Abstract 3904: Clonal analysis of classical subtypes of pancreatic cancer stem cells in ascites

It is now established that pancreatic cancer often displays an intratumor heterogeneity at the levels of epithelial cell types, stromal activation, and immune signaling that is likely germane to therapeutic resolution. While the extent of epithelial subtypes is under investigation, there is general agreement that pancreatic ductal adenocarcinoma (PDAC) is comprised of p63+ "basal" and GATA6+ "classical" subtypes, as well as various "intermediate", hybrid, and immune subtypes. In this initial report, we have applied technology that clones stem cells of the human gastrointestinal tract (Wang et al., 2015) and of esophageal adenocarcinoma and its precursors (in review) to ascites samples from patients with PDCA. Libraries of clonogenic cells were sorted to CEACAM6+ and CEACAM6- populations that were cloned by single cell sorting. The majority of CEACAM6+ clones form colonies with morphologies distinct from the CEACAM6- clones, and yet both form aggressive tumors in immunodeficient mice. Both CEACAM6+ and CEACAM6- clones express high levels of GATA6 and LGALS4, suggesting their general inclusion into the classical subtype seen in PDCA. However, gene expression profiling and tumor histology indicate that the CEACAM6+ clones display an intestinal fate (high CDH17, CDX2, MUC17) whereas the CEACAM6- clones show a gastric profile (TFF1, TFF2, AQP5, EGR1, EGR2, SOX21, MUC5AC). In addition, the CEACAM6- clones showed high levels of interferon signaling and high levels of chemokine expression including CXCL1, 2, 3, and 8, CCL20. The stromal properties of tumors generated from CEACAM6+ and CEACAM6- clones were also distinct, with the CEACAM6- clones marked by tumors with a highly cellularized extracellular matrix including αSMA+ and FAP+ CAFs, and the intestinal CEACAM6+ clones largely devoid of these CAF subpopulations. Consistently, CEACAM6- clones expressing high levels of pro-fibrotic genes, including PLAU, FN1, and CCN1. Importantly, exome sequencing of the CEACAM6+ and CEACAM6- clones from the same patient reveal shared mutant alleles of the p53 and KRAS genes, suggesting that these phenotypically distinct classical subtypes arose from a post-transformation stage likely by epigenetic mechanisms. Ongoing studies aimed at cloning basal subtypes from ascites and resolving the epigenetic control of CEACAM6+ and CEACAM6- classical subtypes should help to define the stem cell heterogeneity in PDAC. Citation Format: Wa Xian, Frank McKeon, Paul Daniel, Saeed Khan, Caycel Desales, Ashley Hoffman, Jaffer Ajani. Clonal analysis of classical subtypes of pancreatic cancer stem cells in ascites [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3904.