Epigenetic Plasticity as a Source of Tumor Evolution and Adaptation

Abstract public domain (NIH RePORTER)

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers, with a five-year survival rate of just 11%. While genetic mutations drive progression, epigenetic regulation, including chromatin remodeling, DNA methylation, and histone modifications, plays a crucial role in adaptation, metastasis, and therapy resistance. This study aims to define how chromatin remodeling sustains tumor heterogeneity and resistance, identifying targetable vulnerabilities for therapy. This proposal hypothesizes that epigenetic dysregulation enhances PDAC cell-state heterogeneity, thereby promoting tumor evolution. Using single cell multiomics, genome editing, and functional genomics, chromatin accessibility and transcriptional changes in PDAC organoids with and without ARID1A loss will be mapped (Aim 1). Next, an ARID1A-KO orthotopic mouse model will be used to assess tumor evolution under therapeutic pressure, identifying drug-tolerant subpopulations and compensatory oncogenic pathways such as WNT and MYC (Aim 2). Finally, an in vivo CRISPR-Cas9 screen will further pinpoint epigenetic regulators driving metastasis and resistance (Aim 3), with small-molecule inhibitors tested in combination with targeted therapy. Genetically engineered and orthotopic mouse models are essential to this work: the epigenetic plasticity, metastatic dissemination, and in vivo therapy responses under study emerge only within an intact tumor microenvironment and immune context that cell-based systems cannot reproduce. Moreover, there are no defined media compositions that sustain the differential epigenetic states of interest ex vivo, making in vivo models indispensable for capturing them. Wherever possible, organoid and in vitro assays are used first to refine hypotheses and minimize animal use. During the mentored phase of this award, I will gain essential training in mouse modeling, cancer biology, single-cell technologies, and bioinformatics. This support, along with the outstanding environment at MIT and mentorship from Dr. Jacks, will set me up for success for the independent portion of this award. Importantly, I will continue to foster collaborations and receive additional mentoring from my Advisory Committee, who will provide crucial expertise in functional genomics, cancer biology, and computational tools, and facilitate my transition to independence. Together, this training and support will promote my scientific career, and the completion of this research proposal will advance our understanding of epigenetic plasticity as a central driver of PDAC evolution.

Public health relevance public domain (NIH RePORTER)

PROJECT NARRATIVE Pancreatic cancer is one of the deadliest cancers, largely because tumors quickly adapt, spread, and become resistant to treatment. This project investigates how changes in chromatin, the structure that controls gene activity, help cancer cells survive and evade therapy. By identifying key epigenetic regulators and testing new drug combinations, this research aims to develop better treatment strategies that prevent tumor progression and improve patient outcomes.