As tumors evolve, cancer cells acquire somatic mutations and these mutations generate tumor specific neoantigens that are different from self and can be recognized by T-cells, inducing anti-tumor immune responses. Such immunogenic antigens can be effective targets for neoantigen-based cancer vaccines. However, the identification of immunogenic neoantigens remains limited with the current prediction models. Here we designed mouse experiments to model tumor evolution under immune pressure and its association with T-cell clones to identify these antigens agnostically and improve current prediction models. We injected three lung cancer cell lines (KPA, KPC, and HKP1) in wildtype immune-competent C57BL/6 mice and immune-deficient Rag1 defective (Rag1 KO) mice, respectively. The three tumor cell lines have common driver mutations, Kras G12D/+ and p53 flox/flox. Two weeks post tumor implantation, whole exome sequencing and RNA-seq was performed on tumor samples. We also performed T cell receptor (TCR) sequencing to profile tumor infiltrated TCR clones. Despite the shared driver mutations, tumor growth patterns in vivo over time are very distinct for each cell line. Interestingly, KPA tumors show differential evolutionary patterns in wild type mice versus Rag1 KO mice, regressing in the former but rapidly progressing in the latter, suggesting that the difference can be attributed to immunoediting of KPA specific neoantigens. HKP1 tumors do not show substantial differences in that aggressive tumor progression is observed in both types of mice. Using WES data, we estimated the cancer cell fraction of each mutation based on phylogeny re-construction. We found that evolved KPA tumors (immunogenic) had significantly lower mutation burden in wild type mice compared to Rag1 KO mice (3410 vs 4199 on average), and the fraction of cell line mutations edited in vivo is significantly higher in wild type than in Rag1 KO (26% vs 14% on average), suggesting again the active on-going immunosurveillance in immune competent mice. In contrast, HKP1 tumors (non-immunogenic) do not show significant differences in mutation burden nor fraction of mutations edited between wild type and Rag1 KO mice. Furthermore, TCR-seq data show that the clonal expansion of T-cells is strongly associated with tumor immunogenicity. KPA tumor samples show significantly higher TCR clustering but with less diversity, quantified by modified Simpson’s Index, that is strongly correlated with the suppression of mutational burden (r=0.74). In summary, we found that tumor evolution in immune competent mice is dependent on mutational context of the tumor. By analyzing longitudinal tumor and TCR sequencing data, we showed that the immunogenicity of tumors is associated with significant decrease in mutational burden and higher T-cell clustering that is indicative of tumor mutation and TCR clone expansion co-evolution in immune competent mice.

Citation Format: Jayon Lihm, Hyejin Choi, Mariam M. George, Yuval Elhanati, David Hoyos, Marta Luksza, Taha Merghoub, Benjamin D. Greenbaum. Modeling tumor immunoediting coupled with T-cell repertoire dynamic [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 610.