{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:49:13Z","timestamp":1787028553352,"version":"build-2736575974"},"reference-count":57,"publisher":"MDPI AG","issue":"22","license":[{"start":{"date-parts":[[2024,11,12]],"date-time":"2024-11-12T00:00:00Z","timestamp":1731369600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["22-15-00487"],"award-info":[{"award-number":["22-15-00487"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Targeted treatment of advanced or metastatic urothelial carcinomas (UCs) requires the identification of druggable mutations. This study describes the development of a 3\u2032 Rapid Amplification of cDNA Ends (3\u2032 RACE)-based targeted RNA sequencing panel which accounts for the status of all genes relevant to UC treatment, namely, FGFR1-4, KRAS, NRAS, BRAF, ERBB2 (HER2), CD274 (PD-L1) and PIK3CA. FGFR2\/3-activating point mutations or fusions were found in 54\/233 (23.2%) tumors. FGFR3 rearrangements were identified in 11 patients, with eight of them being undetectable by commonly used PCR kits. In addition, one tumor contained a high-copy FGFR2 gene amplification accompanied by strong overexpression of the gene. Mutations in RAS\/RAF genes were present in 30\/233 (12.9%) UCs and were mutually exclusive with alterations affecting FGFR2\/3 genes. On the contrary, activating events in the HER2 oncogene (point mutations and overexpression), as well as PIK3CA mutations, which were relatively common, occurred with similar frequencies in RAS\/RAF- or FGFR2\/3-positive vs. negative samples. High PD-L1 mRNA expression was associated with advanced disease stage and was not observed in tumors with increased HER2 mRNA expression or in UCs with evidence for FGFR2\/3 activation. Three of the studied carcinomas had high-level microsatellite instability (MSI). Overall, more than half of the UCs had potentially druggable genetic alterations. The proposed NGS panel permits comprehensive and cost-efficient analysis of UC-specific molecular targets and may be considered in clinical routine.<\/jats:p>","DOI":"10.3390\/ijms252212126","type":"journal-article","created":{"date-parts":[[2024,11,12]],"date-time":"2024-11-12T05:21:59Z","timestamp":1731388919000},"page":"12126","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Use of 3\u2032 Rapid Amplification of cDNA Ends (3\u2032 RACE)-Based Targeted RNA Sequencing for Profiling of Druggable Genetic Alterations in Urothelial Carcinomas"],"prefix":"10.3390","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0179-3191","authenticated-orcid":false,"given":"Natalia V.","family":"Mitiushkina","sequence":"first","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0157-5952","authenticated-orcid":false,"given":"Vladislav I.","family":"Tiurin","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksandra A.","family":"Anuskina","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5583-4221","authenticated-orcid":false,"given":"Natalia A.","family":"Bordovskaya","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. 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Petrov Institute of Oncology, 197758 St. Petersburg, Russia"},{"name":"Department of Medical Genetics, St. Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandr V.","family":"Togo","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia"},{"name":"Department of Medical Genetics, St. Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4529-7891","authenticated-orcid":false,"given":"Evgeny N.","family":"Imyanitov","sequence":"additional","affiliation":[{"name":"Department of Tumor Growth Biology, N.N. 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