MHCSeqNet: a deep neural network model for universal MHC binding prediction.
BACKGROUND
Immunotherapy 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.


RESULTS
In 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.


CONCLUSIONS
The improved performance and the flexibility offered by MHCSeqNet should make it a valuable tool for screening effective neoepitopes in cancer vaccine development.
['Phloyphisut|Poomarin|P|', 'Pornputtapong|Natapol|N|', 'Sriswasdi|Sira|S|http://orcid.org/0000-0002-4117-3632', 'Chuangsuwanich|Ekapol|E|']
D000483:Alleles D000818:Animals D019540:Area Under Curve D030562:Databases, Protein D015395:Histocompatibility Antigens Class I D006801:Humans D051379:Mice D008954:Models, Biological D016571:Neural Networks, Computer D010455:Peptides D011485:Protein Binding D020543:Proteome D012984:Software
Deep learning MHC epitope prediction Recurrent neural networks