Abstract 5825: Non-genetic determinants driving the evolutional trajectories of drug-tolerant-persisters in KRAS Non-small cell lung cancer
Authors: Li Chendi , Graser Christopher J. , Qin Qian , Nimbalkar Anahita , Syed Usman , Karakyriakou Barbara , Clark Sarah , Saiki Anne Y. , Hughes Paul E. , Ott Christopher , Pinello Luca , Michor Franziska , Hata Aaron 
Published: March 2024

Abstract
Rare cell populations manage to evade the effects of cancer therapies, ultimately leading to drug resistance and subsequent cancer relapse. These resilient populations, often referred to as "persisters," exhibit distinct molecular characteristics when compared to the broader tumor population. In the current standard of clinical care for non-small cell lung cancer (NSCLC), patients typically undergo a series of standard treatments, such as surgery followed by chemotherapy/immunotherapy, and then targeted therapy, based on the disease stages. This continues until drug resistance emerges, with little attention given to the state of these persister cells in response to these treatments. In the case of drug resistance in KRAS-mutated NSCLC, ongoing clinical investigations are exploring the combined efficacy of KRAS G12Ci inhibitors with drugs that target mitogen-activated protein kinase (MAPK) feedback reactivation, immunotherapy, and chemotherapy. Despite the myriad of combination therapies, persister populations invariably emerge. The manner in which these persisters evolve to withstand therapies remains elusive. We employed a DNA barcode lineage tracing analysis coupled with mathematical modeling to decode persister evolution to therapies targeting different pathways, e.g., KRAS+ SHP2, KRAS+CDK4/6, and KRAS+MCL-1. Our model reveals that rapidly emerging persister populations are predetermined and do not exhibit clear genetic alterations. In some cells, common persisters exist in response to different therapies. Single-cell ATAC-RNA sequencing showed that these persisters are enriched in chromatin-binding of transcription factors that regulate classic non-homologous end-joining (cNHEJ) DNA repair (ZNF384), interferon response (IRF1), and stem-like characteristics (FOXP1), along with the activation of an IFN-γ transcriptional signature. These findings underscore the connection between specific DNA repair processes, chromosomal instability, and resistance to KRAS G12Ci. In other cells, however, distinct persister populations exist to different therapies, leading to the hypothesis that these diverse persister populations can be targeted orthogonally or sequentially to achieve tumor regression. In summary, our study unveils the heterogeneity in persister evolution trajectories in KRAS NSCLC. Our platform identifies targetable persister populations in NSCLC models and offers a proof-of-concept for non-standard strategies to combat drug resistance based on persister cell states.
Citation Format: Chendi Li, Christopher J. Graser, Qian Qin, Anahita Nimbalkar, Usman Syed, Barbara Karakyriakou, Sarah Clark, Anne Y. Saiki, Paul E. Hughes, Christopher Ott, Luca Pinello, Franziska Michor, Aaron Hata. Non-genetic determinants driving the evolutional trajectories of drug-tolerant-persisters in KRAS Non-small cell lung cancer [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(6_Suppl):Abstract nr 5825.