Single cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma

For many cancers, including head and neck squamous cell carcinoma (HNSCC), response rates to immunotherapy remain modest, with limited ability to predict responders. Previous studies that characterized cellular changes associated with immunotherapy in HNSCC focused on immune cells, providing limited insight into malignant cell responses. Motivated by this gap, we performed single cell RNA-sequencing on 16 HNSCC patients pre- and post-neoadjuvant pembrolizumab treatment. We identified a malignant-interferon (IFN)/MHC-II program in malignant cells, characterized by expression of MHC-II and interferon response genes, which was associated with tumor response to pembrolizumab. We validated malignant cell MHC-II expression at the protein level and characterized its relationship with surrounding immune subsets via multiplexed immunofluorescence. In a murine HNSCC model, IFN-γ-induced malignant cell MHC-II expression marked tumors with favorable immune microenvironments and sensitivity to immunotherapy. Finally, we confirmed pre-treatment expression of the malignant-IFN/MHC-II program as marker of response through deconvolution of bulk RNA-seq data from an independent cohort of 25 pembrolizumab-treated HNSCC patients. Beyond identifying malignant cell MHC-II expression and the malignant-IFN/MHC-II program as potential biomarkers for immunotherapy response in HNSCC, our work provides additional insights into the specific and important role of malignant cells in immunotherapy.