Single cell RNA-Seq uncovers a head and neck cancer senescence program

Cellular senescence is commonly viewed as a stable state of cell cycle arrest, triggered by multiple types of stress. Though senescent cells share several common features, the nature of the senescence program is highly context and cell type-dependent, making it a complex and highly heterogeneous phenotype. Accumulating evidence indicates that senescent tumor cells promote tumor relapse, aggressiveness, and metastasis. In this work, we first analyzed single cell RNA-seq data from two treatment-naive human Head and neck squamous cell carcinoma (HNSCC) patient cohorts and identified a recurrent gene signature of epithelial senescence (EpiSen). Next, we sought in vitro models of EpiSen through analysis of ~200 cell lines and selected two with the highest differential score for the EpiSen signature. Based on cell surface markers derived from the EpiSen signature, we isolated the senescent cells and tested the sorted population for differential drug sensitivities and population dynamics. The senescent cells were specifically sensitive to senolytics and resistant to chemotherapies. Furthermore, senescent cells were more sensitive to inhibition of the EGFR-PI3K-AKT axis, suggesting a biological mechanism and potentially a biomarker for EGFR inhibition, which is currently the only standard targeted therapy for HNSCC. Untreated sorted senescent cells transitioned to the original state distribution and re-entered the cell cycle, suggesting a possible mechanism for post treatment relapse. These results provide better understanding of the senescence phenotype, its contribution to intra-tumor heterogeneity and may aid in the development of future cancer therapies.