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| Home > Publications database > A unified single-cell atlas of HNSCC: Toward characterizing HPV- and sex-associated TME variability |
| Home > Publications database > A unified single-cell atlas of HNSCC: Toward characterizing HPV- and sex-associated TME variability |
| Journal Article | DKFZ-2026-01168 |
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2026
Elsevier
St. Louis
Abstract: Head and neck squamous cell carcinoma (HNSCC) is highly heterogeneous, with variations driven by humanpapillomavirus (HPV) status and sex. However, existing single-cell RNA sequencing (scRNA-seq) studies areoften limited in sample size and lack standardized methodologies, limiting cross-study comparisons. Toaddress this, we integrated scRNA-seq data from 78 patients (274,911 cells) across multiple studies, creatinga 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 andscGate, we improved tumor and immune cell classification. Leveraging our atlas, we identified HPV-specificshifts 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 suggesteddistinct microenvironmental patterns, warranting further investigation. This publicly available atlas providesa comprehensive framework for reproducibly studying HNSCC biology, improving patient stratification, andmay help inform personalized therapies.
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