The N-Myc-responsive lncRNA MILIP promotes DNA double-strand break repair through non-homologous end joining

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 119; no. 49; p. e2208904119
• Main Authors: Wang, Pei Lin, Teng, Liu, Feng, Yu Chen, Yue, Yi Meng, Han, Man Man, Yan, Qianqian, Ye, Kaihong, Tang, Cai Xia, Zhang, Sheng Nan, Fei Qi, Teng, Zhao, Xiao Hong, La, Ting, Zhang, Yuan Yuan, Li, Jin Ming, Hu, Bin, Xu, Dengfei, Cang, Shundong, Wang, Li, Jin, Lei, Thorne, Rick F, Zhang, Yuwei, Liu, Tao, Zhang, Xu Dong
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 06.12.2022
• Subjects: Apoptosis; Biological Sciences; Cell proliferation; Cell viability; Cisplatin; Damage accumulation; Deoxyribonucleic acid; DNA; DNA - genetics; DNA Breaks, Double-Stranded; DNA damage; DNA End-Joining Repair - genetics; DNA repair; DNA Repair - genetics; Double-strand break repair; Gene amplification; Humans; Myc protein; MYCN gene; Neuroblastoma; Neuroblastoma - drug therapy; Neuroblastoma - genetics; Neuroblastoma cells; Non-homologous end joining; RNA, Long Noncoding - genetics; Xenografts; Xenotransplantation; N-Myc; neuroblastoma; MYCN; lncRNA; DNA repair
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.2208904119

The protooncoprotein N-Myc, which is overexpressed in approximately 25% of neuroblastomas as the consequence of gene amplification, has long been postulated to regulate DNA double-strand break (DSB) repair in neuroblastoma cells, but experimental evidence of this function is presently scant. Here, we show that N-Myc transcriptionally activates the long noncoding RNA MILIP to promote nonhomologous end-joining (NHEJ) DNA repair through facilitating Ku70-Ku80 heterodimerization in neuroblastoma cells. High MILIP expression was associated with poor outcome and appeared as an independent prognostic factor in neuroblastoma patients. Knockdown of MILIP reduced neuroblastoma cell viability through the induction of apoptosis and inhibition of proliferation, retarded neuroblastoma xenograft growth, and sensitized neuroblastoma cells to DNA-damaging therapeutics. The effect of MILIP knockdown was associated with the accumulation of DNA DSBs in neuroblastoma cells largely due to decreased activity of the NHEJ DNA repair pathway. Mechanistical investigations revealed that binding of MILIP to Ku70 and Ku80 increased their heterodimerization, and this was required for MILIP-mediated promotion of NHEJ DNA repair. Disrupting the interaction between MILIP and Ku70 or Ku80 increased DNA DSBs and reduced cell viability with therapeutic potential revealed where targeting MILIP using Gapmers cooperated with the DNA-damaging drug cisplatin to inhibit neuroblastoma growth in vivo. Collectively, our findings identify MILIP as an N-Myc downstream effector critical for activation of the NHEJ DNA repair pathway in neuroblastoma cells, with practical implications of MILIP targeting, alone and in combination with DNA-damaging therapeutics, for neuroblastoma treatment.