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.

头颈部鳞状细胞癌 (HNSCC) 包括一部分由人乳头瘤病毒 (HPV) 驱动的癌症。在这里，我们使用单细胞 RNA-seq 来分析 HPV 阳性和 HPV 阴性口咽肿瘤，揭示肿瘤内部和肿瘤之间的高水平细胞多样性。首先，我们在单个肿瘤中检测到多种染色体畸变，表明基因组不稳定，即使在病理阴性边缘也能识别恶性细胞。其次，我们发现了 HNSCC 亚型和其他细胞状态（例如细胞周期、衰老和上皮-间质转化）的多样性。第三，我们发现 HPV 阳性肿瘤中病毒基因表达的异质性。HPV 表达在一部分细胞中丢失或受到抑制，这与 HPV 相关细胞周期表型的减少、对治疗的反应降低、侵袭增加和预后不良有关。这些发现表明，在 HPV 阳性肿瘤的诊断和治疗过程中必须考虑 HPV 表达多样性，并具有重要的预后影响。