Immune stratification in HPV-negative HNSCC: prognostic significance and prediction of immunotherapy response

The tumor immune microenvironment (TIME) played a crucial role in head and neck squamous cell carcinoma (HNSCC), significantly impacting disease progression and immunotherapy. To address these complexities, we analyzed gene expression profiles of 790 HNSCC tumors by combining data from The Cancer Genome Atlas (TCGA; n = 520) and the Gene Expression Omnibu database (GEO, n = 270). We identified five distinct TIME-based phenotypes, with the E class-characterized by tertiary lymphoid structures (TLS)-showing the highest survival rates and immunotherapy responses. To assess TLS prognostic value, we evaluated two cohorts of human papillomavirus (HPV) infection negative HNSCC: 247 surgical resection patients and 35 immunotherapy-treated patients with postoperative recurrence/metastasis. Additionally, we analyzed the GEO dataset (n = 102) comprising HNSCC patients with metastasis/recurrence who received PD-1/PD-L1 inhibitors, integrating clinical and transcriptomic data. Immune stratification systems integrating TIME composition and immune cell counts revealed that TLS-positive patients exhibited superior survival and enhanced immunotherapy responses in HPV-negative HNSCC. The two immune stratification systems exhibited greater accuracy and predictive power in estimating the overall survival of HPV-negative HNSCC patients compared to the use of TNM staging and tumor pathological stage. These findings provided a framework for establishing TLS-based personalized treatment in HPV-negative HNSCC, potentially enhancing disease surveillance, informing clinical practice, and improving patient prognosis.