LAUSR

Cancer vaccines have shown promise in treating late-stage cancers that have failed traditional therapies. Somatic mutations provide a rich source of potential cancer vaccines with minimal T-cell tolerance. We have built a robust screening assay to test somatic mutations for CD8+ T cell activation in a T cell-dendritic cell co-culture assay with synthetic peptides added from outside. Our screening assay revealed that non-mutated wild-type peptides in many instances induced T-cell activation, although their HLA binding affinity was weak. We suspect that addition of high concentration of the peptides from outside may overcome their weak HLA-binding property, allowing them to bind HLA and activate T cells. To reduce the bias of artificial HLA presentation, we have built a minigene platform to screen pairs of wild-type and mutant peptides to assess their immunogenicity. We applied our proprietary cancer vaccine prediction platform to a set of somatic single-nucleotide variants (SNVs) and indels and selected immunogenic peptides by a combination of features that include TCR binding, HLA binding, gene expression and proteasomal processing. Predicted mutant immunogenic peptides and their wild-type counterpart were cloned as minigenes and expressed in HLA restricted antigen-presenting cells (APCs). The minigene-expressing APCs were co-cultured with allogenic CD8+ T cells and activation was monitored by the combined expression of IFN-gamma, TNF-alpha and granzyme-A (CTL phenotype of T cells) by flow cytometry. Our screening assay reveals that a significant number of indels are not presented when they are expressed as a longer peptide because of the stability of the transcripts. However, their presentation and immunogenicity are preserved when they are expressed as short 9-mer peptides with engineered proteasomal cleavage sites. Our study also reveals a range of HLA-binding affinities for peptide presentation. In conclusion, our analysis demonstrates that the two approaches for investigating immunogenicity of peptides—minigene approach and external addition of peptide approach—have differential utilities for testing and validating the immunogenicity of indels and SNVs. Citation Format: Xiaoshan Shi, Vasumathi Kode, Kayla Lee, Amit Chaudhuri, Papia Chakraborty. A minigene platform to validate novel immunogenic peptides arising from somatic mutations as therapeutic cancer vaccines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 731.