The genomic breakpoint and chimeric transcripts in the EWSR1-ETV4/E1AF gene fusion in Ewing sarcoma

Chromosome translocation creates a fusion between the EWSR1 gene and an ETS family gene. The fusion between these two genes is a characteristic featur e of Ewing sarcoma. We previously identified a fourth translocation, t(17;2 2)(q12;q12), in genomic DNA isolated from cells of patients affected with E wing sarcoma. The discovery of this translocation suggested that there migh t be a novel EWSR1-ETV4 fusion gene. In the present study, we determined th e genomic breakpoint and characterized the chimeric transcript of the EWSR1 -ETV4 fusion gene in two t(17;22) Ewing sarcomas. Reverse transcriptase-PCR assay showed an in-frame fusion between the 5'-terminal region of EWSR1 an d the 3' end of ETV4 (alias E1AF, PEA3); the chimeric transcript could thus serve as a template for expression of a protein composed of the N-terminal portion of EWSR1 fused to the DNA-binding domain of ETV4. Long PCR and seq uence analysis of genomic DNA revealed that either exon 8 or intron 7 of EW SR 1 is fused to the same intron of ETV4 in both tumors. Several palindromi c oligomer sequences were found close to the breakpoints in both genes. The 159-bp Alu-like sequence was repealed in the breakpoint region of the ETV4 gene. These observations suggest a mechanism of EWSR1-ETV4 gene fusion.