PhD Student Icahn Sch. of Med., Mount Sinai, New York, United States
Introduction/Rationale: Immunotherapy has reshaped cancer care, yet most people with pancreatic ductal adenocarcinoma (PDAC) gain little from immune checkpoint blockade (ICB). Antitumor immunity is limited by spatially organized niches within an immunosuppressive tumor microenvironment (TME) with suppressive myeloid cells, dense stroma, and exhausted T cells. In a CRISPR Perturb-Map screen, we found that PDAC-secreted PAI-1 and PAI-2 shifted the TME toward immunosuppression.
Methods: Motivated by these results, we asked which secreted factors in PDAC promote growth and immune evasion across spatially distinct tumor clones. We assembled a multimodal PDAC atlas by integrating single-cell RNA-seq from five studies and deconvoluted over 100 10x Genomics Visium resections to chart cancer-cell states, secreted factors, and neighborhood context. We labeled periphery, intermediate, and core layers using a ring-based framework derived from spatial adjacency.
Results: Classical, basal, and exocrine-like states were spatially compartmentalized yet often coexisted within the same tumor. Unsupervised analysis identified subtype-restricted and regionally localized cancer-cell factors: CCL28, CXCL14, and CXCL16 in classical, and IL18, NECTIN1, and TGFB1 in basal. We also observed clear core-to-edge cytokine gradients. The tumor stroma interface and periphery showed higher epithelial-to-mesenchymal transition and extracellular matrix remodeling and enrichment of immune-recruiting cytokines and chemokines such as BAFF, CXCL13, CXCL12, CCL5, and CSF1. An intermediate belt peaked for CCL2, whereas the core favored epithelial and secretory programs with stronger ROS signatures.
Conclusion: Overall, spatially distinct clones created cytokine gradients and sub-TMEs that altered the cues perceived by nearby cells. Using the 10x Genomics Xenium platform with custom panels targeting cancer-intrinsic states and key microenvironmental mediators, we are resolving cytokine signaling ranges and quantifying direct effects on immune populations.
