The KAG motif of HLA-DRB1 (β71, β74, β86) predicts seroconversion and development of type 1 diabetes

Abstract

Background HLA-DR4, a common antigen of HLA-DRB1, has multiple subtypes that are strongly associated with risk of type 1 diabetes (T1D); however, some are risk neutral or resistant. The pathobiological mechanism of HLA-DR4 subtypes remains to be elucidated. Methods We used a population-based case-control study of T1D (962 patients and 636 controls) to decipher genetic associations of HLA-DR4 subtypes and specific residues with susceptibility to T1D. Using a birth cohort of 7865 children with periodically measured islet autoantibodies (GADA, IAA or IA-2A), we proposed to validate discovered genetic associations with a totally different study design and time-to-seroconversions prior to clinical onset of T1D. A novel analytic strategy hierarchically organized the HLA-DRB1 alleles by sequence similarity and identified critical amino acid residues by minimizing local genomic architecture and higher-order interactions. Findings Three amino acid residues of HLA-DRB1 (β71, β74, β86) were found to be predictive of T1D risk in the population-based study. The “KAG” motif, corresponding to HLA-DRB1×04:01, was most strongly associated with T1D risk ([O]dds [R]atio=3.64, p = 3.19 × 10 −64 ). Three less frequent motifs (“EAV”, OR = 2.55, p = 0.025; “RAG”, OR = 1.93, p = 0.043; and “RAV”, OR = 1.56, p = 0.003) were associated with T1D risk, while two motifs (“REG” and “REV”) were equally protective (OR = 0.11, p = 4.23 × 10 −4 ). In an independent birth cohort of HLA-DR3 and HLA-DR4 subjects, those having the “KAG” motif had increased risk for time-to-seroconversion (Hazard Ratio = 1.74, p = 6.51 × 10 −14 ) after adjusting potential confounders. Interpretations DNA sequence variation in HLA-DRB1 at positions β71, β74, and β86 are non-conservative (β74 A→E, β71 E vs K vs R and β86 G vs V). They result in substantial differences in peptide antigen anchor pocket preferences at p1, p4 and potentially neighboring regions such as pocket p7. Differential peptide antigen binding is likely to be affected. These sequence substitutions may account for most of the HLA-DR4 contribution to T1D risk as illustrated in two HLA-peptide model complexes of the T1D autoantigens preproinsulin and GAD65. Funding National Institute of Diabetes and Digestive and Kidney Diseases and the Swedish Child Diabetes Foundation and the Swedish Research Council.

Family‐based association of HLA‐DRB1 and DQB1 alleles and haplotypes in a group of Iranian Type 1 diabetes children

“…In mechanistic point of view, sequence substitutions mainly at positions β71, β74, and β86 in the beta chain of predisposing subtypes of DR4 molecule shape a distinct structural motif (KAG, EAV, RAG, and RAV) that result in substantial differences in peptide antigen anchor pocket preferences at P1 and P4. This, in turn, may affect the differential peptide antigen (autoantigens) binding and consequently T‐cell activation and the development of autoimmune responses against beta cells in T1D 32 . The clear association of DRB1*04:02 (consisting EAV motif) and DRB1*04:05 (consisting RAG motif) with T1D in our study subjects is in accordance with the proposed molecular‐based mechanism at amino acid level for contribution of HLA risk alleles in developing T1D.…”

Possible heterogeneity of initial pancreatic islet beta‐cell autoimmunity heralding type 1 diabetes

“…The longitudinal studies of TEDDY, DIPP, and similar investigations underscore that “timing is everything” [90]. The risk for a first‐appearing autoantibody may be related to the number of variable amino acid residues in the groove of the HLA Class II heterodimer, be it DQ [91, 92] or DR [93, 94]. Analyses will be needed to relate the DR and DQ heterodimer polymorphisms to the first‐appearing autoantibody incidence (Fig.…”

A new, all‐encompassing aetiology of type 1 diabetes

“…Therefore, they have an important role in diagnosis of T1D. However, this does not mean that all proteins are involved in the aetiology of T1D [36]. To the contrary, GWAS only shows a significant correlation with insulin; the other proteins do not fulfil GWEA criteria and therefore must be the result of expansion of the immunological destruction of β‐cells.…”

“…acids 26-28 are encoded by zero to two out of 6 possible SHM hotspots; amino acids 26 and 28 contribute to pocket P4. Amino acids 69-74 are encoded by one out of three SHM hotspots and GC-rich DNA; amino acids 70, 71 and 74 contribute to pocket P4 and are part of the 'shared epitope' in rheumatoid arthritis and 'KAG' motif in T1D[35,36]. Amino acids 85, 89 and 90 contribute to pocket P1; each is located within SHM hotspots.…”