Deep Sequencing in Conjunction with Expression and Functional Analyses Reveals Activation of FGFR1 in Ewing Sarcoma

• Published in: Clinical cancer research 2015-11, Vol.21 (21), p.4935-4946
• Main Authors: Agelopoulos, Konstantin, Richter, Günther H S, Schmidt, Eva, Dirksen, Uta, von Heyking, Kristina, Moser, Benjamin, Klein, Hans-Ulrich, Kontny, Udo, Dugas, Martin, Poos, Kathrin, Korsching, Eberhard, Buch, Thorsten, Weckesser, Matthias, Schulze, Isabell, Besoke, Regina, Witten, Anika, Stoll, Monika, Köhler, Gabriele, Hartmann, Wolfgang, Wardelmann, Eva, Rossig, Claudia, Baumhoer, Daniel, Jürgens, Heribert, Burdach, Stefan, Berdel, Wolfgang E, Müller-Tidow, Carsten
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Animals; Cell Line, Tumor; Child; Disease Models, Animal; DNA Copy Number Variations; Female; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene Frequency; High-Throughput Nucleotide Sequencing; Humans; Male; Mice, Knockout; Mutation; Neoplasm Recurrence, Local; Neoplasm Staging; Receptor, Fibroblast Growth Factor, Type 1 - genetics; Receptor, Fibroblast Growth Factor, Type 1 - metabolism; Sarcoma, Ewing - genetics; Sarcoma, Ewing - metabolism; Sarcoma, Ewing - pathology; Signal Transduction; Young Adult
• ISSN: 1078-0432; 1557-3265
• DOI: 10.1158/1078-0432.CCR-14-2744

A low mutation rate seems to be a general feature of pediatric cancers, in particular in oncofusion gene-driven tumors. Genetically, Ewing sarcoma is defined by balanced chromosomal EWS/ETS translocations, which give rise to oncogenic chimeric proteins (EWS-ETS). Other contributing somatic mutations involved in disease development have only been observed at low frequency. Tumor samples of 116 Ewing sarcoma patients were analyzed here. Whole-genome sequencing was performed on two patients with normal, primary, and relapsed tissue. Whole-exome sequencing was performed on 50 Ewing sarcoma and 22 matched normal tissues. A discovery dataset of 14 of these tumor/normal pairs identified 232 somatic mutations. Recurrent nonsynonymous mutations were validated in the 36 remaining exomes. Transcriptome analysis was performed in a subset of 14 of 50 Ewing sarcomas and DNA copy number gain and expression of FGFR1 in 63 of 116 Ewing sarcomas. Relapsed tumors consistently showed a 2- to 3-fold increased number of mutations. We identified several recurrently mutated genes at low frequency (ANKRD30A, CCDC19, KIAA0319, KIAA1522, LAMB4, SLFN11, STAG2, TP53, UNC80, ZNF98). An oncogenic fibroblast growth factor receptor 1 (FGFR1) mutation (N546K) was detected, and the FGFR1 locus frequently showed copy number gain (31.7%) in primary tumors. Furthermore, high-level FGFR1 expression was noted as a characteristic feature of Ewing sarcoma. RNA interference of FGFR1 expression in Ewing sarcoma lines blocked proliferation and completely suppressed xenograft tumor growth. FGFR1 tyrosine kinase inhibitor (TKI) therapy in a patient with Ewing sarcoma relapse significantly reduced 18-FDG-PET activity. FGFR1 may constitute a promising target for novel therapeutic approaches in Ewing sarcoma.