(GGAA)₃-Based TF-PROTACs Enable Targeted Degradation of ETV6 to Inhibit Ewing Sarcoma Growth

Ewing sarcoma is a rare pediatric cancer primarily driven by the EWS::FLI1 oncofusion transcription factor. Despite being an ideal drug target, EWS::FLI1 has proven challenging to inhibit with conventional approaches. Recent studies identified ETV6 as a vulnerability in Ewing sarcoma, where it competes with EWS::FLI1 at short GGAA repeats to restrain EWS::FLI1 function. However, no therapies targeting ETV6 have been developed. In this study, we report the discovery of a unique (GGAA)₃ DNA oligonucleotide that specifically binds to ETV6 but not EWS::FLI1. We developed (GGAA)₃-based TF-PROTACs, termed d(GGAA)₃s, by coupling (GGAA)₃ with VHL ligands. d(GGAA)₃s effectively degraded endogenous ETV6 but not EWS::FLI1 proteins in Ewing sarcoma cells, thus suppressing Ewing sarcoma growth. Mechanistically, d(GGAA)₃s enhanced oncogenic EWS::FLI1 transcriptional activity, inducing cellular stress and cell death. Additionally, d(GGAA)₃s sensitized Ewing sarcoma cells to standard chemotherapy, suggesting their potential use in combination therapies. Beyond Ewing sarcoma, d(GGAA)₃s also targeted ETV6-fusion proteins found in breast cancer, broadening their potential clinical applications. In summary, d(GGAA)₃s represent a nucleotide-based approach for degrading ETV6, inhibiting Ewing sarcoma growth and targeting ETV6-dependent cancers. This strategy offers a promising therapeutic avenue for Ewing sarcoma and other malignancies involving ETV6 fusions.