An integrated immune-related signature reveals prognostic and immune–microbiome–genomic interactions in head and neck squamous cell carcinoma

Background Head and neck squamous cell carcinoma (HNSCC) is characterized by substantial biological diversity and heterogeneous clinical outcomes. Immune-based therapies have improved treatment options for some patients; however, reliable biomarkers capable of accurately defining patient risk and immune status remain insufficient. Methods Transcriptomic data from TCGA-HNSC and multiple independent GEO validation cohorts were integrated to establish and evaluate the immune-related prognostic framework. Immune checkpoint-related gene expression was analyzed to classify tumors into distinct immune phenotypes. Candidate biomarkers were identified through cross-cohort screening and incorporated into an immune-derived prognostic index using survival modeling. The clinical relevance of this index was assessed in independent datasets by evaluating immune infiltration, tumor mutational burden (TMB), intratumoral microbiome characteristics, and functional effects following gene perturbation. Results Two immune phenotypes with distinct biological characteristics and survival outcomes were identified. Four immune-associated genes, including CXCL9, CXCL10, CCL5, and GZMB, were consistently identified across datasets and incorporated into an immune-derived prognostic index. This model effectively separated patients with different survival risks and retained prognostic value after adjustment for clinical variables. The immune index showed significant associations with immune cell activity, microbial composition, and genomic alterations based on cross-sectional analyses, suggesting potential relationships among these biological features. Experimental inhibition of the four genes enhanced malignant behaviors of HNSCC cells, including proliferation, migration, and invasion, while reducing apoptosis. Conclusion By integrating immune-related features, this signature facilitates simultaneous prediction of clinical prognosis and assessment of the tumor microenvironment in HNSCC. This framework may provide a basis for individualized prognostic stratification and improve understanding of immune-associated tumor heterogeneity in HNSCC.