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 location of Arg47α (magenta) in the protein structure of DQ0602 (PDB: 1uvq) (70). α1 domain (white), α2 domain (pink), and bound peptide (yellow). (B–D) Interdomain H-bonds formed between the α1 and α2/β2 domains in the presence of Arg47α in DQA1*01:02 (DQ0602) (PDB: 1uvq) (70) (B), Gln47α in DQA1*03 (DQ8.3) (PDB: 2nna) (69) (C), and Cys47α in DQA1*05 (DQ2.5) (PDB: 1s9v) (72) (D). α1 and α2 domains (magenta in B, orange in C, and pink in D); β2 domains (gray); water molecules (red spheres); and distances of less than 3.4 Å (green dots). (E) Effects of variants at 47α on the ΔMHC values of DQ2.5 and DQ8.3. (F) Effects of variants at 47α on the ΔMHC values of DQA1*06:01. (G) Differences in ΔMHC between DQB1*03:02 and *03:03, which differ at 57β, and between HLA-DQB1*03:01 and *03:03, which differ at 13β, 26β, and 45β in the β1 domain (Supplemental Figure 12B and 13B). *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001 by 2-tailed t test. Error bars represent the SEM (n ≥3).