Inflammatory Signaling and Fibroblast-Cancer Cell Interactions Transfer from a Harmonized Human Single-cell RNA Sequencing Atlas of Pancreatic Ductal Adenocarcinoma to Organoid Co-Culture

Pancreatic ductal adenocarcinoma (PDAC) is a devastating malignancy driven by a heterogeneous tumor microenvironment enriched with cancer associated fibroblasts (CAFs) that influence its overall immunosuppressive composition. We examined inflammation in PDAC by leveraging our existing patient-derived organoid (PDO) model and a novel PDO-CAF co-culture. We first identified induction of major histocompatibility complex class II expression following treatment with interferon gamma. In parallel, we collated an atlas of 6 published single-cell RNA-sequencing datasets (174,394 cells) combining 61 PDAC (142,807 cells) and 16 non-malignant samples. By combining in silico modeling and in vitro PDO co-culture, we define a gene expression pattern of inflammatory processes in epithelial tumor cells. Following computational inferences, we examined interactions between epithelial tumor cells and CAFs, focusing on VEGF-A and ITGB1 pathways. This work, integrating computational and biological approaches, highlights the value of convergence to accelerate our understanding of key drivers of PDAC. Statement of Significance We established PDO-CAF co-cultures to model tumor cell interactions and validated discoveries using transfer learning into a single-cell RNA-seq atlas of PDAC tumors. This bidirectional approach from human to experimental systems facilitates interrogation of PDAC biology, including the role of inflammation associated with VEGF-A crosstalk between CAFs and tumor cells.