Distinct NK Cell Signatures Define Prognosis in HPV-Positive Versus HPV-Negative Head and Neck Cancer

Background/Objectives: HPV status is a key prognostic determinant in head and neck squamous cell carcinoma (HNSCC), yet the immunological mechanisms underlying the survival advantage of HPV-positive (HPV⁺) over HPV-negative (HPV^-) disease remain poorly defined. This study aimed to characterize the tumor-infiltrating natural killer (NK) cell landscape in HPV-stratified HNSCC and identify novel therapeutic targets. Methods: We performed an NK-cell-centric re-analysis of published scRNA-seq data from 28 HNSCC patients (10 HPV⁺, 18 HPV^-; GEO: GSE139324, GSE164690), encompassing NK subset identification, pseudotime trajectory inference, and cell-cell interaction analysis. Key findings were validated by immunohistochemistry (IHC) in an independent cohort of 10 FFPE tissue sections, and prognostic associations were assessed using TCGA-HNSC data. Results: Four transcriptionally distinct NK cell subsets were identified: adaptive, cell-killing, CD56^bright, and virus-responsive. A cytotoxic CX3CR1⁺KLRB1^dim NK subset was specifically enriched in HPV⁺ tumors and independently associated with favorable survival. Conversely, HPV^- tumors upregulated CLEC2C and CLEC2D ligands on tumor cell surfaces, engaging the inhibitory receptor KLRB1 on NK cells; this CLEC2-KLRB1 axis correlated with suppressed NK activity and poorer prognosis, and was confirmed at the protein level by IHC. Conclusions: NK cell function in HNSCC is dichotomously regulated by HPV status. The CX3CR1⁺KLRB1^dim subset represents a candidate prognostic biomarker in HPV⁺ disease, and the CLEC2-KLRB1 axis is a targetable immune evasion mechanism in HPV^- HNSCC. These insights support the development of HPV-stratified immunotherapies; however, clinical translation requires validation in large, prospectively designed, subsite-matched cohorts to disentangle HPV-specific effects from anatomical site-dependent immune contextures.