Prediction of HLA-DQ8 β cell peptidome using a computational program and its relationship to autoreactive T cells

Abstract

The goal was to identify HLA-DQ8-bound β cell epitopes important in the T cell response in autoimmune diabetes. We first identified HLA-DQ8 (DQA1*0301/DQB1*0302) β cell epitopes using a computational approach and then related their identification to CD4 T cell responses. The computational program (TEA-DQ8) was adapted from one previously developed for identifying peptides bound to the I-Ag7 molecule and based on a library of naturally processed peptides bound to HLA-DQ8 molecules of antigen-presenting cells. We then examined experimentally the response of NOD.DQ8 mice immunized with peptides derived from the Zinc transporter 8 protein. Log-of-odds scores on peptides were experimentally validated as an indicator of peptide binding to HLA-DQ8 molecules. We also examined previously published data on diabetic autoantigens, including glutamic acid decarboxylase-65, insulin and insulinoma-associated antigen-2, all tested in NOD.DQ8 transgenic mice. In all examples, many peptides identified with a favorable binding motif generated an autoimmune T cell response, but importantly many did not. Moreover, some peptides with weak-binding motifs were immunogenic. These results indicate the benefits and limitations in predicting autoimmune T cell responses strictly from MHC-binding data. TEA-DQ8 performed significantly better than other prediction programs

Dendritic Cells Guide Islet Autoimmunity through a Restricted and Uniquely Processed Peptidome Presented by High-Risk HLA-DR

“…Table I). Two overlapping PPI peptides were eluted from HLA-DR4: PPI [14][15][16][17][18][19][20][21][22][23][24] and PPI [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] ( Fig. 2).…”

“…Peptides of all three islet autoantigens were retrieved from HLA-DR3/4 and were derived from the same core regions of the islet Ags as those retrieved from the homozygous DC. Two PPI signal-sequence peptides were eluted: PPI [17][18][19][20][21][22][23][24] and PPI [17][18][19][20][21][22][23] encompassing the same core sequence of PPI (WGPDPAA) as those retrieved from HLA-DR4 (Fig. 2, Supplemental Table I).…”

“…Peptides eluted from HLA-DR purified from PPI-, IA-2-, and GAD65-pulsed DC were synthesized and analyzed by MS for validation of the identified eluted peptide spectra. Shown are the peptide spectra of PPI [17][18][19][20][21][22][23][24] (A), IA-2 470-486 (B), and GAD65 266-286 (C) eluted from HLA-DR (upper spectra) and the corresponding spectra of the synthesized peptides (lower spectra in gray). The peptide spectra of eluted and synthesized peptides fully overlapped.…”

“…PPI [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] , containing the WGPDPAAA core sequence, bound to HLA-DR4 (Fig. 6, Table I).…”

“…Until now, T cell-activating regions in islet autoantigens have been identified on the basis of proliferative and cytokine responses to synthetic overlapping peptides spanning the entire amino acid sequence of the Ag (8,9,(17)(18)(19) by in silico prediction of potential T cell epitopes using HLA class II peptide-binding motifs (20)(21)(22) or by eluting naturally processed and presented epitopes (NPPE) from islet Ag-pulsed B cells (23,24). Although the first two approaches can identify core epitopes recognized by the TCR, the actual sequences with naturally generated flanking regions presented by T1D high-risk HLA-DR cannot be predicted.…”