Abstract Introduction: Preclinical data suggests that priming T cell immunity to mutated or overexpressed proteins can induce tumor rejection, and may potentiate the effects of checkpoint blockade. PIK3CA and p53 are the most commonly mutated genes in breast cancer, and are enriched in high-grade and metastatic tumors. Here, we evaluated the immunogenicity of neo-epitopes derived from common PIK3CA and p53 mutations. Methods: We applied a custom informatics pipeline, EpitopeHunter, to predict neo-epitopes (8-11mers) from twelve PIK3CA and ten p53 mutations restricted to thirty-nine MHC class I alleles. We selected high affinity neo-epitopes (IEDB score < 500) with predicted poor binding of the matched wild type epitope. We used the predicted peptides to stimulate PBMC from healthy donors in vitro, and measured T cell immunity by interferon-γ ELISPOT. We compared the T cell specificity of mutant vs wild type epitopes. A positive response to an epitope was defined as a response that met both of the following criteria: 1) net number of spots (after subtracting background) was >5 spots/50,000 cells and 2) net number of spots exceeded the background spots plus two SDs. Results: In total, 1,824 PIK3CA and 1,520 p53 derived peptide sequences were generated. Of these, 42 PIK3CA (2%) and 45 p53 (3%) peptides were predicted to bind to the HLA class I molecules included in our study. Over 90% of the neo-epitopes were 9- and 10-mers, and the predicted neo-epitopes varied across mutations (range 2-10 per mutation). PIK3CAH1047L and p53R248W had the highest number of potential binding neo-epitopes (n=10 each). We successfully generated T cell lines specific for A*0201 PIK3CAH1047L, A*1101 PIK3CAH1047L, A*1101 PIK3CAE542K and A*0201 p53R248W. Conclusions: Common mutations of PIK3CA and p53 can lead to the generation of potential HLA class I restricted neo-epitopes. We identified four immunogenic neo-epitopes, which may serve as candidates for targeted immunotherapy in breast cancer. Citation Format: Chen M, Yuvaraj P, Sharma AA, Narang P, Wilson Sayres MA, Anderson KS. Targeting neo-epitopes from PIK3CA and p53 mutations for immunotherapy of breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-06-04.
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