An expanded, phenotypically distinct tumor cell subset with low HPV mRNA increases recurrence risk
Human papillomavirus-related (HPV+) cancers harbor a subset of tumor cells expressing certain senescence-related transcripts and reduced levels of HPV mRNAs. We aimed to define this HPV-low population's biologic traits and clinical significance via integrated analysis of recurrence-prone human HPV+ oropharyngeal cancers (OPCs) and patient-derived xenografts (PDXs) of variable therapy sensitivity. Single-cell mRNA sequencing of PDXs and human tumors detected gene expression profiles in HPV-low cells indicating lack of senescence or terminal differentiation and intact tumorigenic capacity. HPV-low cells in cisplatin-refractory PDXs and particular human OPCs differentially upregulated multiple pathways linked to aggressive tumor biology, including RAS signaling, IL-6 signaling, and EMT. Predicted loss of cell-cell interactions among HPV-low cells reflected reduced epithelial identity, further supporting their more aggressive biology. Accordingly, the size of the pre-treatment HPV-low fraction had strong, independent association with recurrence risk. Genetic subclones within OPCs varied widely in content of HPV-low cells, which were enriched in particular lineages. Our findings uncover novel pro-tumor functions of HPV-low cells and support a central role for them in therapy resistance as well as potential utility as a clinical biomarker. Further elucidating mechanisms of cooperativity and plasticity between HPV-low and high states holds promise to reveal targets in treatment-refractory HPV+ malignancies.