Integrated Multiomic Analysis Reveals an EBV‐Associated MIF–SPP1 + Macrophage Axis Linking Tumor Stemness and Immune Dysfunction in Nasopharyngeal Carcinoma

Elucidating how Epstein–Barr virus (EBV) shapes tumor–immune interactions is important for improving therapy in nasopharyngeal carcinoma (NPC). This multi‐cohort analysis integrates single‐cell, spatial, and bulk transcriptomic data with multiplex immunofluorescence and functional assays. Single‐cell profiling identifies stemness‐associated epithelial states and enrichment of SPP1 + tumor‐associated macrophages (TAMs) in EBV + NPC. SPP1 + TAM abundance is associated with stemness‐associated epithelial features and dysfunctional T‐cell states, while high MIF and SPP1 + macrophage signatures are associated with shorter progression‐free survival. Within the EBV + spatial cohort, SPP1 + TAMs co‐occur with stemness‐associated tumor cells, exhausted CD8 + T cells, and regulatory T cells in Niche 5, which is more frequent in non‐response tumors following chemoimmunotherapy. Functional experiments show increased MIF expression and secretion by EBV + epithelial cells. MIF inhibition attenuates conditioned‐medium‐induced monocyte migration and SPP1‐associated TAM‐like programming, whereas recombinant MIF reproduces these effects. Conversely, macrophage‐derived SPP1 increases stemness‐associated marker expression and tumorsphere formation in EBV + epithelial and tumor models. It also impairs primary CD8 + T‐cell proliferation, effector function, and cytotoxic activity while increasing exhaustion‐associated markers; CD44 blockade partially reverses these effects. Collectively, these findings support an EBV‐associated MIF–SPP1 macrophage–tumor/T‐cell crosstalk model linking stemness‐associated epithelial phenotypes with immune dysfunction and adverse clinical outcomes.