Abstract 2685: Activated phenotype of intraepithelial type 1 innate lymphoid cells is enriched in HPV-positive head and neck cancers

Abstract Innate lymphoid cells (ILCs) and natural killer (NK) cells are a heterogeneous family of innate immune cells that regulate inflammation, immune tolerance and tissue homeostasis in infection, chronic inflammation, metabolic diseases and cancer. The ILC family lacks the expression of antigen-specific receptors and demonstrate effector function by generating cytokines and secreted proteins. In tumor microenvironment, ILCs play a dual role including both tumor regression and tumor promotion, suggesting their diverse phenotypes and functional states. Among the ILC family, ILC1s and NK cells share some features, including the expression of the transcription factor T-bet and the ability to produce IFN-γ. In the present study, we analyzed single-cell RNA sequencing (scRNAseq) data to investigate the landscape and functional status of ILC families in patients with head and neck squamous cell carcinoma (HNSCC). The GSE164690 dataset, including pre-processed scRNAseq data and clinical data, was obtained from Gene Expression Omnibus. A total of 17 pairs of tumor-derived CD45-positive cells and peripheral blood lymphocytes, consisting of 6 HPV-positive HNSCCs and 11 HPV-negative HNSCCs, were analyzed using the Seurat v4 R package. After quality control, a total of 95,809 cells were obtained and clustered into 16 immune cell clusters. Next, a total of 7,278 NK cells were extracted and sub-clustered into 11 clusters. To characterize the 11 clusters, the abundances of NK subsets were estimated by CIBERSORTx. This approach identified eight NK cell clusters, two intraepithelial ILC1 (ieILC1) clusters, and one ieILC1-NK-intermediate (ieILC1-NK-int) cluster. Single-sample GSEA (ssGSEA) analysis was performed to further characterize each subset. ieILC1 clusters expressed tissue-resident markers ITGA1, CD69, and CXCR6, whereas ieILC1-NK-int cluster expressed ILC1 markers CCR7, IL7R, and SELL. Principle component analysis (PCA) based on ssGSEA indicated that ieILC1 clusters and ieILC1-NK-int showed the different PCA distribution from NK clusters. Inflammation and effector function-related pathways, including inflammatory response, interferon-gamma response, and interferon-alpha response, were enriched in ieILC1 clusters compared with the others. Among ieILC1 clusters, several pathways, including hypoxia, TNFA signaling via NFKB, allograft rejection, TGF beta signaling, were more enriched in ieILC1-1 than in ieILC1-2, suggesting that ieILC1-1 is the most immunologically active phenotype among NK subclusters. Of note, ieILC1-2 mainly comprised cells isolated from HPV-negative tumors, whereas ieILC1-1 mainly comprised cells isolated from HPV-positive tumors. In conclusion, we have demonstrated the diverse landscape of NK and ieILC1 cells in patients with HNSCC. Further characterization of the ILC family would lead to a novel therapeutic approach against HNSCC. Citation Format: Hideyuki Takahashi, Shota Ida, Hiroe Tada, Kazuaki Chikamatsu. Activated phenotype of intraepithelial type 1 innate lymphoid cells is enriched in HPV-positive head and neck cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2685.