Discovery of Human Papilloma Virus and patient-specific neoantigens targeted by CD8+T cells in HNSCC

Abstract Head and neck squamous cell carcinoma (HNSCC) is amongst the rapidly growing form of cancer associated with high mutation burden and Human Papilloma virus (HPV) infection presenting approximately 800,000 new cases and 400,000 deaths annually. HPV-positive (HPV) HNSCC has been strongly associated with better prognosis than HPV-negative HNSCC due to the immune activation in the tumor microenvironment including cytotoxic CD8+ T cells. One of the key missing links is the relative contribution of HPV-reactive and neoantigen-reactive CD8+ T cells in anti-tumor response. To address this, we utilized epitope libraries presented in Signaling and Antigen-presenting Bifunctional Receptors (SABRs), which were previously described by our lab. As a proof-of-concept, we generated SABR libraries presenting 8392 epitopes derived from HPV or from personalized neoantigens from five HNSCC patients. In parallel, we used single cell RNA sequencing to identify 25 clonally expanded TCRs from tumor-infiltrating lymphocytes of the patients. Using SABR screens, we have identified several putative HPV-derived and neoantigen-derived epitopes targeted by CD8+ T cells in HNSCC patients. We have established a robust pipeline for identification of patient-specific epitope specificities from tumor-infiltrating CD8+ T cells. The goal is to determine whether and how effective anti-HPV or anti-neoantigen T cell responses may contribute to therapeutic efficacy using human samples from clinical trials and murine HNSCC models. Our study will aid in the discovery of novel tumor-associated antigens in HPV+ HNSCC patients, which can be successfully employed for precise adoptive T cell transfer therapies.