Abstract PR06: TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

Abstract

Abstract Recently, we have presented the genomic landscape of 87 neuroblastoma tumors. This cohort has been extended to include 108 tumor/normal pairs of all INSS stages. As recurrent somatic mutations are rare in this cancer and enhancer hijacking has been demonstrated in medulloblastoma, we hypothesized that recurrent structural variations, possibly intergenic, could be identified in our neuroblastoma cohort. Methods: Whole genome sequencing was performed on a total of 108 tumor/lymphocyte DNA samples using Complete Genomics technology. Somatic structural variations were identified and analyzed for recurrent locations. Sequence coverage based CGH break analyses, mRNA expression analyses, telomere length analyses as well as super-enhancer proximity analyses were performed. Results: For each 1 Mb region in the genome, we calculated the number of tumors with one or more structural events. The second-most frequently affected region after MYCN was located on chromosome 5 where breakpoints centered round the TERT locus in 17/75 of the high stage tumors (23%). TERT was the only gene in the vicinity with a significantly increased expression in the rearranged cases as compared to the normal cases (p=8.51x10-5, Wilcoxon Ranksum test). Most of the TERT rearrangements occurred in a region 6-30 kb upstream of the gene. 12 of the rearrangements were resolved by paired-end analysis. We identified neuroblastoma-specific super-enhancers in seven of the translocation partners, which is a significant enrichment compared to randomly generated breaks (p<0.003). Telomere restriction fragment analysis showed increased telomere lengths for rearranged cases, confirming increased telomere repeat counts in the corresponding sequence data. TERT rearrangements were significantly associated with poor prognosis (p=0.04 Logrank test) and almost mutually exclusive with MYCN amplification and ATRX defects. In a multivariate Cox regression analysis all 3 showed independent significance. Kaplan Meier analysis showed that each of the MYCN, TERT and ATRX groups had a significantly poorer outcome than the remaining tumors. Conclusions: We conclude that TERT rearrangements form the second-most frequent gene defect in neuroblastoma, after MYCN. TERT defects are almost mutually exclusive with ATRX and MYCN defects, and each of them identify a separate group of neuroblastoma at very high risk. These tumors have elevated TERT expression due to rearrangement of the upstream 30 kb or downstream 40 kb regions and in over half of the informative breakpoints, TERT was ostensibly activated by hijacking a super-enhancer. Pharmacological inhibition of TERT might in future improve the outcome for this patient group. This abstract is also presented as Poster A40. Citation Format: Jan Koster, Linda J. Valentijn, Danny A. Zwijnenburg, Nancy E. Hasselt, Peter G. van Sluis, Max M. van Noesel, Rani E. George, Godelieve A. Tytgat, Jan J. Molenaar, Rogier Versteeg. TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr PR06.