Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061218/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061218/E20242000600b.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061218/E20242000606b.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061218/E20242000604b.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061218/E20242000610b.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061218/E20242000602b.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061218/E20242000608b.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD061218/P1751-2_CircRNA_interactome_pulldown_normalization.pdResultprimaryOK200P.A.van_Veelen@lumc.nlRayman TjokrodirijoMass SpectrometryBottom-up proteomicsInsulin-like growth factor 2 mrna binding protein 3Circtbrii(3-6)Epithelial-to-mesenchymal transitionTransforming growth factor (tgf)-βhttps://www.ebi.ac.uk/pride/archive/projects/PXD061218Cell CulturePeptides were dissolved in water/formic acid (100/0.1 v/v) and analyzed by on‐line C18 nanoHPLC MS/MS with a system consisting of an Ultimate3000nano gradient HPLC system (Thermo, Bremen, Germany), and an Exploris480 mass spectrometer (Thermo). Fractions were injected onto a cartridge precolumn (300 μm × 5 mm, C18 PepMap, 5 um, 100 A, and eluted via a homemade analytical nano-HPLC column (30 cm × 75 μm; Reprosil-Pur C18-AQ 1.9 um, 120 A (Dr. Maisch, Ammerbuch, Germany). The gradient was run from 2% to 36% solvent B (20/80/0.1 water/acetonitrile/formic acid (FA) v/v) in 120 min at 250 nl/min. The nano-HPLC column was drawn to a tip of ∼10 μm and acted as the electrospray needle of the MS source. The mass spectrometer was operated in data-dependent Top 20 MS/MS mode, with a HCD collision energy at 30% and recording of the MS2 spectrum in the orbitrap, with a quadrupole isolation width of 1.2 Da. In the master scan (MS1) the resolution was 120,000, the scan range 300-1500, at standard AGC target and a maximum fill time of 50 ms. A lock mass correction on the background ion m/z=445.12003 was used. Precursors were dynamically excluded after n=1 with an exclusion duration of 45 s, and with a precursor range of 20 ppm. Included charge states were 1-6. For MS2 the first mass was set to 120 Da, and the MS2 scan resolution was 30,000 at an AGC target of standard at a maximum fill time of 60 ms.PrideIn a post-analysis process, raw data were first converted to peak lists using Proteome Discoverer version 2.5 (Thermo Scientific), and then submitted to the Uniprot human minimal database (20596 entries), using Mascot v. 2.2.07 (www.matrixscience.com) for protein identification. Mascot searches were done with 10 ppm and 0.02 Da deviation for precursor and fragment mass, respectively, and trypsin was specified as the enzyme. Methionine oxidation was set asa variable modification. Carbamidomethyl was set as a fixed modification on cysteines. The false discovery rate was set < 1%.ProteomicsPeter A. van VeelenHead Proteomics Group, Leiden University Medical Center, Center for Proteomics and Metabolomics, PO Box 9600, Postal zone P1-Q, 2300 RC Leiden, The NetherlandsPARTIALHomo Sapiens (human)41145815 Wang Q, Tjokrodirijo RTN, Mei H, van Veelen PA, Ten Dijke P, Fan C. circTGFBR2(3-6) acts as an assembly platform for RNA-binding protein IGF2BP3 and TGFBR1 mRNA to enhance breast cancer cell plasticity. Cell Death Differ. 2026 33(4):779-797 10.1038/s41418-025-01597-2r.t.n.tjokrodirijo@lumc.nlLeiden University Medical Center, Proteomics groupNetherlandsTransforming growth factor (TGF)-β signaling is a key driver to induce epithelial-to-mesenchymal transition (EMT), a process that enhances cancer cell plasticity and metastatic potential. However, the role of circular RNAs (circRNAs) in TGF-β signaling remains largely unexplored. Here, we identify circTGFBR2(3-6), a circRNA derived from TGF-β receptor 2 (TGFBR2) pre-mRNA, as a critical enhancer of TGF-β/SMAD signaling in breast cancer cells. Depletion of circTGFBR2(3-6) inhibits TGF-β-induced EMT, cell migration, and in vivo extravasation of breast cancer cells. Mechanistically, circTGFBR2(3-6) acts as a scaffold that facilitates the interaction between the RNA-binding protein insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) and TGF-β receptor 1 (TGFBR1) mRNA in an N⁶-methyladenosine (m⁶A)-dependent manner, and thereby stabilizes TGFBR1 mRNA and promotes its expression. Furthermore, IGF2BP3 knockdown reduces circTGFBR2(3-6)-mediated enhancement of TGF-β/SMAD signaling, as well as TGF-β-induced EMT and cell migration. Our findings identify circTGFBR2(3-6) as a novel potentiator of TGF-β/SMAD signaling at the receptor level and highlight IGF2BP3 as a critical m⁶A reader that mediates circTGFBR2(3-6)-driven breast cancer cell plasticity.circTGFBR2(3-6) acts as an assembly platform for RNA-binding protein IGF2BP3 and TGFBR1 mRNA to enhance breast cancer cell plasticity.Wang Qian Q, Tjokrodirijo Rayman T N RTN, Mei Hailiang H, van Veelen Peter A PA, Ten Dijke Peter P, Fan Chuannan CfalsecircTBRII(3-6) acts as assembly platform for IGF2BP3 protein and TBRI mRNA to enhance breast cancer cell plasticityTransforming growth factor (TGF)-β signaling is a key driver to induce epithelial-to-mesenchymal transition (EMT), a process that enhances cancer cell plasticity and metastatic potential. However, the role of circular RNAs (circRNAs) in TGF-β signaling remains largely unexplored. Here, we identify circTBRII(3-6), a circRNA derived from TGF-β type II receptor (TBRII) pre-mRNA, as a critical enhancer of TGF-β/SMAD signaling in breast cancer cells. Depletion of circTBRII(3-6) inhibits TGF-β-induced EMT, migration, and in vivo extravasation of breast cancer cells. Mechanistically, circTBRII(3-6) acts as a scaffold that facilitates the interaction between the RNA-binding protein insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) and TGF-β type I receptor (TBRI) mRNA in an N6-methyladenosine (m6A)-dependent manner, and thereby stabilizes TBRI and promotes its expression. Furthermore, IGF2BP3 knockdown reduces circTBRII(3-6)-mediated enhancement of TGF-β/SMAD signaling, as well as TGF-β-induced EMT and migration. Our findings identify circTBRII(3-6) as a novel enforcer of TGF-β/SMAD signaling at the receptor level and highlight IGF2BP3 as a critical m6A reader that mediates circTBRII(3-6)-driven breast cancer cell plasticity.2026-04-272025-02-26PXD061218NEWT:6945NEWT:184922NEWT:6703NEWT:3555NEWT:71647NEWT:2NEWT:157546NEWT:474186NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:1496NEWT:544496NEWT:2102NEWT:2042546NEWT:259447NEWT:45351NEWT:445974NEWT:43179NEWT:4513NEWT:180454NEWT:5722NEWT:1247NEWT:6938NEWT:1129NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:281395NEWT:10360NEWT:1211601NEWT:876138NEWT:47664NEWT:317548NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:272563NEWT:1147161NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:82688NEWT:95648NEWT:3885NEWT:3888NEWT:5821NEWT:1589NEWT:44139NEWT:135622NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:28909NEWT:515849NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:913645NEWT:1000589NEWT:85963NEWT:85962NEWT:143361NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4442NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NEWT:2164133NCBITaxon:183674NEWT:1316931NEWT:224308NEWT:167387NEWT:84645NEWT:44586NEWT:626528NEWT:3347NEWT:511145NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:431241NEWT:931281NEWT:4550NEWT:1000561NEWT:2133NEWT:294381NEWT:197NEWT:1390363NEWT:77133NEWT:288705NEWT:29176NEWT:145481NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:556182NEWT:1270NEWT:374990NEWT:1392NEWT:498217NEWT:156471NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:156476NEWT:286NEWT:391619NEWT:360104NEWT:246196NEWT:287NEWT:246197NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:161934NEWT:1148NEWT:580240NEWT:5508NEWT:294128NEWT:5507NEWT:11676NEWT:55571NEWT:35500NEWT:1140NEWT:100226NEWT:4530NEWT:1143NEWT:4896NEWT:75058NEWT:13616NEWT:1390NEWT:1094343NEWT:1336795NEWT:644042NEWT:296543NEWT:316435NEWT:42157NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:82380NEWT:1034304NEWT:105023NEWT:866628NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:375146NEWT:9378NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NEWT:8175NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:47946NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:1077286NEWT:243277NEWT:990119NEWT:7067NEWT:2850NEWT:1111708NEWT:408172NEWT:227321NEWT:408170NEWT:493760NEWT:106590NEWT:260710NEWT:257313NEWT:3827NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:930945NEWT:106592NEWT:536231NEWT:46704NEWT:1436733NEWT:460519NEWT:1187947NEWT:572307NEWT:1432138NEWT:269796NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:1194599NEWT:272844NEWT:54571NEWT:9598NEWT:8030NEWT:1513458NCBITaxon:40559NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:759272NEWT:432359NEWT:46835NEWT:1182263NEWT:109757NEWT:943146NEWT:2711NEWT:300852NEWT:537457NEWT:1502NEWT:376686NEWT:95486NEWT:9103NEWT:508771NEWT:1883446NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:29158NEWT:3635NEWT:5811NEWT:235443NEWT:180923NEWT:108458NEWT:272623NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:118499NEWT:169963NEWT:32644NEWT:527796NEWT:225117NEWT:746128NEWT:499175NEWT:109779NEWT:43665NEWT:1266464NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:649908NEWT:410289NEWT:373153NEWT:375451NEWT:352472NEWT:357NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:411469NEWT:84023NEWT:1679NEWT:559292NEWT:39491NCBITaxon:5811NEWT:29491NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:1328426NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NCBITaxon:138NEWT:40483NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:38293NEWT:1428NEWT:327159NEWT:178876NEWT:1660NEWT:327160NEWT:573NEWT:9031NEWT:1872122NEWT:7091NEWT:108931NEWT:241368NEWT:1055524NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:7237NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:187878NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1821314NEWT:1249668NEWT:7108NEWT:40479NEWT:317NEWT:5286NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:9644NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:273068NEWT:554NEWT:27592NEWT:98334NEWT:426428NEWT:451516NEWT:63459NEWT:36185NEWT:588858NEWT:1225786NEWT:9639NCBITaxon:11071NEWT:242231NEWT:7574NEWT:1715256NEWT:197221NEWT:7215NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:2172103NEWT:6494NEWT:7460NEWT:6491NEWT:507601NEWT:434271NEWT:643680NCBITaxon:6157NEWT:42752NEWT:746360NEWT:6239NEWT:89764NEWT:470150NEWT:162425NEWT:216257NEWT:102169NEWT:543734NEWT:9986NEWT:4054NEWT:73239NEWT:38018NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:118503NEWT:2059687NEWT:115357NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NEWT:13164NEWT:216129NCBITaxon:2NEWT:985076NEWT:1215323NEWT:2664179NEWT:986NEWT:52641NEWT:7038NEWT:7159NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:27448NEWT:366581NEWT:216599NEWT:216595NEWT:1194669NEWT:40559NEWT:243230NEWT:8355NEWT:633NEWT:9685NEWT:7029NEWT:1080772NEWT:8479NEWT:1283300NEWT:186990NEWT:632NEWT:6183NEWT:6063NEWT:630NEWT:49240NEWT:334747NEWT:61235NEWT:343691NEWT:15368NEWT:6289NEWT:1491466NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:469008NEWT:260707NEWT:256318NEWT:206411NCBITaxon:6191NEWT:596153NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:1719NEWT:703612NEWT:260705NEWT:80863NEWT:692672NEWT:2697049NEWT:105231NEWT:1216981NEWT:52638NEWT:7004NEWT:4097NCBITaxon:6073NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:1329349NEWT:7370NEWT:83906NEWT:607699NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:208963NEWT:208964NEWT:27337NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:9935NEWT:89453NEWT:4120NEWT:51515NEWT:5693NEWT:2186NEWT:8724NEWT:51511NEWT:8845NEWT:92867NEWT:8723NEWT:92866NEWT:5334NEWT:37334NEWT:51750NEWT:382352NEWT:413071NCBITaxon:10359NEWT:1203258NEWT:242619NEWT:160791NEWT:632957NEWT:34073NEWT:373995NEWT:544404NEWT:9925NEWT:89462NEWT:8839NEWT:4232NEWT:2758385NEWT:37349NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:36015NEWT:421932NEWT:312017NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:375939NEWT:61674NEWT:870435NEWT:1117957NEWT:6526NEWT:9913NEWT:8709NEWT:105841NEWT:337330NEWT:4100NEWT:2666255NEWT:1159556NEWT:5671NEWT:2285NEWT:1076NEWT:4101NEWT:6763NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:1486917NEWT:981087NEWT:180066NEWT:226900NEWT:468911NEWT:7604NEWT:818NEWT:135588NEWT:1843183NEWT:5661NEWT:29719NEWT:58002NEWT:326423NEWT:452467NEWT:36111NEWT:326424NEWT:6997NEWT:452589NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:1678078NEWT:749906NEWT:418985NEWT:146479NEWT:749907NEWT:1042986NEWT:1911079NEWT:69373NEWT:145263NEWT:264203NEWT:1480154NEWT:694569NEWT:1274414NEWT:27606NEWT:9739NEWT:59202NEWT:9975NEWT:9612NEWT:38626NEWT:38865NEWT:51953NEWT:3077NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:112273NEWT:36329NEWT:1147787NEWT:62615NCBITaxon:3044782NEWT:1440772NEWT:72407NEWT:1355477NEWT:349741NEWT:9605NEWT:9606NEWT:90371NEWT:157295NEWT:641501NEWT:4153NEWT:2096NEWT:7668NEWT:915099NEWT:74940NEWT:13551NEWT:9721NEWT:137221NEWT:9600NEWT:9963NEWT:1450511NEWT:1143193NEWT:1617910NEWT:174934NEWT:565050NEWT:2823525NEWT:2785785NEWT:411901NEWT:9838NEWT:105884NCBITaxon:9615NEWT:9839NEWT:58334NEWT:1193501NEWT:3055NEWT:58331NEWT:4146NEWT:5478NEWT:6326NEWT:6689NEWT:5476NEWT:1450520NEWT:1042311NEWT:299767NEWT:28835NEWT:1274432NEWT:2053667NEWT:1274426NEWT:70448NEWT:9825NEWT:1274423NEWT:393765NEWT:698936NEWT:39946NEWT:9823NEWT:9940NEWT:95602NEWT:8732NEWT:521001NEWT:192011NEWT:1813887NEWT:39947NEWT:224911NEWT:1274420NEWT:57845841145815