Integrating multi-modal transcriptomics identifies cellular subtypes with distinct roles in PDAC progression

Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, largely due to its highly immunosuppressive and fibrotic tumor microenvironment (TME). However, the spatial and functional organization of its cellular components remains poorly understood.

We present an integrated transcriptomic atlas of the PDAC TME by combining single-cell RNA sequencing (n = 88; 187,520 cells), Visium spatial transcriptomics (n = 20; 67,933 spots), bulk RNA sequencing (n = 1,383), and high-resolution Xenium spatial transcriptomics (n = 2; 307,679 cells). Key findings were validated using scRNA-seq, bulk datasets, multiplex immunohistochemistry, and spatial imaging.

POSTN⁺ fibroblasts and SPP1⁺ macrophages consistently co-infiltrated across 12 independent bulk RNA-seq cohorts, and showed spatial correlation in both Visium and Xenium platforms. Those tumor-promoting cell states were enriched in hypoxic, angiogenesis, and epithelial-mesenchymal transition, and were linked to poor prognosis. In contrast, CCL4⁺ CD8⁺ effector T cells and IGHG1⁺ plasma cells co-occurred within immune-active niches, were enriched for cytotoxic and activation-related pathways, and were associated with improved patient survival. Notably, these protective immune subsets remained detectable despite the immunosuppressive nature of the PDAC TME. Expression specificity of POSTN, SPP1, CCL4, and IGHG1 was validated at the transcriptomic and protein levels.

We delineate two opposing cellular programs in the PDAC TME-tumor-promoting stromal remodeling and anti-tumor immune activation-spatially organized in distinct niches. Those findings suggest that targeting POSTN⁺ fibroblasts and SPP1⁺ macrophages-mediated stromal interactions while promoting CCL4⁺ T cell and IGHG1⁺ plasma cell immunity, may offer new therapeutic strategies for PDAC.