Abstract 1181: Structure and evolution of double minutes in a pediatric high-grade glioma

Abstract

Abstract Double minutes (DMs) are circular extrachromosomal DNA frequently found in brain tumors, often associated with overexpression of oncogenes. To understand the evolution of DMs, we developed a graph-based method to identify simple cycles in a directed graph consisting of highly amplified copy number alteration (CNA) segments and structural variants (SVs) found at the boundaries of each segment. With this method, we presented a case of DM evolution in a pair of diagnosis and relapse whole genome sequencing (WGS) samples from a pediatric high-grade glioma patient, followed by validation with Chromium linked-read sequencing. Using an empirical value of CNA threshold, we extracted 44 and 29 highly amplified CNA segments from the diagnosis and relapse samples respectively. We then identified 29 and 19 unique SVs associated with these CNA segments from the two samples. We constructed five major DMs in the diagnosis sample and five major DMs in the relapse sample, covering all the CNA segments and the SVs. One DM harboring EGFR is identified in both samples. Two of the five relapse DMs are also found in the diagnosis sample but in a trace amount, suggesting a shifting from minor clones in the diagnosis to dominant clones in the relapse. Two major DMs, one carrying MYC and the other carrying CDK6, were only identified in the relapse sample. Analysis of mutations on the DMs revealed that new somatic mutations were acquired on sub-populations of the DMs. Importantly, for the EGFR-carrying DM shared in both samples, we identified an 8-bp deletion at a splicing site of EGFR that has 2% allele frequency in the diagnosis but reached 96% in the relapse. This deletion leads to a mRNA transcription skipping of exon 16 with an 87 fold up-regulation of EGFR compared with other high-grade gliomas, suggesting a possible drug resistance mechanism and positive selection of tumor cells resulting from the mutated DM. We propose an evolutionary model that simultaneously involves a branching model for DM formation and a selection model for mutations on DM. We applied the same methods to the WGS data from two adult glioblastoma patients in TCGA, and found that our proposed model could also explain the DM evolution in these patients. Therefore, our study reveals that DMs follow an evolutionary trajectory independent of linear chromosomes and contribute to tumor heterogeneity. Citation Format: Ke C. Xu, Liang Ding, Ti-Cheng Chang, Shuoguo Wang, Yong-Dong Wang, Heather Mulder, Ying Shao, John Easton, Jinghui Zhang, Suzanne J. Baker, Gang Wu. Structure and evolution of double minutes in a pediatric high-grade glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1181.