BepiTBR: T-B reciprocity enhances B cell epitope prediction
James Zhu,
Anagha Gouru,
Fangjiang Wu,
Jay A. Berzofsky,
Yang Xie,
Tao Wang
Affiliations
James Zhu
Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Anagha Gouru
Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Fangjiang Wu
Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Jay A. Berzofsky
Vaccine Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
Yang Xie
Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Corresponding author
Tao Wang
Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Corresponding author
Summary: The ability to predict B cell epitopes is critical for biomedical research and many clinical applications. Investigators have observed the phenomenon of T-B reciprocity, in which candidate B cell epitopes with nearby CD4+ T cell epitopes have higher chances of being immunogenic. To our knowledge, existing B cell epitope prediction algorithms have not considered this interesting observation. We developed a linear B cell epitope prediction model, BepiTBR, based on T-B reciprocity. We showed that explicitly including the enrichment of putative CD4+ T cell epitopes (predicted HLA class II epitopes) in the model leads to significant enhancement in the prediction of linear B cell epitopes. Curiously, the positive impact on B cell epitope generation is specific to the enrichment of DQ allele binders. Overall, our work provides interesting mechanistic insights into the generation of B cell epitopes and points to a new avenue to improve B cell epitope prediction for the field.
