Spatial multi-omics uncovers an invasive-desmoplastic cellular community with prognostic and therapeutic implications in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense desmoplastic stroma and profound spatial heterogeneity, yet the multicellular organizational principles governing its tumor microenvironment remain poorly understood. Here, we performed single-cell RNA sequencing (scRNA-seq; n = 9) and spatial transcriptomics (n = 4), integrating 61,234 single cells and 30,430 spots to identify an invasive-frontier myofibroblastic cancer-associated fibroblast (IF-myCAF), which is characterized by elevated expression of ACTA2, TAGLN, COL11A1, THBS2, CTHRC1, and POSTN. IF-myCAFs were validated in eight independent PDAC cohorts (159 samples with 67,959 CAFs), showing conserved transcriptional programs and representing a major CAF subpopulation across datasets. Spatial cellular community (CC) analysis identified five recurrent CCs that delineated the multicellular organization of PDAC. Notably, the invasive-desmoplastic CC (ID-CC), which localized to the tumor-stroma interface, was defined by a 5.8-fold enrichment of IF-myCAF; within this community, IF-myCAF colocalized with malignant ductal cells and macrophages. We also found that the ID-CC transcriptional signature was independently associated with worse outcome in TCGA-PAAD. Furthermore, ligand-receptor (LR) analysis of 4,009 IF-myCAF-associated LR pairs identified IF-myCAF as the predominant cell population mediating ECM-related intercellular signaling within ID-CC. Structure-based virtual screening against four IF-myCAF-derived ligand-receptor axes mediating intercellular communication within this community (THBS2-CD47, CTHRC1-FZD8, PPIA-BSG/CD147, MIF-CD74) identified five multi-target drug-repurposing candidates, including conivaptan, lonafarnib, rucaparib, desloratadine, and ketotifen. Collectively, this study first identified a novel CAF subpopulation, IF-myCAF, and established a CC-based organizational scheme for PDAC spatial architecture. Our findings advance our understanding of spatial ecosystem-level stromal heterogeneity in PDAC and suggest targeting IF-myCAF-driven signaling within ID-CC.