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) Frequencies of DQ haplotypes in T1D cases and controls in the Swedish (77, 78) and Japanese populations (10). See Supplemental Table 5 for the association table. (B) Frequencies of DQ haplotypes of various ΔMHC levels in the Swedish (77, 78) and Japanese populations (10). Lines indicate the boundaries for the ΔMHC less than 0.2 (yellow) and the ΔMHC greater than 0.8 (white). (C) ΔMHC profiles for the major DQ haplotypes (haplotype frequency >0.03) in the European (133) and Japanese populations (134). Colors indicate the DQ haplotypes that confer risk (magenta), protection (blue), or neutrality (gray) with regard to T1D in the Swedish (77, 78) and Japanese populations (10). (D) Relationship between the ΔMHC and the ORs for the major DQ haplotypes (haplotype frequency >0.03) in the Swedish and Japanese populations. The left axis indicates the OR, and the right axis indicates the ΔMHC. The dashed lines indicate a 95% CI for the ORs or standard errors for the ΔMHC. T1D risk (magenta), protective (blue), and neutral (gray) haplotypes. Haplotypes that are most strongly associated with susceptibility to or protection against T1D in each population are indicated by bold lines. P values indicate the association between the rankings in the ΔMHC and the ORs (Spearman’s rank test).