Deep sequencing in conjunction with expression and functional analyses reveals activation of FGFR1 in Ewing sarcoma.

Purpose: A low mutation rate seems a general feature of pediatric cancers, in par-ticular in oncofusion gene driven tumors. Genetically, Ewing sarcoma (ES) is de-fined by balanced chromosomal EWS/ETS translocations, which give rise to onco-genic chimeric proteins (EWS-ETS). Other contributing somatic mutations involved in disease development have only been observed at low frequency. Experimental design: Tumor samples of 116 Ewing sarcoma (ES) 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 ES and 22 matched normal tissues. A discovery data set of 14 of these tu-mor/normal pairs identified 232 somatic mutations. Recurrent non-synonymous mu-tations were validated in the 36 remaining exomes. Transcriptome analysis was per-formed in a subset of 14/50 ES and DNA copy number gain and expression of FGFR1 in 63/116 ES. Results: 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 ES. RNA-Interference of FGFR1 expression in ES lines blocked proliferation and completely suppressed xenograft tumor growth. FGFR1 TKI inhibitor therapy in a patient with ES relapse significantly reduced 18-FDG-PET activity. Conclusions: FGFR1 may constitute a promising target for novel therapeutic ap-proaches in ES.