the Transcriptional and Epigenetic Regulation of Epithelial-Mesenchymal Plasticity in Patient-Derived Pancreatic Cancer Cell Lines

Abstract Epithelial-mesenchymal transition (EMT) is a hallmark of pancreatic ductal adenocarcinoma (PDAC) invasion. In general, cellular plasticity is a major contributor to both tumor progression and therapy resistance. The major goals of our study are to 1) directly and quantitatively measure plasticity in PDAC3 cell lines, and 2) identify candidate genes that could alter the plasticity of cancer cells. By understanding the regulation of tumor cell plasticity, we may find ways to perturb cells and prevent the transition towards treatment resistant cell states. A strict definition of plasticity in cancer has yet to be established, however, and is imperative to our understanding of cell state regulation and for identifying vulnerabilities in plastic cells. We argue that in order to prove plasticity occurs within a population of cells, one must either 1) demonstrate that a new cell state has emerged that was previously not present, or 2) trace the lineage of a cell to show it can adopt multiple cell states. For our study, we profile 12 patient-derived PDAC cell lines to find convergent EMT programs and perform lineage tracing on these cell lines using a modified CROP-seq vector, called ClonMapper, to quantitatively measure plasticity. Towards this goal, we perform single-cell RNA-seq (scRNA) and single-cell multiomic measurements of 1000 uniquely barcoded cells expanded over a time course of 2, 3 and 4 weeks. We refer to cells that have the same lineage barcode - originating from the same initial cell - as families. We found that ~50% of families are composed of cells that are epithelial and mesenchymal, thus proving plasticity must exist, as it shows that a given parental cell of unknown state can give rise to progeny that are in multiple states. We then develop mathematical models to show that families have different levels of plasticity, defined by the rates of transition between distinct cell states. We next leverage our barcode-resolution time course data to identify factors at early time points that may influence plasticity at later time points. We show there is differential accessibility of several of these factors across families with different plasticity properties, thus proposing a role for epigenetic regulation of EMT. Importantly, we find that specific factors drive gene regulatory networks important for epithelial and mesenchymal programs, and therefore propose candidates for the modulation of EMT for therapeutic benefit. Citation Format: Deepika Yeramosu, Lynn Bi, Abigail Collins, Mike Bogaev, Martin Jankowiak, Aziz Al’Khafaji, Milan Parikh, Mehrtash Babadi, Alex Bloemendal, Surya Nagaraja, Ray Jones, Jay Shendure, David T. Ting, Andrew Aguirre, Nir Hacohen, Dana Pe’er, Eric S. Lander, Arnav Mehta. The transcriptional and epigenetic regulation of epithelial-mesenchymal plasticity in patient-derived pancreatic cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6940.