Systematic Discovery Of Kras Neoantigens.

Response rates to immunotherapies in pancreatic ductal adenocarcinoma (PDAC) patients are low. However, cases with long-term survival have been correlated with both T cell infiltration and quality of neoantigens (i.e., epitopes from mutations presented by Human Leukocyte Antigen (HLA) molecules). It is known that mutations in the KRAS oncogene, which occur in the majority of PDAC patients, can be recognized by T cells as neoantigens on specific HLA molecules and lead to tumor control. KRAS neoantigens may thus be an attractive therapeutic target in a substantial fraction of PDAC patients. In this study, we systematically evaluated a broad range of KRAS neoantigens using an integrated discovery and validation pipeline. To date, the discovery and validation of KRAS neoantigens has mainly relied on the detection of stochastic T cell responses in patient samples or the use of transgenic mouse models. As such, the reported coverage of common HLA alleles is relatively limited. To overcome these issues, we established a systematic pipeline that addresses two fundamental principles: (1) the presentation of the neoantigen on cells with the mutation and (2) ability of the neoantigen to elicit T cell responses. The presentation of potential neoantigens was evaluated by applying a targeted mass spectrometry approach to detect peptides eluted from specific class I HLA molecules isolated from cells harboring a KRAS mutation of interest. T cell responses were elicited to MS-observed peptides using a proprietary in vitro stimulation protocol, after which the T cells can further be used in cytotoxicity assays to orthogonally confirm neoantigen presentation. We substantiated our pipeline using KRAS codon 12 neoantigens reported in the literature (e.g., G12D on HLA-C*08:02), then evaluated novel neoantigens predicted to be presented by common class I HLA molecules in the U.S. population. Through this pipeline, we have increased the number of validated KRAS neoantigens and thus the targetable patient population expected to harbor at least one KRAS neoantigen. A more comprehensive understanding of KRAS neoantigens will help drive focused therapies, such as the development of tumor-specific T cell receptor (TCR) therapies or neoantigen vaccines in appropriate patient populations in PDAC or other indications. Citation Format: Jaewon Choi, Scott P Goulding, Brandon P. Conn, Christopher D. McGann, Jared L. Dietze, Jessica Kohler, Divya R. Lenkala, Antoine Boudot, Daniel A. Rothenberg, Paul J. Turcott, John S. Srouji, Michael S. Rooney, Marit M. van Buuren, Richard B. Gaynor, Jennifer G. Abelin, Terri A. Addona, Vikram R. Juneja. Systematic discovery of KRAS neoantigens [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-015.