In silico validation of RNA-Seq results can identify gene fusions with oncogenic potential in glioblastoma

Autor: Hernández, Ainhoa, Muñoz-Mármol, Ana Maria, Esteve-Codina, Anna, Alameda, Francesc, Carrato, Cristina, Pineda, Estela, Arpí Lluciá, Oriol, Martinez-García, Maria, Mallo, Maria del Mar, Gut, Marta, Del Barco Berrón, Sonia, Gallego Rubio, Oscar, Dabad, Marc, Mesia, Carlos, Bellosillo Paricio, Beatriz, Domènech Viñolas, Marta, Vidal, Noemí, Aldecoa, Iban, de la Iglesia, Nuria, Balañá, Carmen, Universitat Autònoma de Barcelona
Rok vydání: 2022
Předmět:
Zdroj: Dipòsit Digital de la UB
Universidad de Barcelona
Scientific Reports
r-IGTP. Repositorio Institucional de Producción Científica del Instituto de Investigación Germans Trias i Pujol
instname
r-IIB SANT PAU. Repositorio Institucional de Producción Científica del Instituto de Investigación Biomédica Sant Pau
ISSN: 2045-2322
DOI: 10.1038/s41598-022-18608-8
Popis: RNA-Sequencing (RNA-Seq) can identify gene fusions in tumors, but not all these fusions have functional consequences. Using multiple data bases, we have performed an in silico analysis of fusions detected by RNA-Seq in tumor samples from 139 newly diagnosed glioblastoma patients to identify in-frame fusions with predictable oncogenic potential. Among 61 samples with fusions, there were 103 different fusions, involving 167 different genes, including 20 known oncogenes or tumor suppressor genes (TSGs), 16 associated with cancer but not oncogenes or TSGs, and 32 not associated with cancer but previously shown to be involved in fusions in gliomas. After selecting in-frame fusions able to produce a protein product and running Oncofuse, we identified 30 fusions with predictable oncogenic potential and classified them into four non-overlapping categories: six previously described in cancer; six involving an oncogene or TSG; four predicted by Oncofuse to have oncogenic potential; and 14 other in-frame fusions. Only 24 patients harbored one or more of these 30 fusions, and only two fusions were present in more than one patient: FGFR3::TACC3 and EGFR::SEPTIN14. This in silico study provides a good starting point for the identification of gene fusions with functional consequences in the pathogenesis or treatment of glioblastoma.
Databáze: OpenAIRE
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