Spatial transcriptomic analysis of head and neck squamous cell carcinoma reveals novel regulators of hybrid epithelial-to-mesenchymal transition

Head and neck squamous cell carcinoma (HNSCC) is characterized by a high degree of intra- and inter-tumoral heterogeneity. Here we use spatial transcriptomics (ST) to profile both HPV-positive and HPV-negative HNSCC, uncovering distinct patterns of spatial organization of malignant cells and the surrounding tumor microenvironment across groups of tumors. First, we find that HPV-positive HNSCC is characterized by high cellular density in all cellular compartments with distinct expression of hypoxia, senescence, and cell cycle-associated genes in the malignant compartment. In HPV-negative HNSCC, we find two distinct spatial patterns of a partial epithelial-to-mesenchymal transition (p-EMT) program. One pattern is spatially associated with fibroblasts, characterized by p-EMT at the leading edge of tumor nests (“p-EMT edge”), and mediated by TGFB-signaling. The other pattern features high p-EMT expression in the core of tumor nests (“p-EMT core”). In p-EMT core tumors, we observe high co-localization of p-EMT cells with an inflammatory response program including neutrophils and macrophages, as well as differential expression of distinct ligands, including OSM. In vitro experiments demonstrate that OSM can induce the p-EMT state in multiple HNSCC models. Together these findings suggest that multiple p-EMT phenotypes exist across HPV-unrelated HNSCC and are mediated by distinct cell-to-cell signaling mechanisms, highlighting potential novel therapeutic vulnerabilities.