CD161 serves as a prognostic biomarker and predicts immunotherapy response in head and neck squamous cell carcinoma

Despite advances in immune checkpoint inhibitors (ICIs), the prognosis of patients with head and neck squamous cell carcinoma (HNSCC) remains poor, and reliable biomarkers for predicting clinical outcomes are still lacking. CD161, a lectin-like receptor expressed on multiple T-cell subsets, has been reported to inhibit T-cell cytotoxicity; however, its prognostic and immunological significance in HNSCC remains unclear.

We analyzed transcriptomic data from the HNSCC cohort in the TCGA database and four GEO datasets (GSE6631, GSE102349, GSE159067, and GSE103322) to evaluate CD161 expression, its prognostic significance, and its association with immune infiltration and functional pathways. Single-cell RNA sequencing data were used to identify CD161-expressing cell subsets. Differential expression was further validated by immunohistochemistry (IHC) in 20 paired HNSCC and adjacent normal tissues. The association between CD161 expression and immunotherapy response was additionally assessed in an independent cohort of 33 ICI-treated patients.

CD161 expression was significantly lower in HNSCC tissues than in normal tissues in the TCGA cohort and the GSE6631 dataset, which was further confirmed by IHC analysis. High CD161 expression was associated with a favorable prognosis, with longer overall survival (OS) and disease-specific survival (DSS), and remained an independent protective factor in multivariate analysis (OS: hazard ratio [HR] = 0.92, 95% confidence interval [CI]: 0.86-0.99, p = 0.019; DSS: HR = 0.86, 95% CI: 0.78-0.96, p = 0.008). CD161 expression correlated with infiltration of CD8⁺ T cells and regulatory T cells, as well as with multiple immune checkpoint molecules, including CD27, TIGIT, BTLA, and PD-1. Single-cell analysis further localized CD161 predominantly to CD4⁺ T cells. In the GSE159067 dataset, high CD161 expression was associated with longer progression-free survival and overall survival. In our ICI-treated cohort, high CD161 expression correlated with longer PFS and higher objective response rate.

CD161 is downregulated in HNSCC. Higher CD161 expression is associated with favorable prognosis and an immune-inflamed tumor microenvironment, and may predict response to ICI-containing therapy. These findings suggest that CD161 has potential as a prognostic biomarker and may help characterize tumor-immune interactions in HNSCC.