Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptomic, regulatory, and spatial programs

BACKGROUND: The mechanisms of peritoneal dissemination in pancreatic ductal adenocarcinoma (PDAC) remain unclear partly owing to the lack of patient-derived models that recapitulate this process. This study aimed to establish an orthotopic model of PDAC peritoneal dissemination and to uncover the transcriptional and regulatory programs underlying this process. METHODS: Organoids were established from primary pancreatic tumors and malignant effusions of patients with PDAC and orthotopically transplanted into the pancreas of immunodeficient mice to generate patient‒derived orthotopic xenograft (PDOX) models. Subsequently, the organoids were rederived from pancreatic and peritoneal lesions of a representative model (PDOX12) and orthotopically reimplanted to assess the dissemination capacity. Single-nucleus RNA sequencing (snRNA-seq), single-cell ATAC sequencing (scATAC-seq) and spatial transcriptomic analysis were performed to analyze the tumors from these models. RESULTS: The organoids that were derived from malignant effusions reproducibly generated peritoneal metastases after orthotopic implantation. To dissect this process more precisely, we focused on one representative model (PDOX12) and rederived organoids from its pancreatic and peritoneal lesions (PDXO12P and PDXO12A, respectively). These organoids generated matched PDOX models that differed only in dissemination potential when reimplanted orthotopically. The results of snRNA-seq revealed a distinct subpopulation enriched in the high-dissemination model, suggesting a dissemination-primed state. Integration with scATAC-seq identified potential upstream regulators of the gene programs in the subpopulation. Furthermore, the cellular plasticity was revealed by the PDOX system. In vitro, PDXO12P and PDXO12A organoids exhibited nearly indistinguishable transcriptional and proliferative profiles. However, their latent differences were unmasked when placed in vivo: PDXO12A demonstrated stronger peritoneal dissemination, accompanied by the clear transcriptional divergence. We hypothesized that these differences were unveiled by the influence of the tumor microenvironment (TME) and performed spatial transcriptomic analysis to profile the TME in the high-dissemination model and comprehensively characterize the transcriptional features of fibroblasts. CONCLUSIONS: We established PDOX models that isolate the peritoneal dissemination phenotype and reveal the transcriptional and regulatory programs driving this process.