Prospective Clinical Genomic Profiling of Ewing Sarcoma: <i>ERF</i> and <i>FGFR1</i> Mutations as Recurrent Secondary Alterations of Potential Biologic and Therapeutic Relevance.

Abstract

Ewing sarcoma (ES) is a primitive sarcoma defined by EWSR1-ETS fusions as the primary driver alteration. To better define the landscape of cooperating secondary genetic alterations in ES, we analyzed clinical genomic profiling data of 113 patients with ES, a cohort including more adult patients (> 18 years) and more patients with advanced stage at presentation than previous genomic cohorts. The data set consisted of patients with ES prospectively tested with the US Food and Drug Administration-cleared Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets large panel, hybrid capture-based next-generation sequencing assay. To assess the functional significance of <i>ERF</i> loss, we generated ES cell lines with increased expression of <i>ERF</i> and lines with knockdown of <i>ERF</i>. We assessed cell viability, clonogenic growth, and motility in these ES lines and performed transcriptomic and epigenetic analyses. Finally, we validated our findings in vivo using cell line xenografts. Novel subsets were defined by recurrent secondary alterations in <i>ERF</i>, which encodes an ETS domain transcriptional repressor, in 7% of patients (five truncating mutations, one deep deletion, and two missense mutations) and in <i>FGFR1</i> in another 2.7% (one amplification and two known activating mutations). <i>ERF</i> alterations were nonoverlapping with <i>STAG2</i> alterations. <i>In vitro</i>, increased expression of <i>ERF</i> decreased tumor cell growth, colony formation, and motility in two ES cell lines, whereas <i>ERF</i> loss induced cellular proliferation and clonogenic growth. Transcriptomic analysis of cell lines with <i>ERF</i> loss revealed an increased expression of genes and pathways associated with aggressive tumor biology, and epigenetic, chromatin-based studies revealed that <i>ERF</i> competes with <i>EWSR1-FLI1</i> at ETS-binding sites. Our findings open avenues to new insights into ES pathobiology and to novel therapeutic approaches in a subset of patients with ES.