Journal
BMC BIOINFORMATICS
Volume 20, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12859-019-2892-4
Keywords
MHC epitope prediction; Deep learning; Recurrent neural networks
Categories
Funding
- Grant for Special Task Force for Activating Research, Ratchadapisek Sompoch Endowment Fund, Chulalongkorn University
- Grant for New Scholar, Thailand Research Fund [MRG6080087]
- Vidyasirimedhi Institute of Science and Technology
- Chulalongkorn Academic Advancement into Its 2nd Century Project
- Grant for Development of New Faculty Staff, Ratchadaphisek Sompoch Endowment Fund, Chulalongkorn University
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BackgroundImmunotherapy is an emerging approach in cancer treatment that activates the host immune system to destroy cancer cells expressing 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 elicits 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.ResultsIn this study, we developed MHCSeqNet, an open-source deep learning model, which not only outperforms state-of-the-art predictors on both MHC binding affinity and MHC ligand peptidome datasets but also exhibits promising generalization to unseen MHC class I 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.ConclusionsThe improved performance and the flexibility offered by MHCSeqNet should make it a valuable tool for screening effective neoepitopes in cancer vaccine development.
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