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) ΔMHC profile for the DQ0602-peptide fusion constructs. HLA-DQA1*01:02–stable cells were transduced with pMXs-IG/DQB1*06:02, which carries the peptide sequence between the signal and the mature protein sequence (see Methods). (B) ΔMHC profile in the presence and absence of the artificial negative control peptide GGS. HLA-DQA1–stable cells were transduced with pMXs-IG/DQB1 (without peptide fusion) (white bars) or with pMXs-IG/DQB1-GGS peptide (black bars). (C) ΔMHC profile for HLA-DQ in the presence (black bars) and absence (white bars) of the human invariant chain. ΔMHC was measured in NIH3T3 cells that stably expressed the human invariant chain (Supplemental Figure 10) and HLA-DQA1. (D) ΔMHC profile for the DQB1-CLIP81–107 fusion constructs. Error bars represent the SEM (n ≥3).