An amino acid motif in HLA-DRß1 distinguishes patients with uveitis in juvenile idiopathic arthritis

A.J.W. Haasnoot; M.W. Schilham; S.S.M. Kamphuis; P.C.E. Hissink Muller; A. Heiligenhaus; D. Foell; R.A. Ophoff; T.R.D.J. Radstake; A.I. Den Hollander; T.H.C.M. Reinards; S. Hiddingh; N. Schalij-Delfos; E.P.A.H. Hoppenreijs; M.A.J. van Rossum; C. Wouters; R.K. Saurenmann; N. Wulffraat; R. ten Cate; J.H. de Boer; S.L. Pulit; J.J.W. Kuiper

To identify HLA-DRB1 alleles that encode proteins with similar predicted binding preferences, we performed unsupervised hierarchical clustering. Clustering of the peptide affinity data discerned two major clusters of classical alleles strikingly similar to the distribution of serine at position 11 (Supplementary Figure 7) . We observed that the average binding affinity of the peptide panel was higher for the HLA-DRB1 alleles that encode serine at position 11 versus alleles that have other amino acids at this position (Wilcoxon signed-rank test, p = 3.44 x 10 -136 , Supplementary Table 5) . To compare these two clusters, we then computed the ratio of the average binding affinity of the 6 HLA-DRB1 allotypes that contain serine-11 and the 7 that have other amino acids at this position (Supplementary Table 5 ). Since MHC class II molecules at the cell surface present . CC-BY-ND 4.0 International license is made available under a repertoires that are skewed in favor of high affinity binders, 39 we selected for peptides with an (IC 50 ) affinities <500 nM (an affinity of <500 nM is routinely used as a threshold for potential immunogenicity) or <50nM (strong binding peptides) for HLA-DRB1 allotypes with serine-11 (Materials and Methods). The data indicated that peptides with an intermediate or high affinity for allotypes containing serine-11 have less affinity to allotypes that contain other amino acids at position 11 (Supplementary Table 5 ).