Polymorphisms within HLA gene loci are strongly associated with susceptibility to autoimmune disorders; however, it is not clear how genetic variations in these loci confer a disease risk. Here, we devised a cell-surface MHC expression assay to detect allelic differences in the intrinsic stability of HLA-DQ proteins. We found extreme variation in cell-surface MHC density among HLA-DQ alleles, indicating a dynamic allelic hierarchy in the intrinsic stability of HLA-DQ proteins. Using the case-control data for type 1 diabetes (T1D) for the Swedish and Japanese populations, we determined that T1D risk–associated HLA-DQ haplotypes, which also increase risk for autoimmune endocrinopathies and other autoimmune disorders, encode unstable proteins, whereas the T1D–protective haplotypes encode the most stable HLA-DQ proteins. Among the amino acid variants of HLA-DQ, alterations in 47α, the residue that is located on the outside of the peptide-binding groove and acts as a key stability regulator, showed strong association with T1D. Evolutionary analysis suggested that 47α variants have been the target of positive diversifying selection. Our study demonstrates a steep allelic hierarchy in the intrinsic stability of HLA-DQ that is associated with T1D risk and protection, suggesting that HLA instability mediates the development of autoimmune disorders.
Authors
Hiroko Miyadera, Jun Ohashi, Åke Lernmark, Toshio Kitamura, Katsushi Tokunaga
(A) Neighbor-joining tree for HLA-DQA1 showing the amino acid substitutions at 2α and 47α. (B and C) dn-ds for codons in HLA-DQA1 (14 alleles) (B), and ape DQA1 (20 alleles) (C). The x axis indicates the amino acid residue numbers starting at 18α and ending at 79α. The y axis indicates the dn-ds at each codon, as calculated by the Nei-Gojobori method (124) using SNAP (126) (http://www.hiv.lanl.gov). The codons with a positive dn-ds (P< 1 × 10–7, calculated for pn and ps) are plotted in orange. (D) Location of the amino acid residues that showed a positive dn-ds (P < 1 × 10–7) in both human and ape DQA1. See Supplemental Tables 3 and 4 for the association tables.