GPS-MBA: Computational analysis of MHC class II epitopes in type 1 diabetes

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Abstract

As a severe chronic metabolic disease and autoimmune disorder, type 1 diabetes (T1D) affects millions of people worldwide. Recent advances in antigen-based immunotherapy have provided a great opportunity for further treating T1D with a high degree of selectivity. It is reported that MHC class II I-A g7 in the non-obese diabetic (NOD) mouse and human HLA-DQ8 are strongly linked to susceptibility to T1D. Thus, the identification of new I-A g7 and HLA-DQ8 epitopes would be of great help to further experimental and biomedical manipulation efforts. In this study, a novel GPS-MBA (MHC Binding Analyzer) software package was developed for the prediction of I-A g7 and HLA-DQ8 epitopes. Using experimentally identified epitopes as the training data sets, a previously developed GPS (Group-based Prediction System) algorithm was adopted and improved. By extensive evaluation and comparison, the GPS-MBA performance was found to be much better than other tools of this type. With this powerful tool, we predicted a number of potentially new I-A g7 and HLA-DQ8 epitopes. Furthermore, we designed a T1D epitope database (TEDB) for all of the experimentally identified and predicted T1D-associated epitopes. Taken together, this computational prediction result and analysis provides a starting point for further experimental considerations, and GPS-MBA is demonstrated to be a useful tool for generating starting information for experimentalists. The GPS-MBA is freely accessible for academic researchers at: http://mba.biocuckoo.org. © 2012 Cai et al.

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Cai, R., Liu, Z., Ren, J., Ma, C., Gao, T., Zhou, Y., … Xue, Y. (2012). GPS-MBA: Computational analysis of MHC class II epitopes in type 1 diabetes. PLoS ONE, 7(3). https://doi.org/10.1371/journal.pone.0033884

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