Single-Cell Atlas of Nasopharyngeal Carcinoma Reveals Epithelial Heterogeneity and Immune Evasion Networks

Background Although the tumor microenvironment of nasopharyngeal carcinoma (NPC) is rich in lymphocytic infiltration, tumors still evade immune clearance. The transcriptomic heterogeneity within epithelial compartments and the epithelial states associated with this immune context remain incompletely resolved. This study aimed to map epithelial heterogeneity in NPC at single-cell resolution and infer candidate ligand–receptor communication patterns associated with the immunosuppressive microenvironment. Methods A single-cell atlas of 1,122,790 cells was constructed from seven published cohorts, in-house tumor specimens, and patient peripheral blood mononuclear cells. Among these, 75,480 epithelial cells were independently reanalyzed and characterized using chromosome-aware CNV inference with inferCNVpy, root-dependent transcriptional-continuum mapping, pathway enrichment, exploratory survival modeling, spatial transcriptomics, and CellChat-based inference of potential ligand–receptor communication. Public bulk-transcriptomic PFS data and spatial-transcriptomic data were obtained from GSE102349 and GSE200310, respectively. Funding: None. Results Twenty-four epithelial transcriptional states were identified, including seven malignant-associated states supported by reproducible inferCNV patterns and coordinated immune-evasion and proliferation programs. The Epi_09 state, annotated by MEX3A expression, was prioritized based on concordant inferred-CNV, prognostic, and spatial evidence; its multigene signature was associated with progression-free survival in the GSE102349 cohort and enriched in malignant regions of a representative spatial transcriptomics specimen. Ligand–receptor analysis further identified candidate signaling relationships between malignant-associated epithelial states and exhausted T cells, regulatory T cells, and macrophages, including CXCL10-CXCR3, CD274-PDCD1, TNF-TNFRSF1A, and LGALS9-HAVCR2. These findings are association-based and require independent clinical and experimental validation. Conclusions Malignant epithelial subpopulations were associated with coordinated immunoregulatory ligand–receptor programs. The Epi_09 transcriptional state, marked by MEX3A, represents a computationally prioritized malignant-associated population that warrants functional investigation. The present data do not establish MEX3A as a causal regulator or validated therapeutic target in NPC.