头颈部鳞状细胞癌（HNSCC）包括一些由人乳头瘤病毒（HPV）驱动的癌症亚型。我们使用单细胞RNA测序对HPV阳性和HPV阴性的口咽肿瘤进行了分析，揭示了肿瘤内部和之间高水平的细胞多样性。首先，我们发现个体肿瘤内存在不同的染色体异常，这种基因组不稳定性能够在病理阴性边缘下鉴别恶性细胞。其次，我们揭示了HNSCC亚型和其他细胞状态（如细胞周期、衰老和上皮间质转化）之间的差异。第三，我们发现在HPV阳性的肿瘤内病毒基因表达存在异质性。在一部分细胞中失去或抑制了HPV表达，这些细胞与HPV相关的细胞周期表型降低、对治疗的响应下降、侵袭能力增强和预后不良有关。这些发现表明，HPV表达的多样性必须在诊断和治疗HPV阳性肿瘤时考虑，并具有重要的预后影响。© 2023.作者（们）独家许可Springer Nature America，Inc.

Head and neck squamous cell carcinoma (HNSCC) includes a subset of cancers driven by human papillomavirus (HPV). Here we use single-cell RNA-seq to profile both HPV-positive and HPV-negative oropharyngeal tumors, uncovering a high level of cellular diversity within and between tumors. First, we detect diverse chromosomal aberrations within individual tumors, suggesting genomic instability and enabling the identification of malignant cells even at pathologically negative margins. Second, we uncover diversity with respect to HNSCC subtypes and other cellular states such as the cell cycle, senescence and epithelial-mesenchymal transitions. Third, we find heterogeneity in viral gene expression within HPV-positive tumors. HPV expression is lost or repressed in a subset of cells, which are associated with a decrease in HPV-associated cell cycle phenotypes, decreased response to treatment, increased invasion and poor prognosis. These findings suggest that HPV expression diversity must be considered during diagnosis and treatment of HPV-positive tumors, with important prognostic ramifications.© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.