Neoadjuvant chemotherapy induces clinically distinct spatial remodeling of the tumor microenvironment in PDAC

Neoadjuvant chemotherapy (NACT) followed by surgical resection is increasingly becoming the standard treatment paradigm for pancreatic ductal adenocarcinoma (PDAC). However, post-surgical therapeutic strategies remain largely unguided by tumor. To address this critical gap, we performed an integrated multi-omics analysis using matched tumor specimens from the same clinical cohort (n=18 patients per group) to define how NACT reshapes stromal architecture and antitumor immunity in PDAC.Spatial transcriptomic analysis revealed pronounced NACT-induced reorganization of tumor and stromal compartments. Basal-like and classical-like tumor programs formed distinct spatial domains accompanied by heterogeneous CAF niches, including myCAF-, iCAF-, and apCAF-like regions. Although overall cellular composition was largely preserved, NACT triggered marked subtype-specific remodeling: basal-like tumors exhibited activation of inflammatory signaling, whereas classical-like tumors showed reduced KRAS signaling and epithelial-mesenchymal transition activity. In stromal compartments, myCAF-like regions displayed suppression of collagen biosynthesis and ECM organization programs, while iCAF- and apCAF-like niches retained inflammatory transcriptional states. Notably, NACT selectively increased spatial proximity between CD8⁺ T cells and classical-like tumor regions, whereas basal-like tumors remained embedded within CAF- and myeloid-enriched immune-restrictive microdomains.Proteomic profiling supported these spatial findings by demonstrating coordinated stromal reprogramming after NACT, with increased abundance of collagen- and coagulation-related proteins and reduced proliferative signatures. Cross-modal integration further revealed concordant activation of ECM remodeling pathways in CAF-rich niches and immune-modulatory programs near tumor regions. Consistently, multiplex immunohistochemistry demonstrated significantly increased infiltration of CD8⁺ cytotoxic and CD4⁺ helper T cells with enhanced proximity to malignant epithelial regions, while FOXP3⁺ regulatory T cells remained largely unchanged. Spatial immune organization was clinically relevant, as tumor proximity to activated CD8⁺ T cells predicted superior survival, whereas association with MDSC-dominant niches correlated with poor outcome.NACT therefore reshapes the PDAC microenvironment into clinically actionable spatial states, enabling post-surgical patient stratification and providing a rationale for personalized adjuvant strategies, including immunotherapy and CAF-targeted treatments strategy.