Abstract B123: Phenotypic, Microenvironmental, and Genetic Crosstalk Shapes Pancreatic Cancer Organization

Tumors acquire a set of functional capabilities, known as the Hallmarks of Cancer, to thrive and grow. While extensive research has revealed how gene and protein expression networks contribute to these traits, the relationships between tumor cell states, spatial organization of immune and stromal cells in the tumor microenvironment, and tumor genetics, remains poorly understood. To address this, we constructed a cohort of primary tumor tissues from 117 pancreatic ductal adenocarcinoma (PDAC) patients. Using Multiplexed Ion-Beam Imaging (MIBI) with a 40-antibody panel, we mapped the spatial organization of major cell types and their phenotypes. We also conducted targeted genomic and bulk proteomic analyses to explore how spatial organization patterns align with tumor genetics and proteome profiles. We identified phenotypic subtypes of tumor epithelium that shape distinct microenvironmental niches: (i) Glycolytic tumors expressing proteins such as GLUT1, LDHA, MCT1 and HIF1α reside in hypoxic niches. They are encased by dense fibrotic stroma and lacking vasculature and immune cell infiltration. (ii) Tumor and metaplastic epithelium that exhibit an oxidative proteome profile, are highly enriched for ECAD and PD-L1 expression, and are situated near pancreatic epithelium and vasculature, with significant immune infiltration. (iii) Myeloid-interacting tumors expressing CXCL5, heavily infiltrated with neutrophils and characterized by low-collagen and high FAP positive fibroblasts. Notably, neutrophils accumulate within the lumen of tumor ducts where they exhibit increased apoptosis, DNA damage, and netosis. These highly neutrophil-infiltrated tumors, associate with poor disease outcome. The genetic landscape of PDAC influences these spatial and phenotypic patterns. Patients with TGFβ/SMAD pathway mutations, demonstrate an increased proportion of basal tumor cells accompanied by reduced lymphocytic infiltration. Similarly, distinct TP53 variants shape immune-cell infiltration: patients harboring missense mutations show increased lymphocytic infiltration compared to those with truncating mutations. These findings underscore the strong link between tumor genetics, phenotypic heterogeneity and cellular architecture of the PDAC microenvironment, offering new insights into collective tumor behavior. Citation Format: Ofer Elhanani, Guy Truzman, Martin Wartenberg, Yuval Bussi, Dana Shainshein, Bar Engelberg, Ido Harlev, Adi Lilien, Inti Zlobec, Tamar Geiger, Leeat Keren. Phenotypic, Microenvironmental, and Genetic Crosstalk Shapes Pancreatic Cancer Organization [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_3): nr B123.