Abstract 419: Evolutionary trajectories of complex genome rearrangements in osteosarcoma

Abstract Whole-genome sequencing (WGS) studies have revealed that osteosarcoma genomes are riddled by remarkably intricate forms of structural variants (SV), collectively known as complex genomic rearrangements (CGR). Yet, most CGR detected in osteosarcoma remain unexplained, hinting at the possibility of undiscovered mechanisms that might lead to novel therapeutic strategies. To elucidate the mechanisms underpinning cancer genome complexity in osteosarcomas and the downstream consequences of CGR during tumor evolution, we uniformly processed exiting osteosarcoma WGS data sets and performed high-depth (120x) multi-regional short- and long-read WGS for hundreds of osteosarcomas. We found that whole genome doubling and diverse types of CGR are frequent clonal events in most osteosarcomas. Through the integration of multi-regional WGS data, we discovered that in tumors with whole-genome doubling, cancer genome evolution and oncogene amplification are the consequence of multi-generational CGR triggered by whole-genome doubling and involving multiple mechanisms, especially chromothripsis and breakage-fusion-bridge cycles. By contrast, in tumors without whole-genome doubling, biallelic inactivation of TP53 and oncogene amplification frequently occur as part of a cascade of genomic instability initiated by a single double-strand break upstream of the TP53 locus. This process results in clonal diversification and rapid tumor growth suggestive of punctuated evolution. In addition, we found that subclonal CGRs are also frequent events. Indeed, clonal expansions triggered by the acquisition of subclonal CGR often colonize distant tumor regions, suggesting that CGR act as subclonal driver events. Finally, we show that some recurrent genomic alterations are prognostic of poor survival, which we validate in independent cohorts. In sum, using WGS data, we have elucidated the mechanisms underpinning the complexity and evolution of osteosarcoma genomes. Our results indicate that diverse types of CGR, such as chromothripsis, are triggered by whole genome doubling and occur throughout tumor evolution, which primes the cancer genome for ongoing genomic instability, rapid karyotype evolution and clonal diversification. These results have implications for our understanding of the molecular basis of intra-tumor heterogeneity and drug resistance in osteosarcomas and other cancers driven by genomic instability. Citation Format: Isidro Cortes Ciriano, Jose Espejo Valle-Inclán, Solange de Noon, Katherine Trevers, Hillary Elrick, Adrienne M. Flanagan. Evolutionary trajectories of complex genome rearrangements in osteosarcoma abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts) ; 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84 (6Suppl): Abstract nr 419.