A Framework for Comparing Mouse Neoantigen Immunogenicity

SUMMARY Cytotoxic CD8+ T cell responses targeting tumor neoantigens are critical for immunotherapy efficacy and are widely studied across different preclinical mouse tumor models. Defined neoantigens are commonly introduced to enable tracking of tumor-specific T cells; however, variation in neoantigen choice may yield immune phenotypes attributable to differences in neoantigen immunogenicity, complicating interpretation of tumor-intrinsic mechanisms. Here, we determined the relative immunogenicity of a set of 25 commonly used mouse tumor-derived and model neoantigens to facilitate comparison of neoantigens across studies. We found that in silico predicted major histocompatibility complex (MHC) binding affinity poorly stratified in vivo immunogenicity. In contrast, experimental measurement of peptide-MHC complex stability (K off ), more so than measured affinity (K D ), closely correlated with the relative magnitude of neoantigen-targeted vaccine responses in vivo . Thus, we report the relative stability of a known set of commonly used neoantigens as a reference and provide a simple method to benchmark novel neoantigens against this library. This framework will allow contextualization of the level of immunogenicity of newly identified neoantigens and aid in comparative interpretation of tumor-immune phenotypes across studies.