MHCSeqNet: A deep neural network model for universal MHC binding prediction

Abstract

Immunotherapy is an emerging approach in cancer treatment that activates the host immune system to destroy cancer cells that express unique peptide signatures (neoepitopes). Administrations of cancer-specific neoepitopes in the form of synthetic peptide vaccine have been proven effective in both mouse models and human patients. Because only a tiny fraction of cancer-specific neoepitopes actually elicit immune response, selection of potent, immunogenic neoepitopes remains a challenging step in cancer vaccine development. A basic approach for immunogenicity prediction is based on the premise that effective neoepitope should bind with the Major Histocompatibility Complex (MHC) with high affinity. In this study, we developed MHCSeqNet, an open-source deep learning model, which not only competes favorably with state-of-the-art predictors but also exhibits promising generalization to new MHC class I and class II alleles. MHCSeqNet employed neural network architectures developed for natural language processing to model amino acid sequence representations of MHC allele and epitope peptide as sentences with amino acids as individual words. This consideration allows MHCSeqNet to accept new MHC alleles as well as peptides of any length. The flexibility offered by MHCSeqNet should make it a valuable tool for screening effective neoepitopes in cancer vaccine development.\n\nAvailability and implementationhttps://github.com/cmbcu/MHCSeqNet