Abstract B126: Single-cell and spatially resolved atlas of pancreatic cancer reveals immunophenotypes associated with clinical outcome

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive and lethal tumor. PDAC also shows poor response to many conventional treatments and is refractory to immunotherapy. We hypothesize that these challenges arise from the highly heterogeneous and immunosuppressive tumor microenvironment (TME) in PDAC. Therefore, to comprehend the players behind this immunosuppressive TME, we integrated 10 publicly available datasets into a robust PDAC scRNA atlas of 941.608 cells covering 201 patients (159 PDAC, 24 non-cancer, and 18 metastatic PDAC). The TME showed distinct composition for each tissue, predominating a fibro-inflammatory phenotype with infiltrating Tregs and dysfunctional CD8 T cells in primary PDACs. In contrast, adjacent normal tissue exhibited enrichment of tissue-resident memory CD8 T cells (p < 0.05). Metastatic PDAC was characterized by a reduction in stromal cells combined with myeloid and naive T cells infiltration. Comparison between treated and untreated PDAC revealed the enrichment of cancer-associated fibroblasts (CAFs) in treated patients. Besides, CD8 T cells from untreated patients exhibited higher levels of genes previously linked to immunotherapy response compared to treated patients. Non-negative matrix factorization (NMF) of the malignant cells unraveled 8 distinct metaprograms (MP). MP3 and MP7 overlapped with the well-known Classical subtype, whereas MP5 correlated with the Basal subtype. MP2 exhibited high expression of MHC-II genes and was enriched in metastatic lesions. Next, we investigated the tumor architecture using public spatial transcriptomic datasets. Spot-level deconvolution revealed 12 distinct cellular niches. Deconvolution of these spatial niches in a large cohort of bulk RNA samples uncovered unique clusters associated with patient survival, providing novel insights into TME biology and its clinical implications. Citation Format: Gabriel Francisco Pozo de Mattos Pereira, Julia Crispim da Fontoura, Marvin Paulo Lins, Alessandro Bersch Osvaldt, Simone Marcia Dos Santos Machado, Eduardo Cremonese Filippi-Chiela, Cristina Bonorino. Single-cell and spatially resolved atlas of pancreatic cancer reveals immunophenotypes associated with clinical outcome [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_3):Abstract nr B126.