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

Poomarin Phloyphisut,Ekapol Chuangsuwanich,Natapol Pornputtapong,Sira Sriswasdi

doi:10.1186/s12859-019-2892-4

Abstract

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.

Highlights

Immunotherapy is an emerging approach in cancer treatment that activates the host immune system to destroy cancer cells expressing unique peptide signatures
The improved performance and the flexibility offered by MHCSeqNet should make it a valuable tool for screening effective neoepitopes in cancer vaccine development
MHCSeqNet exhibits performance improvement over existing tools for predicting Major Histocompatibility Complex (MHC) class I ligands on both binding affinity and peptidome datasets

Summary

Introduction

Immunotherapy is an emerging approach in cancer treatment that activates the host immune system to destroy cancer cells expressing unique peptide signatures (neoepitopes). 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. Immunotherapy is a promising approach in cancer treatment that activates the host immune system to destroy cancer cells, with far fewer adverse effects than chemotherapy or radiotherapy. This is possible because cancer cells produce unique peptide signatures (neoepitopes), some of which are presented on the cancer cells’ outer surface and recognized by T cells [1, 2]. Recent approaches that employed deep learning models [9, 10] have demonstrated considerable performance gains over

Results

Discussion

Conclusion