3. Complex and cryptic EWSR1-FLI1 gene fusions and 1q jumping translocation in pediatric Ewing sarcomas

Ewing sarcomas are the second most frequent bone tumor of childhood that can also occur in soft tissue. They are highly aggressive with a survival of 30% for those with metastatic disease. They are genetically characterized by balanced reciprocal chromosomal translocations in which a member of the FET gene family is fused with an ETS transcription factor, with the most common translocation being the t(11;22)(q24;q12). The t(11;22) reciprocal translocation fuses the N-terminal transactivation domain of the Ewing sarcoma breakpoint region 1 protein (EWSR1) with the C-terminal DNA binding domain of the Friend leukemia integration 1 transcription factor (FLI1). The EWSR1-FLI1 fusion occurs in ∼90% of Ewing sarcoma cases and is a tumor-specific chimeric transcription factor that massively revamps the transcriptome. Therefore, the detection of EWSR1-FLI1 fusions is of important diagnostic value. Here, we present two pediatric Ewing sarcomas with atypical EWSR1-FLI1 fusions. The first case had a complex t(9;11;22)(q22;q24;q12) three-way translocation and a 1q jumping translocation by chromosome analysis. EWSR1 rearrangements using a EWSR1 break-apart FISH probe set revealed 5’ EWSR1 on der(22)(q12) and 3’ EWSR1 on der(9)(q22). Metaphase FISH using dual-color dual-fusion EWSR1-FLI1 FISH probe set revealed a EWSR1-FLI1 fusion at the derivative chromosome 22 involving the three-way translocation. 1q amplification by jumping translocations were confirmed by SNP microarray. The second case had a t(4;22)(q35;q12) reciprocal translocation and tetrasomy 8 by chromosome analysis. EWSR1 rearrangements using a EWSR1 break-apart FISH probe set revealed 5’ EWSR1 on der(22)(q12) and 3’ EWSR1 on der(4)(q35). Metaphase FISH using dual-color dual-fusion EWSR1-FLI1 FISH probe set revealed a EWSR1-FLI1 fusion at the derivative chromosome 22 involving the 4;22 translocation. Both cases had EWSR1-FLI1 gene fusions detected by Nanostring gene fusion panel. Recognizing complex and cryptic EWSR1-FLI1 gene fusions using various diagnostic methods is important for diagnosis, prognosis, and treatment outcome of pediatric Ewing sarcomas.