Single-cell RNA-seq and spatial transcriptomics characterize CD8+ exhausted T cells in pancreatic ductal adenocarcinoma

Abstract

Summary Pancreatic cancer resists immunotherapy due to a suppressive immune microenvironment where CD8+ T cells play a key role. Using single-cell RNA sequencing and spatial transcriptomics, we characterized CD8+ exhausted T (Tex) cells in pancreatic ductal adenocarcinoma (PDAC). We generated single-cell profiles from PDAC tumors and matched peripheral blood mononuclear cells, and performed T cell sub-analysis. We found CXCL13 upregulated and GZMK downregulated in CD8+ Tex cells. Cell-cell interaction analysis showed that T cells most frequently interacted with myeloid cells and cancer cells via ligand-receptor pairs; INHBA+ macrophages and cancer cells communicated most with CD8+ Tex cells. Two key LR pairs (SPP1-integrin α4β1 and PLAUR-integrin α4β1) mediated crosstalk between cancer cells and CD8+ Tex cells, confirmed by immunofluorescence, spatial mapping, and protein docking. High SPP1 and PLAUR expression correlated with poor prognosis in TCGA-PAAD. These findings provide a resource for understanding CD8+ T cell exhaustion in PDAC.