Single-cell sequencing reveals an immunotherapy-relevant IFITM1-marked epithelial interferon state in nasopharyngeal carcinoma

BACKGROUND: Nasopharyngeal carcinoma (NPC) is an immune-rich epithelial malignancy with marked malignant-cell heterogeneity and variable benefit from immune checkpoint blockade. METHODS: Single-cell RNA-seq data were integrated with inferCNV, Monocle3, DoRothEA/decoupleR, donor-aware pseudobulk differential expression and CellChat ligand-receptor modeling. External validation used NPC bulk cohorts (GSE53819, GSE12452, GSE64634 and GSE102349), TCGA-HNSC, and the anti-PD-1/PD-L1-treated HNSCC cohort GSE159067. HK1 cells were used for preliminary IFITM1 knockdown assays. RESULTS: Among nine epithelial states, Epi7 emerged as a late-pseudotime interferon-responsive malignant epithelial state with marked IRF9, STAT2, IRF1 and STAT1 activity. IFITM1 was identified as its lead marker and was associated with CD274 at cell and donor levels. Donor-aware pseudobulk analysis confirmed that IFITM1-high cells carried a type I interferon and antiviral program, whereas Epi7 was enriched for chemokine signaling, antigen presentation and lymphocyte costimulation. CellChat analysis showed enhanced MIF, MHC-I, MHC-II, Midkine, APP and Galectin signaling from Epi7. Across external cohorts, IFITM1 was upregulated in NPC tumors, while the multigene Epi7 signature showed stronger correlations than IFITM1 alone across most checkpoint and immune-infiltration endpoints. IFITM1/Epi7-high tumors showed an inflamed but checkpoint-enriched microenvironment and higher composite ICB-likelihood. IFITM1 knockdown in HK1 cells reduced proliferation, colony formation and Matrigel-based invasion. CONCLUSIONS: Single-cell sequencing identified an IFITM1-marked Epi7 epithelial interferon program, in which IFITM1 serves as a lead marker rather than an exclusive determinant, linking NPC malignant-cell heterogeneity with tumor-immune communication and immunotherapy-relevant microenvironmental remodeling. The Epi7 program may provide a translational biomarker framework for immune stratification in NPC.