Single-Cell Transcriptomics Identifies Novel Prognostic Signatures in HNSCC Immunotherapy Response.

Head and neck squamous cell carcinoma (HNSCC) poses a major therapeutic challenge. In this study, we aimed to analyze tumor immune microenvironment changes and develop a prognostic model based on immunotherapy response. We analyzed single-cell RNA sequencing data from three HNSCC patients receiving TLR8 agonist and anti-PD1 combination therapy, identified cell subpopulations before and after treatment with a focus on six major immune cell types, and developed a LASSO-Cox risk stratification model using combined single-cell and bulk RNA sequencing data. We identified 19 pre-treatment and 13 post-treatment cell subpopulations. Analysis of six major immune cell types revealed differential gene expression patterns. Based on treatment-induced differential genes, we developed a LASSO-Cox model with 51 survival-associated genes, which showed robust predictive performance (AUC: 0.749-0.800) across different timepoints for both HPV-positive and HPV-negative patients. High-risk groups had elevated MDSCs and CAFs, decreased immune cell infiltration (except Th2 CD4+ T cells and common lymphoid progenitors), and increased expression of ICB-related genes. In conclusion, our model effectively captures patients' immune status and provides insights for optimizing HNSCC immunotherapy strategies.