PT - JOURNAL ARTICLE AU - Hannah Reimann AU - Andrew Nguyen AU - J Zachary Sanborn AU - Charles J Vaske AU - Stephen C Benz AU - Kayvan Niazi AU - Shahrooz Rabizadeh AU - Patricia Spilman AU - Andreas Mackensen AU - Matthias Ruebner AU - Alexander Hein AU - Matthias W Beckmann AU - Edith D van der Meijden AU - Judith Bausenwein AU - Sascha Kretschmann AU - Marieke Griffioen AU - Jeffrey Schlom AU - James L Gulley AU - Karin L Lee AU - Duane H Hamilton AU - Patrick Soon-Shiong AU - Peter A Fasching AU - Anita N. Kremer TI - Identification and validation of expressed HLA-binding breast cancer neoepitopes for potential use in individualized cancer therapy AID - 10.1136/jitc-2021-002605 DP - 2021 Jun 01 TA - Journal for ImmunoTherapy of Cancer PG - e002605 VI - 9 IP - 6 4099 - http://jitc.bmj.com/content/9/6/e002605.short 4100 - http://jitc.bmj.com/content/9/6/e002605.full SO - J Immunother Cancer2021 Jun 01; 9 AB - Background Therapeutic regimens designed to augment the immunological response of a patient with breast cancer (BC) to tumor tissue are critically informed by tumor mutational burden and the antigenicity of expressed neoepitopes. Herein we describe a neoepitope and cognate neoepitope-reactive T-cell identification and validation program that supports the development of next-generation immunotherapies.Methods Using GPS Cancer, NantOmics research, and The Cancer Genome Atlas databases, we developed a novel bioinformatic-based approach which assesses mutational load, neoepitope expression, human leukocyte antigen (HLA)-binding prediction, and in vitro confirmation of T-cell recognition to preferentially identify targetable neoepitopes. This program was validated by application to a BC cell line and confirmed using tumor biopsies from two patients with BC enrolled in the Tumor-Infiltrating Lymphocytes and Genomics (TILGen) study.Results The antigenicity and HLA-A2 restriction of the BC cell line predicted neoepitopes were determined by reactivity of T cells from HLA-A2-expressing healthy donors. For the TILGen subjects, tumor-infiltrating lymphocytes (TILs) recognized the predicted neoepitopes both as peptides and on retroviral expression in HLA-matched Epstein-Barr virus–lymphoblastoid cell line and BC cell line MCF-7 cells; PCR clonotyping revealed the presence of T cells in the periphery with T-cell receptors for the predicted neoepitopes. These high-avidity immune responses were polyclonal, mutation-specific and restricted to either HLA class I or II. Interestingly, we observed the persistence and expansion of polyclonal T-cell responses following neoadjuvant chemotherapy.Conclusions We demonstrate our neoepitope prediction program allows for the successful identification of neoepitopes targeted by TILs in patients with BC, providing a means to identify tumor-specific immunogenic targets for individualized treatment, including vaccines or adoptively transferred cellular therapies.Data are available upon reasonable request. Data have largely been presented in the text; other data are available upon request.