Abstract 1089: Extrachromosomal DNA (ecDNA)-driven switching of oncogene dependency facilitates resistance to targeted therapy
Authors: Turner Kristen M. , Perusse Dean , Jadin Laurence , Nguyen Nam-Phuong , Hassig Christian , Christiansen Jason 
Published: July 2021

Introduction: Tumors with oncogene copy number amplification are aggressive, have poor prognosis and, to date, have been very difficult to treat. Computational analyses in a large pan-cancer study revealed that ecDNA comprises over 50% of highly amplified oncogenes. We sought to determine the underlying mechanisms that render tumors with amplified oncogenes on ecDNA largely refractory to targeted oncogene therapy intervention and the subsequent implications regarding emergent resistance of oncogene amplified tumors to targeted inhibitors.

Methods: This study used the SNU16 gastric cancer cell line that contains the common oncogenes, MYC and FGFR2, amplified on ecDNA. We performed a longitudinal assessment of cellular resistance and ecDNA dynamics in response to the FGFR inhibitor, infigratinib (infi), including dosing at EC20, EC50, and EC90.

Results: Prior to infi exposure, we characterized broad differences in ecDNA structure and quantified the supporting massively increased genetic heterogeneity at the subcellular level. Strikingly, upon treatment with infi, we observed dose-dependent therapeutic resistance driven by underlying intracellular heterogeneity of oncogenes residing on ecDNA. Suppressing FGFR signaling at the EC90 dose led to a decrease in FGFR2 ecDNA and concomitant exponential increase in EGFR ecDNA, revealing a rapid switch of functional oncogene dependencies and therefore a fitness advantage uniquely enabled by ecDNA. We subsequently exposed the infi-resistant cells (now harboring EGFR amplification) to erlotinib and documented a return from the emergent ecDNA-enabled EGFR dependency back to the basal FGFR2 dependency on ecDNA. In addition to facilitating resistance to targeted therapeutic pressure, this unique oncogene dependency switching mechanism demonstrates that ecDNA-amplified oncogenes constitute cancer driver alterations. We next tested simultaneous upfront inhibition of both FGFR and EGFR with combination targeted therapies. Although initial cytotoxicity was robust, the cell population inevitably became resistant. Resistance to the up-front dual blockade was also driven by ecDNA, with diverse oncogenes including MET and KRAS becoming amplified on ecDNA in a marked heterogeneous pattern within the population. In sum, the cells had a remarkable propensity to amplify a range of oncogenes on ecDNA to enable survival under therapeutic pressure.

Conclusions: This data validates previous reports of ecDNA copy number dynamics under therapeutic pressure. The inability to predict which oncogenes would amplify on ecDNA in upfront combinations suggests that an up-front targeted therapy approach, including combination therapy, will not be durably effective for patients with tumors carrying ecDNA and highlights the urgent need to take a new therapeutic approach to disable tumor cells' utilization of ecDNA.

Citation Format: Kristen M. Turner, Dean Perusse, Laurence Jadin, Nam-Phuong Nguyen, Christian Hassig, Jason Christiansen. Extrachromosomal DNA (ecDNA)-driven switching of oncogene dependency facilitates resistance to targeted therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1089.