Abstract PR05: APOBEC mutagenesis is tightly linked to the immune landscape and immunotherapy biomarkers in head and neck squamous cell carcinoma
Authors: Lin Yan , Zhai Shuyan , Kuo Fengshen , Chan Timothy A. , Morris Luc G. , Ferris Robert L. , Faden Daniel L. , Ding Fei 
Published: September 2020

Significant interest is focused on the immune microenvironment of head and neck squamous cell carcinoma (HNSCC) due in part to the recent success of immune modulating therapeutics. HNSCC is known to be an immunologically active tumor with immune cell infiltration levels among the highest of all cancers, high mutational burden, and a subset of patients who respond to immune checkpoint blockade. One of the primary sources of mutations in HNSCC is the cytidine deaminase APOBEC3, which is also a known factor in innate immunity. Why particular HNSCCs have higher rates of APOBEC mutations and how these mutations relate to the immune microenvironment and immune activation remain unknown. We utilized whole-exome and RNA-Seq datasets from 276 HNSCC patients from TCGA to annotate APOBEC mutations, immune cell populations, activating and end effectors of immunity and predict neoantigens. In combination with FFPE tissue sections from matched patients, patient demographic data and germline APOBEC polymorphism status, we interrogated the relationship between APOBEC mutations and the immune landscape. Immune cell populations and composite scores of immune activation and infiltration (IFNy score, CYT score, Estimate Immune score) are tightly associated with APOBEC mutational burden, both univariately and after controlling for HPV status (p = 0.013-0.014). HNSCC has the highest levels of IFNy across cancer types with high APOBEC mutational burden, with the highest IFNy scores in HPV mediated HNSCC (HPVmHNSCC) (p = 0.05). Similarly, PD-L1 expression is positively associated with APOBEC mutational burden (p = 0.04). Mutation-induced tumor-specific neoantigen burden is strongly associated with APOBEC mutational burden while other sources of neoantigens are not associated (p = 8e-12). The presence of a germline APOBEC gene polymorphism is more prevalent in non-white, non-black race patients and within this group, patients with the polymorphism have higher APOBEC mutational burden (p= 0.002). Taken together, these data suggest that multiple mechanisms may exist within HNSCC that lead to APOBEC mutations. Immune upregulation, potentially in response to mutation-induced neoantigens, appears to be the primary driver, with viral infection inducing additional IFNy production in the subset of tumors caused by HPV. These mechanisms may be additive and not mutually exclusive, which could explain the higher levels of APOBEC mutations in HPVmHNSCC. The tight interconnectedness of APOBEC mutations and the immune landscape in HNSCC, including numerous known markers of response to immunotherapy, highlights the importance of the immune microenvironment in mutation acquisition in HNSCC.

Citation Format: Yan Lin, Shuyan Zhai, Fengshen Kuo, Timothy A. Chan, Luc G. Morris, Robert L. Ferris, Daniel L. Faden, Fei Ding. APOBEC mutagenesis is tightly linked to the immune landscape and immunotherapy biomarkers in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr PR05.