Clonal dynamics and non-genetic mechanisms mediating resistance to RAS inhibition

Standard of care treatment for pancreatic ductal adenocarcinoma (PDAC) provides limited benefits to patients, highlighting the need for alternative therapies. Given that >90% of PDAC is driven by KRAS mutations, novel KRAS/RAS inhibitors, including pan-RAS inhibitors (RASi), hold the potential to improve patient survival. Despite objective clinical responses observed in early RASi trials, relapses are nearly universal. My preliminary studies indicate that relapse arises from a subset of cells that can enter a drug-tolerant persister cell state, characterized by negligible growth, which eventually adapt bona fide resistance mechanisms to resume proliferation. However, the molecular mechanisms governing these cell states and the drivers of cell state transitions remain poorly understood. Moreover, RASi studies performed in our genetically homogenous PDAC models, genomic analyses of human PDAC treated with allele-specific KRAS inhibitors, and prior studies of the persister cell state in other cancers underscore the importance of studying non-genetic resistance mechanisms, including epigenetic mechanisms. Traditional resistance studies compare pre- and post-treatment, late-stage disease, failing to capture the cell state trajectories of individual cells on the path to resistance. Studying these dynamic cell state transitions may uncover vulnerabilities in the transient persister cell state or even pre-existing states that dictate survival. Importantly, my preliminary lineage tracing experiments suggest that some lineages are intrinsically primed to resist RASi. Thus, this proposal tests the hypothesis that pre-existing epigenetic states promote persistence (survival) when cells are exposed to RASi, permitting the subsequent emergence of drug resistance and clinical relapse. To test this, I will pair DNA-barcoding with single-cell technologies to trace PDAC through RASi treatment in vitro to gain a time-resolved understanding of clonal dynamics and phenotypes that mediate resistance. In Aim 1, I will assess the potential of targeting pre-existing cell state heterogeneity in PDAC by quantifying the degree to which the state of a cell prior to RASi treatment influences cell fate. In Aim 2, I will study the gene expression and chromatin accessibility profiles of resistant PDAC lineages over time, before and after RASi, to elucidate the patterns and drivers of epigenetic plasticity. Ultimately, this work will provide critical insights into the mechanisms enabling PDAC progression to resistance, which will inform the development of combination therapies to prevent RASi relapse and effect a cure. Project Number: 1F31CA310236-01 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Jayne McDevitt | Institution: UNIVERSITY OF PENNSYLVANIA, PHILADELPHIA, PA | Award Amount: $50,114 | Activity Code: F31 | Study Section: Special Emphasis Panel[ZRG1 F09B-W (20)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11314891