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

Abstract

PURPOSE: 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. EXPER-IMENTAL DESIGN: 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. 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 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. CONCLUSIONS: FGFR1 may constitute a promising target for novel therapeutic approaches in Ewing sarcoma.

Identification of a Novel SYK/c-MYC/MALAT1 Signaling Pathway and Its Potential Therapeutic Value in Ewing Sarcoma

“…Although several potential molecular targets have been identified in Ewing sarcoma, their clinical trials aimed at these targets have yet to show success (53). Through high-throughput screens using both siRNA and small-molecule inhibitor libraries, we confirmed a number of previously reported Ewing sarcoma actionable candidates such as ERBB4, EGFR, ROR1, KIT, and FGFRs (9,(30)(31)(32)(33)(34)(35)(36)(37). Most importantly, we identified SYK as an important progrowth kinase in Ewing sarcoma through unbiased integrative approaches.…”

“…As shown in Fig. 1A, the top 20 genes ranked by median inhibition rate values (MV) included a number of known oncogenic kinases in Ewing sarcoma, such as ROR1, KIT, FGFR, PTK families (PTK-2 and 7), Src families (FGR and SRMS), ERBB4, and EGFR (9,(30)(31)(32)(33)(34)(35)(36)(37), which strongly supported the methodology and effectiveness of our high-throughput screen. Importantly, we identified novel targets including SYK and related proteins (SYK and ZAP70), BTK, ABL1, FLT4, and MATK.…”

Transgenic antigen-specific, HLA-A*02:01-allo-restricted cytotoxic T cells recognize tumor-associated target antigen STEAP1 with high specificity

“…[25][26][27][28] However, the addition of adjunctive, immune-activating therapies during first remission demonstrated the potential to reduce recurrence rates and exploit immunotherapy approaches for ES patients. 29 Balanced chromosomal EWS/ETS translocations that give rise to oncogenic chimeric proteins (EWS-ETS), the most common being EWS-FLI1 as a consequence of the t(11;22)(q24; q12) translocation, 30,31 are the characteristic driver event of ES tumorgenesis.…”

Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets

“…ATP1A1 is required for unconventional secretion of FGF 54 , BCL11B promotes FGF-signaling by transcriptional suppression of a negative feedback inhibitor 44,55 , and GLG1 (alias cysteine-rich FGF receptor) is known to regulate intracellular levels of FGF 56 . Several studies have shown that FGF promotes EWSR1-FLI1 expression 57 and growth of Ewing sarcoma cells in vitro and in vivo 46,55 , and that FGF-inhibitors could be used as a targeted treatment for Ewing sarcoma patients 58 . Although more work needs to be done to elucidate the precise role of ATP1A1, BCL11B, and GLG1 in FGF-signaling, it is tempting to speculate that they could serve as predictive biomarkers for the efficacy of FGF-inhibitors.…”