Hpv-driven rewiring of the tumor immune microenvironment through single-cell profiling informs prognosis and therapy in HNSCC.

PURPOSE: Human papillomavirus (HPV) status is a key prognostic factor in head and neck squamous cell carcinoma (HNSCC), yet the precise immunological mechanisms and robust biomarkers for guiding personalized therapy remain elusive. This study aims to comprehensively delineate how HPV infection reprograms the tumor immune microenvironment (TIME) and to develop a novel prognostic model for stratifying patient outcomes and therapeutic responses.

METHODS

Multi-omics data from TCGA and GEO databases were integrated. The immune landscape was compared between HPV+ and HPV- HNSCC using bulk transcriptomic deconvolution and single-cell RNA sequencing (scRNA-seq) profiling. A prognostic risk signature was constructed from HPV-associated genes via LASSO-COX regression and validated in independent cohorts. The model was evaluated for its association with immune infiltration, tumor mutational burden, and drug sensitivity. Cellular communication networks were deciphered using CellChat. Hub genes expression was confirmed by immunohistochemistry (IHC).

RESULTS

Single-cell profiling revealed that HPV+ tumors were characterized by an immunologically active microenvironment with increased infiltration and enhanced crosstalk of cytotoxic CD8+ T cells, helper CD4+ T cells, and B cells. In contrast, HPV- tumors exhibited a stromal-rich, immunosuppressive niche. We developed and validated a prognostic model based on seven HPV-related genes (IER3, FHL2, MBOAT2, DSC3, IRAK3, RGMA, BARD1). This risk score robustly stratified patients into high- and low-risk groups with distinct overall survival (low-risk vs. high-risk, P < 0.0001) and was an independent prognostic factor. The low-risk group, mirroring the HPV+ phenotype, demonstrated an activated immune milieu, higher expression of immune checkpoints (e.g., PD-1, CTLA-4), and was predicted to be more responsive to both chemotherapy and immunotherapy. Conversely, the high-risk group displayed a barren immune landscape, enriched in stromal and pro-tumorigenic pathways (e.g., MIF, COLLAGEN), and heightened sensitivity to specific targeted agents (e.g., Dasatinib). IHC validation confirmed the tumor-promotive role of hub genes (IER3, FHL2).

CONCLUSION

Our study leverages single-cell profiling to elucidate HPV-driven immunological remodeling in HNSCC. The derived prognostic signature effectively captures the essence of the TIME, serving as a reliable biomarker for predicting patient survival and informing precision therapy, potentially bridging the gap between HPV status and clinical decision-making.