Comprehensive mapping of identical epitopes across human proteins reveals implications for immune recognition and therapeutic design

Abstract Shared epitopes create safety and efficacy issues for T-cell immunotherapy. In order to facilitate the monitoring of immune responses and the engineering required to solve this problem, we performed a computational proteome-wide epitope screening to establish the complete atlas of shared epitopes in the human and murine proteomes. Unlike bacterial or viral antigens, self-antigens like tumor-associated antigens (TAAs) frequently contained a high level of shared MHC-II epitopes identical to unintended other self-proteins. Therefore, shared epitopes should be a mandatory and systematic concern in studies using TAA. Noticeably, a subset of TAAs identified in this atlas is free of this drawback. Therefore, this dataset will be essential for immunologists designing cancer vaccines, but also to interpret immunomonitoring studies against self-antigens in oncology and autoimmunity. To facilitate the detection of common epitopes, a web server has been made available at https://epitopscanner.ircan.org/ .