Abstract IA018: Reading and writing extrachromosomal DNA

Abstract

Abstract Cancer patients face an extraordinary challenge when oncogenes unleash themselves from chromosomes. Extrachromosomal DNA (ecDNA) are large, megabase-sized circular episomes containing oncogenes and regulatory DNA elements. EcDNAs have a remarkable transcriptional advantage and rapidly change copy number–a moving target driving accelerated evolution in cancer. We present a method for targeted purification of megabase-sized ecDNA by combining in-vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA (CRISPR-CATCH). Targeted purification of ecDNA versus chromosomal DNA enabled phasing of genetic variants and provided definitive proof of oncogenic mutations exclusively on ecDNAs, discovery of ecDNA-specific demethylation with single molecule resolution, and accurate reconstruction of megabase- sized ecDNA structures with base-pair resolution. We model and test the impact of non-chromosomal oncogene inheritance—random identity by descent—on ecDNA on variation and selection. Integrating mathematical modeling, unbiased image analysis, CRISPR-based ecDNA generation, and live-cell imaging, we identify a set of basic “rules” for how random ecDNA inheritance drives oncogene copy number and distribution, resulting in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted cancer treatment. These new tool kits for reading and writing ecDNAs promise to unravel the genetic and epigenetic landscapes of ecDNA biogenesis, dynamics, and function. Citation Format: Howard Y. Chang. Reading and writing extrachromosomal DNA. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr IA018.