Behçet disease-associated MHC class I residues implicate antigen binding and regulation of cell-mediated cytotoxicity

Abstract

The HLA protein, HLA-B*51, encoded by HLA-B in MHC, is the strongest known genetic risk factor for Behçet disease (BD). Associations between BD and other factors within the MHC have been reported also, although strong regional linkage disequilibrium complicates their confident disentanglement from HLA-B*51. In the current study, we examined a combination of directly obtained and imputed MHC-region SNPs, directly obtained HLA-B locus types, and imputed classical HLA types with their corresponding polymorphic amino acid residues for association with BD in 1,190 cases and 1,257 controls. SNP mapping with logistic regression of the MHC identified the HLA-B/MICA region and the region between HLA-F and HLA-A as independently associated with BD (P < 1.7 × 10(-8)). HLA-B*51, -A*03, -B*15, -B*27, -B*49, -B*57, and -A*26 each contributed independently to BD risk. We directly examined rs116799036, a noncoding SNP upstream of HLA-B that was recently suggested to underlie the association of HLA-B*51 with BD, but we were unable to replicate that finding in our collection. Instead, we mapped the BD association to seven MHC class I (MHC-I) amino acid residues, including anchor residues that critically define the selection and binding of peptides to MHC-I molecules, residues known to influence MHC-I-killer immunoglobulin-like receptor interactions, and a residue located in the signal peptide of HLA-B. The locations of these variants collectively implicate MHC-I peptide binding in the pathophysiology of BD. Furthermore, several lines of evidence suggest a role for altered regulation of cellular cytotoxicity in BD pathogenesis.

Keywords: HLA imputation; antigen presentation; autoinflammation; killer immunoglobulin-like receptors; natural killer cells.

Fig. 1.

HLA-B*51 is the predominant risk allele, but variants between HLA-F and HLA-A are independently associated with BD. (A and B) The results of association testing and stepwise conditional analysis of imputed MHC region SNPs in 1,190 BD cases and 1,257 healthy control subjects from Turkey are displayed in A. Conditional analysis accounting for the effect of HLA-B*51 (B, red dots) produced a pattern of residual association virtually identical to that seen after conditioning for rs79556279 (A, green dots). (C) Association testing results of BD-associated SNPs in proximity to HLA-B/MICA were plotted, and data points were color-coded to demonstrate D′ of each SNP with HLA-B*51.

Fig. 2.

Individual amino acids within HLA-A and HLA-B proteins influence the risk of BD. The allele frequencies of amino acid positions 97, 116, 152, 67, and −10 in HLA-B and positions 161 and 97 in HLA-A are plotted for cases (red) and controls (blue), and univariate ORs are displayed above the bars.

Fig. 3.

BD-associated positions within MHC-I molecules cluster around the antigen-binding groove. 3D modeling of HLA-B*5101 (A) and HLA-A*0301 (B) demonstrates the clustering of BD-associated amino acid positions (red balls) in and around the antigen-binding grooves of HLA-B and HLA-A. The peptide backbone and side chains of the epitope are displayed in green. This figure was prepared with PyMol, using Protein Data Bank entries 2XPG (40) and 1E27 (41).