Targeting transcription-replication conflicts is an effective therapeutic principle for MYCN-driven neuroblastoma [ChIPseq_IMR5]

Targeting the function of MYC proteins for therapy is a major challenge in tumor biology. MYC proteins are transcription factors that can globally release RNA polymerase II (RNAPII) from core promoters. In neuroblastoma, the MYC paralogue, MYCN, and the Aurora-A kinase form a complex during S phase that stabilizes MYCN and enhances Aurora-A kinase activity. Here we show that Aurora-A phosphorylates histone H3 at serine 10 in S phase and suppresses transcription-dependent R-loop formation. Inhibition of Aurora-A causes global stalling of RNAPII at pause sites and exon/intron boundaries and induces transcription/replication conflicts, activating the Ataxia telangiectasia and Rad3 related (ATR) kinase. Activation of ATR is required to prevent the accumulation of double-strand breaks. In genetically-engineered mice with MYCN-driven neuroblastoma, combined inhibition of Aurora-A and ATR induces rampant tumor-specific apoptosis and tumor regression, leading to permanent eradication of tumors in a subset of mice. The therapeutic efficacy is not only due to tumor cell-intrinsic mechanisms, but also engages the host immune system for tumor eradication. Since stabilization of MYCN promotes promoter-proximal transcription termination, we propose that MYCN/Aurora-A complex formation enables tumor cells to prevent transcription-replication conflicts and that targeting this mechanism is an effective therapy for MYCN-driven neuroblastoma. Overall design: S phase synchronized IMR-5 cells treated for 4 h with 1 µM MLN8237 or DMSO; ChIP-Sequencing of H3.3 A combined Input.fastq file was generated by merging the files IR180_Input_DMSO.fastq & IR180_Input_MLN.fastq. The file 'Input.fastq' was then randomly subsampled to 15603418 reads, resulting in the file Input_sorted15603418.bedgraph, which was used as input control for the H3.3-ChIPseq samples.