Interpretable Prediction of SARS-CoV-2 Epitope-Specific TCR Recognition Using a Pre-Trained Protein Language Model

The emergence of the novel coronavirus, designated as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has posed a significant threat to public health worldwide. There has been progress in reducing hospitalizations and deaths due to SARS-CoV-2. However, challenges stem from the emergence of SARS-CoV-2 variants, which exhibit high transmission rates, increased disease severity, and the ability to evade humoral immunity. Epitope-specific T-cell receptor (TCR) recognition is key in determining the T-cell immunogenicity for SARS-CoV-2 epitopes. Although several data-driven methods for predicting epitope-specific TCR recognition have been proposed, they remain challenging due to the enormous diversity of TCRs and the lack of available training data. Self-supervised transfer learning has recently been proven useful for extracting information from unlabeled protein sequences, increasing the predictive performance of fine-tuned models, and using a relatively small amount of training data. This study presents a deep-learning model generated by fine-tuning pre-trained protein embeddings from a large corpus of protein sequences. The fine-tuned model showed markedly high predictive performance and outperformed the recent Gaussian process-based prediction model. The output attentions captured by the deep-learning model suggested critical amino acid positions in the SARS-CoV-2 epitope-specific TCRβ sequences that are highly associated with the viral escape of T-cell immune response.