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Noberini"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Tumor microenvironment","Triple-negative breast cancer"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063630"],"sample_protocol":["For immunoprecipitation analysis, 50 μg of nuclear extracts (DNA content) were incubated with primary antibody (Supplementary Data 2) overnight at 4°C on rotation. A competition assay was performed by adding an excess fold of soluble PML peptide (PSPSPTERAPASEE; LS Bio LS-E44221). For each IP, 5% of nuclear extracts were collected as “input”. Samples were then incubated with beads (ChIP-IT Protein G magnetic beads 53033 or Magna ChIP™ Protein A Magnetic Beads 16–661) for 4 h on rotation at 4°C. IP samples were washed three times in ice-cold RIPA buffer + 1% SDS (10 mM Tris–HCl, pH 8, 140 mM NaCl, 1%Triton X-100, 0.1% Na-deoxycholate, 1 mM EDTA and 0.5 mM EGTA). Elution was performed in SDS sample buffer (100 mM Tris-HCl, pH 6.8, 200 mM DTT, 4% SDS, 20% glycerol, 0.2% bromophenol blue) for 35 min at 95°C. IP-MS samples were run on 4-15% Mini-PROTEAN® TGX™ Precast Protein gel (Bio-Rad) and stained with colloidal Coomassie stain. Gel lanes were sliced, in-gel digested with Trypsin, and the produced proteolytic peptides were analyzed by online nano-flow liquid chromatography-tandem mass spectrometry (nLC-MS/MS) using an EASY-nLC™ 1200 (Thermo Fisher Scientific) connected to a quadrupole/Orbitrap mass spectrometer (Q Exactive, Thermo Fisher Scientific) through a nanoelectrospray ion source.Peptides were injected into a 25-cm analytical column (75 μm inner diameter, 350 μm outer diameter) packed with C18 RP resin at a flow rate of 300 nl/min and separated with a 60 min of 3–60% gradient of solvent B (55 min 3-35%, 5 min 35-60%) at flow rate of 300 nl/min."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Acquired raw data obtained by MS analysis were analyzed using the MaxQuant (MQ) version 1.6.10.43, and peptide lists were searched against the human Uniprot FASTA database (74470 Entries) with the Andromeda search engine."],"omics_type":["Proteomics"],"labhead":["Tiziana Bonaldi"],"instrument_platform":[""],"labhead_affiliation":["European Institute of Oncology, Milan, Italy"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["roberta.noberini@ieo.it"],"submitter_affiliation":["Istituto Europeo di Oncologia"],"submitter_country":["Italy"],"additional_accession":[]},"is_claimable":false,"name":"The promyelocytic leukemia PML protein fuels immune suppression in triple-negative breast cancer","description":"Tumors evade immune surveillance through diverse mechanisms that include modelling of the tumor microenvironment (TME) and impaired antigen presentation. Here, we identify the stress response protein PML as a key driver of immune evasion in triple-negative breast cancer (TNBC)","dates":{"publication":"2026-06-04","submission":"2025-05-06"},"accession":"PXD063630","cross_references":{"TAXONOMY":["NEWT:1773","NEWT:3555","NEWT:38783","NEWT:1182590","NEWT:2","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:35554","NEWT:4120","NEWT:5693","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:92867","NEWT:990346","NEWT:544496","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:284812","NEWT:115104","NCBITaxon:1313","NEWT:43330","NEWT:67825","NEWT:44544","NEWT:13076","NEWT:373995","NEWT:544404","NEWT:3702","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:1736309","NEWT:4113","NEWT:7227","NEWT:11298","NEWT:885318","NEWT:171101","NEWT:876138","NEWT:4081","NEWT:554","NEWT:5691","NEWT:260710","NEWT:106592","NEWT:237561","NEWT:9913","NEWT:10036","NEWT:4100","NEWT:7574","NEWT:1351","NEWT:1076","NEWT:6763","NEWT:7215","NEWT:803","NEWT:8030","NEWT:380394","NEWT:272563","NEWT:507601","NEWT:1639","NEWT:188229","NEWT:4909","NCBITaxon:79857","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:135588","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:95486","NEWT:3880","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:1000589","NEWT:145943","NEWT:85962","NEWT:160488","NEWT:317447","NEWT:3635","NEWT:7955","NCBITaxon:2","NEWT:235443","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:3197","NEWT:9615","NEWT:884019","NEWT:4565","NEWT:1264690","NEWT:169963","NCBITaxon:38727","NEWT:36329","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:9606","NEWT:367830","NEWT:243230","NEWT:931281","NEWT:373153","NEWT:7029","NEWT:1283300","NEWT:334747","NEWT:470","NCBITaxon:79824","NCBITaxon:4563","NEWT:3218","NEWT:5759","NEWT:9838","NCBITaxon:9615","NEWT:1736231","NEWT:1193501","NEWT:6287","NEWT:2242","NEWT:6326","NEWT:9796","NEWT:2762","NEWT:5476","NEWT:562","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:29760","NEWT:260705","NEWT:80863","NEWT:1148","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:39946","NEWT:11676","NEWT:9823","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:573","NEWT:6282","NEWT:7091","NEWT:1134506"]}}