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) The HLA-DQ heterodimers in DQ2/3/4 are organized in the order of their ΔMHC values. Error bars represent the SEM. (B and C) Polymorphic variants in HLA-DQA1 (B) and -DQB1 (C) and their association with ΔMHC. Numbers indicate the amino acid residues. Residue numbers for the α2, β2, transmembrane, and cytosolic domains are shaded in brown. Variants identical to DQA1*02:01-DQB1*04:01 (magenta) and other variants (white or gray). The association between each amino acid variant and ΔMHC was analyzed. The lowest P values at each site are indicated on the left with asterisks (2-tailed t test). The association table is presented in Supplemental Table 2.