Resolving epigenetic determinants of cellular plasticity programs in non-small cell lung cancer

SUMMARY Pioneering research in cancer biology over the past four decades has uncovered a repertoire of oncogenes and tumor suppressors that initiate and maintain tumorigenesis across diverse cancer types. Such genetic alterations constitute an important aspect of intra-tumor heterogeneity which is associated with a poor prognosis and

resistance to therapy. The recent application of single-cell RNA-sequencing to tumor biology has shed further light on the composition and dynamics of intra-tumor heterogeneity. The Yanai & Wong labs and many others have provided evidence that such heterogeneity is not exclusively explained by genetic causes, but rather also

through the process of cellular plasticity. Emerging evidence also points to a crucial role for cellular plasticity in the process of drug resistance. In non-small cell lung cancer (NSCLC), tumors treated with a KRASG12C inhibitor have been shown to adapt by undergoing an adeno-to-squamous transition (AST). While this line of evidence

supports a major role for cellular plasticity in tumor adaptation to treatments, we lack an understanding of the determinants, dynamics and strategies for preventing cell state transitions. In this proposal we seek to determine the molecular programs that maintain the chromatin landscape using cutting-edge multi-omic approaches

coupled with clinically-relevant NSCLC murine models and their derivative organoids. In Aim 1 we propose a systematic study of the adeno-to-squamous plasticity seeking to identify and delineate its chromatin-mediated mechanisms. Our approach seeks to identify and test means for restricting the ability of cancer cells to undergo

AST. We first determine the dynamics of chromatin landscape changes during AST in murine-derived LUAD organoids. Then we will map functional vulnerabilities along AST using a Perturb-Seq approach, and finally, we will test for the potency of restricting AST with small molecule inhibitors against chromatin modifiers. In Aim 2,

we propose to predict the dynamics of cellular adaptation to context-specific targeted therapies used to treat NSCLC. We will further seek to apply these predictions to primary tumor samples and correlate with clinical outcomes with the goal of predicting the adaptive process. Overall, the impact of this work will be to provide

insights into cellular plasticity in lung cancer in clinically-relevant settings, and the identification of strategies for synergistic treatment combinations to inhibit cell-state transitions and to eliminate the emergence of aggressive subpopulations.