Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens

• Published in: Briefings in bioinformatics Vol. 23; no. 3
• Main Authors: Buckley, Paul R, Lee, Chloe H, Ma, Ruichong, Woodhouse, Isaac, Woo, Jeongmin, Tsvetkov, Vasily O, Shcherbinin, Dmitrii S, Antanaviciute, Agne, Shughay, Mikhail, Rei, Margarida, Simmons, Alison, Koohy, Hashem
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 13.05.2022; Oxford Publishing Limited (England)
• Subjects: Cancer; Cancer immunotherapy; CD8 antigen; CD8-Positive T-Lymphocytes - metabolism; Cell recognition; Computer applications; Computer Simulation; Context; Coronaviruses; COVID-19; Epitopes; Epitopes, T-Lymphocyte; Histocompatibility antigen HLA; Human pathology; Humans; Immunogenicity; Lymphocytes; Lymphocytes T; Major histocompatibility complex; Mathematical models; Neoantigens; Neoplasms; Pathogens; Peptides; Performance evaluation; Performance prediction; Predictions; Problem Solving Protocol; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; T cell receptors; Vaccines; Viral diseases; Viruses; cancer neoantigen; peptide immunogenicity; CD8 T-cell target; peptide presentation; immunotherapy; T-cell response
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbac141

Abstract T cell recognition of a cognate peptide–major histocompatibility complex (pMHC) presented on the surface of infected or malignant cells is of the utmost importance for mediating robust and long-term immune responses. Accurate predictions of cognate pMHC targets for T cell receptors would greatly facilitate identification of vaccine targets for both pathogenic diseases and personalized cancer immunotherapies. Predicting immunogenic peptides therefore has been at the center of intensive research for the past decades but has proven challenging. Although numerous models have been proposed, performance of these models has not been systematically evaluated and their success rate in predicting epitopes in the context of human pathology has not been measured and compared. In this study, we evaluated the performance of several publicly available models, in identifying immunogenic CD8+ T cell targets in the context of pathogens and cancers. We found that for predicting immunogenic peptides from an emerging virus such as severe acute respiratory syndrome coronavirus 2, none of the models perform substantially better than random or offer considerable improvement beyond HLA ligand prediction. We also observed suboptimal performance for predicting cancer neoantigens. Through investigation of potential factors associated with ill performance of models, we highlight several data- and model-associated issues. In particular, we observed that cross-HLA variation in the distribution of immunogenic and non-immunogenic peptides in the training data of the models seems to substantially confound the predictions. We additionally compared key parameters associated with immunogenicity between pathogenic peptides and cancer neoantigens and observed evidence for differences in the thresholds of binding affinity and stability, which suggested the need to modulate different features in identifying immunogenic pathogen versus cancer peptides. Overall, we demonstrate that accurate and reliable predictions of immunogenic CD8+ T cell targets remain unsolved; thus, we hope our work will guide users and model developers regarding potential pitfalls and unsettled questions in existing immunogenicity predictors.