A robust deep learning workflow to predict CD8 + T-cell epitopes.

Journal: Genome medicine
Published Date: Sep 13, 2023

Abstract

BACKGROUND: T-cells play a crucial role in the adaptive immune system by triggering responses against cancer cells and pathogens, while maintaining tolerance against self-antigens, which has sparked interest in the development of various T-cell-focused immunotherapies. However, the identification of antigens recognised by T-cells is low-throughput and laborious. To overcome some of these limitations, computational methods for predicting CD8 + T-cell epitopes have emerged. Despite recent developments, most immunogenicity algorithms struggle to learn features of peptide immunogenicity from small datasets, suffer from HLA bias and are unable to reliably predict pathology-specific CD8 + T-cell epitopes.

Authors

  • Chloe H Lee
    MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.
  • Jaesung Huh
    Visual Geometry Group, Department of Engineering Science, University of Oxford, Oxford, OX2 6NN, UK.
  • Paul R Buckley
    MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.
  • Myeongjun Jang
    Intelligent Systems Lab, Department of Computer Science, University of Oxford, Oxford, OX1 3QG, UK.
  • Mariana Pereira Pinho
    MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.
  • Ricardo A Fernandes
    Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford, OX3 7BN, UK.
  • Agne Antanaviciute
    Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and.
  • Alison Simmons
    MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.
  • Hashem Koohy
    MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine , University of Oxford, Oxford, UK.

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