Neoepitope Discovery

Our previous work led to the elaboration of the cancer immunoediting concept wherein the immune system was shown to not only protect individuals against cancer outgrowth but also shape tumor immunogenicity. In the course of these studies we developed an immunogenomics approach involving identification of expressed somatic mutations in tumors and prediction of those mutations that formed tumor-specific mutant neoantigens (TSMA). We went on to show that some of the predicted strong neoantigens expressed in highly immunogenic, unedited tumor cells (derived from immunodeficient mice) were important cancer immunoediting targets. We also showed that the T cell dependent immunoediting of a developing tumor selected for tumor cell variants that lacked expression of strong TSMAs, thereby rendering the edited tumor more fit to survive in an immunocompetent host. We subsequently applied this approach to established, immunoedited tumors that grew progressively in vivo but were rejected when tumor-bearing mice were subjected to immune checkpoint blockade therapy. This work showed that certain weaker TSMA remaining in tumor cells after immunoediting were favored targets of anti-tumor T cells that are rejuvenated in tumor-bearing mice treated with immune checkpoint blocking antibodies. In the case of the T3 sarcoma (that expresses 700 nonsynonymous mutations), we showed that point mutations in the genes encoding Laminin asubunit 4 (Lama4) or the Alg8 glucosyltransferase, led to the generation of two immunodominant mutant neoantigens for CD8+ T cells. Importantly we showed that a vaccine comprised of synthetic long peptides encompassing the mutations in mutant Lama4 (mLama4) and mAlg8 plus adjuvant was as effective in eliminating established T3 tumors in mice as anti-PD-1 and/or anti-CTLA-4 therapy. More importantly, the combination of personalized vaccine plus anti-PD-1 cured >80% of mice bearing large tumors (>1 cm diameter) while monotherapies with individual checkpoint blocking antibodies or vaccine alone were not effective. These observations prompted the opening of several clinical trials at Washington University and elsewhere that are focused on using personalized cancer neoantigen vaccines (either alone or together with immune checkpoint blocking antibodies) to treat different cancers that display quantitatively distinct mutational landscapes. In addition, we continue to use our immunogenomics approaches to delve deeper into the minimal requirements for successful cancer immunotherapy. First, using a CRISPR/Cas9 approach to convert dominant neoantigens in a tumor back with wild type, we have shown that immune responses to stronger neoantigens can obscure responses to weaker ones, i.e. that cancer neoantigens exhibit profound immunodominance. Second, using oncogene driven sarcomas that were completely devoid of mutant neoantigens, we found that protective immune responses to tumors minimally require the host response to bothMHC-I and MHC-II restricted neoepitopes. Third, using a combination of single cell RNAseq and CyTOF approaches, we have found that tumor infiltrating lymphoid and myeloid cells display an unexpected complexity and undergo major transcriptional and functional remodelling (including changes in the frequencies of tumor neoantigen specific T cell receptor sequences) that are dependent on the type of immunotherapy used and whether the tumor continues to grow progressively or is immunologically eliminated. The implications of these findings to development of effective neoantigen vaccines will be discussed.