title: GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes.
abstract: As a severe chronic metabolic disease and autoimmune disorder, type 1 diabetes (T1D) affects millions of people world-wide. 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.
authors.affiliation: Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Ruikun
authors.initials: R
authors.lastname: Cai
authors.forename: Zexian
authors.initials: Z
authors.lastname: Liu
authors.forename: Jian
authors.initials: J
authors.lastname: Ren
authors.forename: Chuang
authors.initials: C
authors.lastname: Ma
authors.forename: Tianshun
authors.initials: T
authors.lastname: Gao
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Zhou
authors.forename: Qing
authors.initials: Q
authors.lastname: Yang
authors.forename: Yu
authors.initials: Y
authors.lastname: Xue
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D003922:Diabetes Mellitus, Type 1 / Q000276:immunology* / Q000378:metabolism; D018604:Epitope Mapping; D000939:Epitopes / Q000737:chemistry / Q000378:metabolism; D006683:HLA-DQ Antigens / Q000737:chemistry / Q000276:immunology* / Q000378:metabolism; D000949:Histocompatibility Antigens Class II / Q000737:chemistry / Q000276:immunology* / Q000378:metabolism; D006801:Humans; D020407:Internet; D051379:Mice; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D015203:Reproducibility of Results; D057386:Search Engine; D012984:Software
chemical_list: D000939:Epitopes; D006683:HLA-DQ Antigens; C109756:HLA-DQ8 antigen; D000949:Histocompatibility Antigens Class II; C407099:I-A g7 antigen; D010455:Peptides