Back to Search
Start Over
IEPAPI: a method for immune epitope prediction by incorporating antigen presentation and immunogenicity.
- Source :
- Briefings in Bioinformatics; Jul2023, Vol. 24 Issue 4, p1-10, 10p
- Publication Year :
- 2023
-
Abstract
- CD8<superscript>+</superscript> T cells can recognize peptides presented by class I human leukocyte antigen (HLA-I) of nucleated cells. Exploring this immune mechanism is essential for identifying T-cell vaccine targets in cancer immunotherapy. Over the past decade, the wealth of data generated by experiments has spawned many computational approaches for predicting HLA-I binding, antigen presentation and T-cell immune responses. Nevertheless, existing HLA-I binding and antigen presentation prediction approaches suffer from low precision due to the absence of T-cell receptor (TCR) recognition. Direct modeling of T-cell immune responses is less effective as TCR recognition's mechanism still remains underexplored. Therefore, directly applying these existing methods to screen cancer neoantigens is still challenging. Here, we propose a novel immune epitope prediction method termed IEPAPI by effectively incorporating antigen presentation and immunogenicity. First, IEPAPI employs a transformer-based feature extraction block to acquire representations of peptides and HLA-I proteins. Second, IEPAPI integrates the prediction of antigen presentation prediction into the input of immunogenicity prediction branch to simulate the connection between the biological processes in the T-cell immune response. Quantitative comparison results on an independent antigen presentation test dataset exhibit that IEPAPI outperformed the current state-of-the-art approaches NetMHCpan4.1 and mhcflurry2.0 on 100 (25/25) and 76% (19/25) of the HLA subtypes, respectively. Furthermore, IEPAPI demonstrates the best precision on two independent neoantigen datasets when compared with existing approaches, suggesting that IEPAPI provides a vital tool for T-cell vaccine design. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14675463
- Volume :
- 24
- Issue :
- 4
- Database :
- Complementary Index
- Journal :
- Briefings in Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 166742630
- Full Text :
- https://doi.org/10.1093/bib/bbad171