The KAG Motif of HLA-DRB1 (β71, β74, β86) Predicts Seroconversion and Development of Type 1 Diabetes

Abstract

Background: 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 DR4 subtypes remains to be elucidated. Methods: We used a population-based case-control study of T1D to decipher genetic associations of DR4 subtypes and specific residues with susceptibility to T1D, and a birth cohort of children with periodically measured islet autoantibodies (GADA, IAA or IA-2A) to investigate the same genetic associations with 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. Finding: 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=3.19x10 -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=4.23x10 -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=6.51x10 -14 ). Interpretations: DNA sequence variation in HLA-DRB1 at positions b71, b74, and b86 alters antigen binding site anchor pockets p1 and p4 (and potentially neighboring regions such as anchor pocket p6) in both dramatic (b74 AaE) and subtle (b71 E vs K vs R; b86 G vs V) ways with major implications for antigen binding. The impact of these sequence substitutions is discussed in the context of two HLA-peptide model complexes for experimentally well-documented T1D autoantigens and may account for most of the HLA-DR4 contribution to T1D risk. Funding: National Institute of Diabetes and Digestive and Kidney Diseases and Swedish Child Diabetes Foundation Declaration of Interest: None to declare. Ethical Approval: This study was approved by the Swedish Better Diabetes Diagnosis (BDD) and the Karolinska Institute Ethics Board.