Abstract 5587: Characterization of shared immunogenic frameshift mutations in microsatellite unstable cancers to guide the design of off-the-shelf immunotherapies
Authors: Bozkus Cansu Cimen , Roudko Vladimir , Orfanelli Theofani , Blank Stephanie , Greenbaum Benjamin , Bhardwaj Nina 
Published: September 2020

Microsatellite instability-high (MSI-H) cancers are an important model for evaluating neoantigen-based immunotherapies, given their high loads of tumor-specific antigens, evidence of T cell infiltration and exceptional response rates to checkpoint blockade. Importantly, MSI-H tumors are enriched in short nucleotide insertion/deletions in microsatellite regions (“hot spots”) within open reading frames, potentially leading to frameshift mutations shared across patients with MSI-H tumors and Lynch Syndrome, a hereditary cancer predisposition syndrome with MSI-H phenotype. We hypothesized that MSI-H tumors are enriched in recurrent frameshift mutations encoding immunogenic neoantigens and pre-selection of an optimal set of recurrent frameshift mutations, based on the multiplicity of encoded neoepitopes, diversity of interaction with common major histocompatibility complex (MHC) alleles and immunogenicity, will inform the design of off-the-shelf immune therapies for patients with MSI-H phenotype. Utilizing the whole-exome sequencing information available at The Cancer Genome Atlas, we evaluated the neoantigen profiles of patients with colorectal (n=461), stomach (n=443) and endometrial carcinoma (n=560) (COAD, STAD and UCEC, respectively) according to the aforementioned criteria and identified 37, 23 and 9 frameshift mutations encoding potentially immunogenic neoantigens, which were shared across the MSI-H population in COAD, STAD and UCEC, respectively. In an array of immunological assays utilizing peripheral blood mononuclear cells (PBMCs) from healthy donors, we characterized the immunogenicity of the neoantigens derived from the 9 frameshift peptides shared in MSI-H UCEC to assess the extent and specificity of the engendered T cell immunity. We found that each frameshift peptide could elicit antigen-specific CD8+ T cell responses in a subset of subjects tested, which suggests that MSI-H UCEC patients have an increased frequency of high-quality T cell epitopes derived from shared frameshift peptides, binding to a broad spectrum of MHC alleles, capable of inducing CD8+ T responses. Currently, utilizing blood and tissue specimens from patients with MSI-H COAD, STAD and UCEC, we are interrogating (1) the expression levels and frequencies of the selected shared neoantigens, (2) whether these neoantigens are presented in the context of MHC and (3) can elicit endogenous T cell responses. Findings from this research will guide the selection of shared neoantigens eliciting antitumor T cell immunity in patients with MSI-H tumors and will ultimately lay the foundation for common neoantigen-based, off-the-shelf cancer immunotherapy designs, which can be utilized in therapeutic and preventative settings in MSI-H cancers and Lynch Syndrome, respectively.

Citation Format: Cansu Cimen Bozkus, Vladimir Roudko, Theofani Orfanelli, Stephanie Blank, Benjamin Greenbaum, Nina Bhardwaj. Characterization of shared immunogenic frameshift mutations in microsatellite unstable cancers to guide the design of off-the-shelf immunotherapies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5587.