.MinProb function from the R package imputeLCMD, which specializes in missing value imputation. The imputation is based on a Gaussian distribution centered at the 5% quantile of each sample (parameters: g = 0.05, tune.sigma = 0.01), and random numbers drawn from this distribution are used as imputed values. 3. Calculate pairwise ratios by sequentially computing the ratios between replicates of the two groups, and take the median of these ratios as the final ratio. 4. Conduct statistical testing using a two-sample t-test to calculate p-values. In the table \"WT vs MUT,\" which shows the processed results, a total of 1709 proteins were quantified. Proteins with a fold change (Ratio) ≥ 1.5 and p-value < 0.05 were screened and marked in red, totaling 1369 proteins. Proteins with a fold change (Ratio) ≤ 0.67 and p-value < 0.05 were screened and marked in green, totaling 13 proteins."],"omics_type":["Proteomics"],"labhead":["Kaibo Wang"],"instrument_platform":[""],"labhead_affiliation":["China Pharmaceutical University"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["42087785 Wang Y, Zhang X, Bian Y, He S, Cheng R, Li J, Dickerhoff J, Liu Y, Zhou Y, Bian J, Zheng K, Yang D, Kong LY, Wang KB. A small molecule disrupts G4-STAT1 interaction and synergizes with olaparib to drive cancer cell death. Nucleic Acids Res. 2026 54(9):gkag383 10.1093/nar/gkag383"],"submitter_mail":["1377599356@qq.com"],"curator_keywords":["Cancer (b/d-hpp)","Human proteome project","Biology/disease-driven human proteome project (b/d-hpp)"],"submitter_affiliation":["China Pharmaceutical University"],"submitter_country":["China"],"pubmed_abstract":["Bloom syndrome protein (BLM), a RecQ family DNA helicase, is consistently overexpressed in multiple malignancies, yet its therapeutic potential remains largely unexplored. Herein, we focused on targeting the BLM promoter G-quadruplex (BLM-G4) to inhibit the BLM signaling pathway. We first characterized the parallel BLM-G4 in the BLM promoter region. Subsequently, it is shown for the first time that BLM-G4 recruits phosphorylated signal transducer and activator of transcription 1 (pSTAT1) to activate BLM expression. Importantly, two natural alkaloids, berberine (BER) and coptisine (COP), compete with STAT1 for binding to BLM-G4, thereby significantly suppressing BLM expression in colon cancer cells. The BER/COP-BLM-G4 complex structures were determined using nuclear magnetic resonance experiments, which provide valuable insights for the rational design of next-generation BLM-G4-targeting ligands. Beyond BLM regulation, the conjoint analysis of genome-wide STAT1-CUT&Tag-seq, G4-CUT&Tag-seq, and COP-RNA-seq demonstrated STAT1 as a general G4-binding transcription factor and COP as a pan-genomic G4 stabilizer. Furthermore, BER/COP exhibited a pronounced synergistic effect with olaparib in inducing colon cancer cell death by disrupting DNA repair pathways and intensifying DNA damage. Collectively, our findings reveal a novel epigenetic mechanism of BLM gene upregulation mediated by BLM-G4-STAT1 interaction and suggest that the combination therapy of G4 stabilizers with poly(ADP) ribose polymerase (PARP) inhibitors is a promising strategy for treating complex cancers."],"pubmed_title":["A small molecule disrupts G4-STAT1 interaction and synergizes with olaparib to drive cancer cell death."],"pubmed_authors":["Wang Yingying Y, Zhang Xuenan X, Bian Yuting Y, He Sihan S, Cheng Rongshuang R, Li Jinzhu J, Dickerhoff Jonathan J, Liu Yushuang Y, Zhou Yu Y, Bian Jinlei J, Zheng Kewei K, Yang Danzhou D, Kong Ling-Yi LY, Wang Kai-Bo KB"],"additional_accession":[]},"is_claimable":false,"name":"BLM-G4 pulldown IP-MS in human colon cancer HT-29 cells","description":"the experiment uses biotin-labelled BLM-G4 to incubate with HT-29 cell lysates, and uses streptavidin agarose beads to pulldown BLM-G4-binding proteins. Utilize LC-MS/MS to annotate and quantify the proteins pulled down by BLM-G4.","dates":{"publication":"2026-06-08","submission":"2026-03-07"},"accession":"PXD075345","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:1211601","NEWT:876138","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:51329","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:260707","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:105231","NEWT:1216981","NCBITaxon:6073","NEWT:884204","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:38783","NEWT:8727","NEWT:4006","NEWT:8726","NEWT:6426","NEWT:6669","NEWT:10090","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","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