A Unified Single-Cell Atlas of HNSCC: Uncovering HPV and Sex Variability in the Tumor Microenvironment

Head and neck squamous cell carcinoma (HNSCC) is highly heterogeneous, with variations driven by HPV status and sex. However, existing single-cell RNA sequencing (scRNA-seq) studies are often limited in sample size and lack standardized methodologies, limiting cross-study comparisons. To address this, we integrated scRNA-seq data from 78 patients (274,911 cells) across multiple studies, creating a unified HNSCC atlas that harmonizes annotations and enables robust tumor microenvironment (TME) analyses. Using STACAS for semi-supervised integration and automated annotation tools such as Ikarus and scGate, we improved tumor and immune cell classification. Leveraging our atlas, we identified HPV- and sex-specific shifts in immune and stromal composition, with HPV+ tumors enriched in adaptive immune cells and HPV− tumors showing more stromal and myeloid populations. Preliminary sex-stratified analyses suggested distinct microenvironmental patterns, warranting further investigation. This publicly available atlas provides a comprehensive framework for reproducibly studying HNSCC biology, improving patient stratification, and may help informing personalized therapies.