ena-STUDY-Institute of Bioinformatics-20-03-2015-16:19:49:650-583
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 particular in oncofusion gene driven tumors. Genetically, Ewing sarcoma (ES) 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. 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 tumor/normal pairs identified 232 somatic mutations. Recurrent non-synonymous muta- tions were validated in the 36 remaining exomes. Transcriptome analysis was performed 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 activ- ity. Conclusions: FGFR1 may constitute a promising target for novel therapeutic approaches in ES.  A manuscript is submitted to Clinical Cancer Research.  The data associated with this submission (2 Ewing patients; patient 1 (male) with normal tissue, relapse 1 and 2 (in time) and patient 2 (female) with normal tissue, primary tumor, relapse 1 and 2, in total 7 experiments; sample assignment: see samples; more details see publication) belongs to the whole genome sequencing approach (coverage app. 80 fold) and was processed by Complete Genomics in mid 2013 until the beginning of 2014. The included downstream results are calculated by Complete Genomics utilizing the normal tissue as a baseline.
Purpose: A low mutation rate seems a general feature of pediatric cancers, in particular in oncofusion gene driven tumors. Genetically, Ewing sarcoma (ES) 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. 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 tumor/normal pairs identified 232 somatic mutations. Recurrent non-synonymous muta- tions were validated in the 36 remaining exomes. Transcriptome analysis was performed 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 activ- ity. Conclusions: FGFR1 may constitute a promising target for novel therapeutic approaches in ES.  A manuscript is submitted to Clinical Cancer Research.  The data associated with this submission (2 Ewing patients; patient 1 (male) with normal tissue, relapse 1 and 2 (in time) and patient 2 (female) with normal tissue, primary tumor, relapse 1 and 2, in total 7 experiments; sample assignment: see samples; more details see publication) belongs to the whole genome sequencing approach (coverage app. 80 fold) and was processed by Complete Genomics in mid 2013 until the beginning of 2014. The included downstream results are calculated by Complete Genomics utilizing the normal tissue as a baseline.