Resolving the co-occurrence and mutual exclusivity patterns of cancer cell states in HPV-negative HNSCC by integrating single-cell and spatial transcriptomics

Diverse cellular states manifest intratumor heterogeneity, underpinning tumor evolution and therapeutic resistance. However, cancer cell states and their interactive patterns in HPV-negative head and neck squamous cell carcinoma (HNSCC) remain unclear. Here, we integrated single-cell RNA-seq and spatial transcriptomics to delineate the cancer cell state landscape. By analyzing 408,606 cells from 81 samples, we identified eighteen cancer cell states (CCSs) and mapped their co-occurrence and mutual exclusivity (CO/ME) patterns along tumor progression. Spatial analyses revealed distinct tumor microenvironment architectures of CSSs, highlighting cDC2 and pDC as potential regulators of co-occurring hormone-related (ER_AR) and complement-related (CC) states. Leveraging state-specific signatures, we defined six novel cell state subtypes, which reflected CO/ME patterns and improved prognostic efficacy, and further presented potential subtype/state-specific therapeutic drugs and response mechanisms. Our study provides a comprehensive map of cancer cell states and coordinate patterns, offering new insights into the development of precision treatment strategies in HNSCC.For complete merged single-cell data, please contact us.