Phase separation-based screening identifies arsenic trioxide as the N-Myc-DNA interaction inhibitor for neuroblastoma therapy

Transcription factors (TFs) like N-Myc are crucial in disease including cancer. MYCN amplification is a pivotal biomarker for stratifying high-risk neuroblastoma patients. The difficulty in targeting N-Myc poses a significant challenge for treating high-risk neuroblastoma. Since transcription factors activate transcription by binding to DNA, inhibiting this DNA-binding could disrupt their function and offer a therapeutic approach. Herein, we develop a high-throughput in vivo model to screen for inhibitors of protein-DNA interaction (PDI), utilizing phase separation and DNA-binding properties. Base on this, we identify arsenic trioxide (ATO) as the first N-Myc-DNA interaction inhibitor. ATO directly binds to N-Myc to disrupt its interaction with DNA, thereby destroying its transcriptional activity and reducing the expression of its target genes. Consistently, ATO significantly inhibits the cell proliferation and clone formation ability of MYCN-amplified neuroblastoma cells. More importantly, we used 5 patient-derived neuroblastoma cells to evaluate the therapy clinical value of ATO. Finally, we found ATO synergizes with the chemotherapy drug cisplatin in treating neuroblastoma in vitro and in vivo. Together, we not only construct a PDI inhibitor screening model for transcriptional factor and uncover ATO as the first DNA binding inhibitor of N-Myc, but also identify ATO as a promising therapeutic regimen for MYCN-amplified neuroblastoma, especially in refractory patients. Overall design: SK-N-Be(2) cells treated with ATO (2, 4 µM) for 12 h.