epiTCR: a highly sensitive predictor for TCR–peptide binding

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 5
• Main Authors: Pham, My-Diem Nguyen, Nguyen, Thanh-Nhan, Tran, Le Son, Nguyen, Que-Tran Bui, Nguyen, Thien-Phuc Hoang, Pham, Thi Mong Quynh, Nguyen, Hoai-Nghia, Giang, Hoa, Phan, Minh-Duy, Nguyen, Vy
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 04.05.2023
• Subjects: Antigens - chemistry; Epitopes - chemistry; Humans; Original Paper; Peptides - metabolism; Receptors, Antigen, T-Cell - chemistry; Systems Biology; T-Lymphocytes - metabolism
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btad284

Abstract Motivation Predicting the binding between T-cell receptor (TCR) and peptide presented by human leucocyte antigen molecule is a highly challenging task and a key bottleneck in the development of immunotherapy. Existing prediction tools, despite exhibiting good performance on the datasets they were built with, suffer from low true positive rates when used to predict epitopes capable of eliciting T-cell responses in patients. Therefore, an improved tool for TCR–peptide prediction built upon a large dataset combining existing publicly available data is still needed. Results We collected data from five public databases (IEDB, TBAdb, VDJdb, McPAS-TCR, and 10X) to form a dataset of >3 million TCR–peptide pairs, 3.27% of which were binding interactions. We proposed epiTCR, a Random Forest-based method dedicated to predicting the TCR–peptide interactions. epiTCR used simple input of TCR CDR3β sequences and antigen sequences, which are encoded by flattened BLOSUM62. epiTCR performed with area under the curve (0.98) and higher sensitivity (0.94) than other existing tools (NetTCR, Imrex, ATM-TCR, and pMTnet), while maintaining comparable prediction specificity (0.9). We identified seven epitopes that contributed to 98.67% of false positives predicted by epiTCR and exerted similar effects on other tools. We also demonstrated a considerable influence of peptide sequences on prediction, highlighting the need for more diverse peptides in a more balanced dataset. In conclusion, epiTCR is among the most well-performing tools, thanks to the use of combined data from public sources and its use will contribute to the quest in identifying neoantigens for precision cancer immunotherapy. Availability and implementation epiTCR is available on GitHub (https://github.com/ddiem-ri-4D/epiTCR).