Abstract B021: Epigenetic Reprogramming of Intraductal Papillary Mucinous Neoplasms (IPMNs) by Pancreatic Cancer Associated Fibroblasts
Hailee I. Porter, Md Shahadat Hossan, Timothy Hoggard, Bethsebie Sailo, Jeremy Kratz, Nita AhujaAbstract
Background:
Intraductal papillary mucinous neoplasms (IPMNs) are established precursors to pancreatic ductal adenocarcinoma (PDAC). While IPMNs are the only pancreatic precursor readily identified by clinical imaging, no tools readily predict progression to cancer. The local pancreatic tumor microenvironment (TME) is heavily composed of cancer-associated fibroblasts (CAFs) with resultant immunosuppressive desmoplastic stroma. Single-cell sequencing has demonstrated that precursor microenvironments contain myofibroblastic (myCAF) and inflammatory CAF (iCAF) phenotypes. Given that CAF-driven remodeling of the pancreatic TME promotes oncogenesis in vivo, we hypothesized that early epithelial epigenetic reprogramming can be modeled using co-culture systems for stromal cross-talk.
Methods:
Patient-derived IPMN organoids and 2D CAF co-cultures were established by 0.4 μm polycarbonate transwell inserts and collected for protein and RNA isolation. Global epigenetic alterations in IPMN organoids were quantified via Western blot for H3K27ac, H3K27me3, H3K4me3, H3K9me3, and total Histone 3 relative to GAPDH using a LiCOR Odyssey M system. Active transcription was evaluated by blotting for phosphorylated RBP1 C-terminal domain (CTD) Serine 5 residues and total RBP1 protein. Statistical analysis was conducted using a Welch’s t-test. Transcriptomic profiling (RNA-seq by Plasmidsaurus) was analyzed using the DESeq2 pipeline.
Results:
Findings demonstrate that within, 72 hours of CAF co-culturing, IPMN organoids undergo epigenetic reprogramming. Western[JK1] [HP2] blotting of histone marks by co-culture revealed a significant (p < 0.05) increase in total Histone 3 residues in IPMN organoids grown in CAF co-culture compared to organoid cultures alone. When normalized to total Histone 3, H3K4me3 and H3K27me3 were markedly decreased, while H3K9me3 and H3K27ac remained enriched in the co-culture condition. Parallel RNA-seq profiling showed a significant upregulation of the TGFβ signaling pathway (p = 0.027) alongside trending increases in epithelial-mesenchymal transition (EMT) genes, KRAS signaling, cholesterol homeostasis, MYC targets, and apoptosis. Notably, genes with changed expression including ANXA10 (log2FC=2.65, p < 0.011), RET (log2FC=1.94, p<0.017), and WNT7A (log2FC=1.73, p<0.031).
Conclusion:
Transwell co-culture of IPMN organoids with CAFs are sufficient to induce rapid, significant global epigenetic remodeling. The sustained enrichment of H3K27ac and H3K9me3 indicates a stromal-driven shift toward open transcriptional states. This epigenetic remodeling aligns with findings by RNA sequencing demonstrating activation of TGFβ signaling and the robust induction of ANXA10, a known driver of progression in the gastric subtype of IPMN. These data highlight a novel stromal-epithelial reprogramming axis that may be part of the global transitional state to invasive PDAC
Citation Format:
Hailee I. Porter, Md Shahadat Hossan, Timothy Hoggard, Bethsebie Sailo, Jeremy Kratz, Nita Ahuja. Epigenetic Reprogramming of Intraductal Papillary Mucinous Neoplasms (IPMNs) by Pancreatic Cancer Associated Fibroblasts [abstract]. In: Proceedings of the AACR Conference on Pancreatic Cancer: New Frontiers in Biology and Therapeutic Development; 2026 Sep 25-28; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(18_Suppl_2):Abstract nr B021.