EGFR gene alterations are found in 15%-30% of lung adenocarcinomas (LUADs). While EGFR-targeted therapies are initially effective, most patients eventually relapse due to treatment resistance. Recent research has identified "persister cells" - tumor cells that survive throughout targeted treatment and are believed to be a primary cause of cancer recurrence in EGFR-mutant LUAD. This project aims to understand how these persister cells survive despite targeted therapy and identify ways to eliminate them. The ultimate goal is to identify resistance factors, develop therapeutic strategies to eradicate persister cells, and provide the scientific foundation for clinical trials to improve outcomes for patients with EGFR-mutant LUAD.
- Research Summary
Alterations in the EGFR gene are present in ~15-30% of all lung adenocarcinomas (LUADs). EGFR targeted therapies are initially effective, but most LUADs eventually relapse. Recent studies suggest some tumor cells survive throughout targeted treatment. These cells, called “persister cells”, are thought to be a primary mechanism of relapse in some patients with EGFR-mutant LUAD. In this project, we aim to study how these persister cells remain healthy despite treatment with targeted therapy and to identify targets to eliminate them. We will use cutting-edge technologies to study the biology of persister cells in clinical samples and mouse models. We will identify and validate factors causing resistance to therapy, propose therapeutic strategies for the eradication of persister cells, and provide the preclinical rationale for the initiation of clinical trials to improve outcomes for patients with EGFR-mutant LUAD.
- Technical Abstract
Up to 40% of resistance mechanisms to EGFR targeted therapies in lung adenocarcinoma (LUAD) are unknown. Drug tolerant persister cells (DTPs) constitute a reservoir of therapy resistant cells that can be found even in never-treated LUAD tumors and survive during the minimal residual disease (MRD) stage despite the ongoing pressure of targeted therapy, leading to lung cancer relapse. These cells do not harbor classical genetic alterations such as secondary mutations in EGFR. Importantly, several preclinical studies have shown that this drug tolerance state is reversible after drug removal, supporting the involvement of epigenetic rather than genetic resistance mechanisms. However, the biology of DTPs, and in particular their epigenetic landscape, is largely unknown. The eradication of DTPs is crucial for improving outcomes for patients with EGFR-mutant LUAD. In this proposal we will integrate single-cell transcriptome and epigenome analyses to nominate drivers of drug tolerance.
We will (1) characterize MRD biospecimens at single-cell level to investigate the distinct transcriptomic MRD subclusters and determine the molecular and cellular dynamics of MRD samples. Collecting MRD clinical samples is highly challenging since re-biopsies are not standard practice. Therefore, insights gained from this analysis will be very valuable in understanding the mechanisms underlying drug tolerance in EGFR-mutant LUAD.
We will (2) leverage our unique set of patient-derived xenografts (PDXs) to mimic MRD in vivo and characterize the dynamics of resistance to osimertinib (3rd generation EGFR targeted therapy) in these models. We will perform a comprehensive transcriptomic and epigenetic characterization by single-cell RNAseq, chromatin immunoprecipitation sequencing, ATACseq and methylation analysis to decipher the epigenetic reprogramming that occurs over time. The integration of our transcriptomic and epigenomic data from these models will nominate molecular pathways and targets associated with drug tolerance and resistance.
Finally, (3) we have identified EP300 in an in vivo CRISPR screen as a druggable epigenetic vulnerability in osimertinib-treated DTPs. EP300 along with other candidates previously identified in clinical samples and PDXs, will be extensively validated in vitro and in vivo. This proposal will provide knowledge of the mechanisms underlying drug tolerance and resistance in patients with EGFR-mutant LUAD and may gather robust preclinical data to propose novel therapeutic strategies to be evaluated in clinical trials.