Abstract A039: Repeat RNA mediated disruption of cellular plasticity in pancreatic cancer

Abstract Aberrant expression of repeat RNAs in pancreatic ductal adenocarcinoma (PDAC) mimics viral-like responses with implications for tumor cell state and the surrounding microenvironment. To better understand the relationship of repeat RNAs in human PDAC, we employed the NanoString CosMx™ spatial molecular imaging (SMI) platform, which utilizes a 1,000-plex RNA panel with custom repeat RNA probes targeting long interspersed nuclear element 1 (LINE-1) retrotransposon ORF1 and ORF2, HSATII satellite (SAT) repeat, and two human endogenous retroviruses (HERV-K and HERV-H) in 46 primary tumors. This analysis revealed correlations of high repeat RNA expression with alterations in the epithelial state of PDAC cells and the myofibroblast phenotype in cancer-associated fibroblasts (CAFs). The loss of cellular identity observed with dosing of extracellular vesicles (EVs) and individual repeat RNAs in PDAC and CAF cell culture models points to cell-cell intercommunication involving these viral-like elements. Differences in the PDAC and CAF response are driven by distinct innate immune signaling pathways through interferon regulatory transcription factor 3 (IRF3). Altogether, our data indicate that cell context-specific viral-like responses driven by tumor cells have broad impacts on single-cell heterogeneity within cancer cells and the pancreatic cancer microenvironment. Citation Format: Eunae You, Patrick Danaher, Chenyue Lu, Siyu Sun, Luli Zou, Ildiko Phillips, Alexandra Rojas, Natalie Ho, Yuhui Song, Michael Raabe, Katherine Xu, Peter Richieri, Hao Li, Natalie Aston, Rebecca Porter, Bidish Patel, Linda Nieman, Nathan Schurman, Briana Hudson, Khrystyna North, Sarah Church, Vikram Deshpande, Andrew Liss, Tae Kim, Yi Cui, Youngmi Kim, Benjamin Greenbaum, Martin Aryee, David Ting. Repeat RNA mediated disruption of cellular plasticity in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A039.