No abstract

High-affinity MHC I-peptide interactions are considered essential for immunogenicity. However, some neo-epitopes with low affinity for MHC I have been reported to elicit CD8 T cell dependent tumor rejection in immunization-challenge studies. Here we show in a mouse model that a neo-epitope that poorly binds to MHC I is able to enhance the immunogenicity of a tumor in the absence of immunization. Fibrosarcoma cells with a naturally occurring mutation are edited to their wild type counterpart; the mutation is then re-introduced in order to obtain a cell line that is genetically identical to the wild type except for the neo-epitope-encoding mutation. Upon transplantation into syngeneic mice, all three cell lines form tumors that are infiltrated with activated T cells. However, lymphocytes from the two tumors that harbor the mutation show significantly stronger transcriptional signatures of cytotoxicity and TCR engagement, and induce greater breadth of TCR reactivity than those of the wild type tumors. Structural modeling of the neo-epitope peptide/MHC I pairs suggests increased hydrophobicity of the neo-epitope surface, consistent with higher TCR reactivity. These results confirm the in vivo immunogenicity of low affinity or ‘non-binding’ epitopes that do not follow the canonical concept of MHC I-peptide recognition.

A high- affinity MHC I-peptide interaction is considered essential for immunogenicity. However, some neoepitopes with low affinities for MHC have been reported to elicit CD8-dependent tumor rejection in immunization-challenge studies. Here, we ask if a non-binder, tumor-rejection- mediating neoepitope influences the natural immunogenicity of a tumor in vivo, in the absence of artificial immunization. A mutation in tumor MUT1 was edited to its WT counterpart; the mutation was then re-introduced into the WT tumor, recapitulating the mutation in a tumor MUT2. TILs from all three tumors show T cell activation. However, TILs of MUT1 and MUT2 show significantly stronger transcriptional signatures of cytotoxicity and TCR engagement as well as the greater breadth of TCR reactivity than those of WT. Structural modeling of the Kd-neoepitope complex suggests increased hydrophobicity of the neoepitope surface consistent with higher TCR reactivity. These results reveal the immunogenicity in vivo of low affinity or “non-binding” epitopes that do not follow the canonical view of MHC I-peptide recognition.

Cancer neoepitopes are the only truly tumor-specific antigens and therefore, the most suitable as cancer vaccines. Current methods to predict neoepitopes, based on studies of viral epitopes, emphasize high affinity MHC-peptide interactions. Increasing evidence in human and murine models indicates that the present neoepitope prediction methods are mostly inaccurate in predicting true MHC I-restricted cancer neoepitopes. Here, in a completely unbiased approach, all possible neoepitopes in a mouse tumor model were tested for their ability to mediate tumor rejection and also CD8+ T cell responses. These studies show that the true tumor rejecting neoepitopes have different properties from those of viral epitopes. Further, CD8+ T cell responses elicited by these neoepitopes possess a more plastic chromatin phenotype with stem-like properties that is known to be associated with anti-viral and anti-tumor immune responses. Such cancer neoepitopes can be exploited for generation of personalized cancer vaccines.