ATR Inhibition Synergizes With Alkylating PI Polyamide Targeting MYCN by Suppressing DNA Repair in MYCN-Amplified Neuroblastoma

Abstract

Amplification of MYCN is a major oncogenic driver of high-risk neuroblastomas. We previously developed CCC-002, a MYCN-selective pyrrole-imidazole polyamide conjugated to a DNA alkylating agent. Administration of CCC-002 to MYCN-amplified (MYCN-amp) neuroblastoma cells triggered the activation of DNA damage responses. Here, we demonstrated that among the DNA damage response inhibitors, ataxia telangiectasia and Rad3-related (ATR) inhibitors synergized with CCC-002 to suppress DNA repair-related genes and induce apoptosis in MYCN-amp neuroblastoma cells. A synergistic antitumor effect was verified in an SK-N-BE(2) xenograft mouse model, in which the combined use of CCC-002 and ATR inhibitor at low doses significantly inhibited tumor progression. Notably, SK-N-BE(2) and SK-N-DZ cells, which showed ATM activation after CCC-002 treatment, exhibited high sensitivity to the combined treatment of ATR inhibitors. Comprehensive analysis of the gene expression profiles revealed that the combination treatment upregulated apoptosis-related pathways and downregulated DNA repair-related pathways. After the combined treatment of CCC-002 and ATR inhibitor, MYCN-amp cells showed less FISH probe signal and mRNA expression of MYCN, which was accompanied by an increase in DNA damage markers in the genomic region of MYCN, highlighting that ATR inhibitors synergize with CCC-002 and play a crucial role in the development of a novel MYCN-targeting therapy for MYCN-amp neuroblastoma.