Abstract 143: A platform for deep evolutionary profiling of cancer resistance

Abstract Despite the introduction of a number of new therapeutic classes including targeted inhibitors, immunotherapy, and antibody-drug conjugates, the ability to achieve long-term disease control in the majority of patients with advanced cancer remains elusive due to the emergence of resistance. While our understanding of resistance mechanisms continues to expand through preclinical and clinical sequencing efforts, comprehensive approaches to map the distribution of potential resistance mechanisms in a given cell line and drug context require the development of novel approaches. Here, we describe the design of a platform for profiling cancer resistance at scale. Beginning with a single sensitive parental cancer cell line, the EGFR-mutant lung cancer line PC9, we optimize pre-existing diversity using a combination of single-cell subcloning and alkylator mutagenesis, and generate 50 independently evolved clones resistant to the EGFR inhibitor osimertinib. Profiling of this library via multiplexed whole genome sequencing (WGS) demonstrates convergent mutations in the MAPK pathway. Taking a similar approach, we profile the NTRK1-fusion-driven KM12 colon cancer cell line, yielding convergent, clinically observed, on-target resistance mutations to the NTRK inhibitor larotrectinib. Taken together, these results provide an initial proof-of-concept for the high-throughput generation of viable drug-resistant cancer clones. Future efforts to increase mutational diversity as well as assess additional drug and disease contexts will broaden the utility of this approach. Citation Format: Arvind Ravi, Sainikhil Sontha, Maisha Chowdhury, Jacob Smigiel, Matthew Rees, Brian Danysh, Jennifer Roth, Laxmi Parida, Eric Lander, Gad Getz. A platform for deep evolutionary profiling of cancer resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 143.