Abstract A122: Molecular barcoding and single cell approaches to investigate drug tolerance in EGFRmut NSCLC

Patients with non-small cell lung cancer (NSCLC) that is driven by an activating mutation in the epidermal growth factor receptor (EGFR) are routinely treated with tyrosine kinase inhibitors (TKI) to specifically target the activated EGFR signaling pathway. EGFR-mutant NSCLC tumors initially respond well to EGFR inhibitors, however a subset of drug-tolerant persister cells remain at minimal residual disease (MRD) and represent a cell reservoir from which acquired genetic mutations, such as EGFRT790M or MET amplification, can emerge to render the tumor fully drug-resistant. Prior to the emergence of genetic mutations, little is known about how drug-tolerant persister cells are able to survive EGFR targeted therapy at MRD. To better understand this cell population, we investigated drug-tolerance using single cell cloning and scRNAseq in NSCLC cell lines. Using ClonTracer barcoding, we found that the same barcodes emerged after EGFR-inhibitor treatment across multiple replicates, indicating that drug-tolerance is both pre-defined and stable over many generations. Within each individual cell line, we observed multiple distinct heterogeneous subpopulations of drug-tolerant persister cells with unique gene expression signatures and proliferation rates. Additionally, we observed evidence of putative mechanisms of drug tolerance that were shared by persister cells across cells lines and used a drug combination treatment approach to target these distinct subpopulations of drug-tolerant persister cells. Taken together, our findings provide evidence that drug-tolerant persister cell subpopulations are both predefined and heterogeneous, as well as suggesting that drug-combination treatment approaches in the clinic would be more effective at targeting multiple persister cell survival mechanisms. Citation Format: Jennifer L. Cotton, Viveksagar KrishnamurthyRadhakrishna, Julie Chen, Michelle Piquet, Joel Wagner, Gaylor Boulay, Kathleen Sprouffske, Youngchul Song, Xiaoyan Li, Katja Schumacher, Raphael Thierry, Nathaniel D. Kirkpatrick, David A. Ruddy, Joshua Korn, Erick J. Morris, Peter S. Hammerman, Jeffrey A. Engelman, Matthew J. Niederst. Molecular barcoding and single cell approaches to investigate drug tolerance in EGFRmut NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A122. doi:10.1158/1535-7163.TARG-19-A122