Motifs of Three HLA-DQ Amino Acid Residues (α44, β57, β135) Capture Full Association With the Risk of Type 1 Diabetes in DQ2 and DQ8 Children
Article Figures & Tables
Figures
- Figure 1
Association scan of individual residues with T1D with the logarithmically transformed P value (y-axis) across all AAs from DQA1 to DQB1. A: The scan is from the marginal associations of individual residues without any adjustment (y-axis is scaled from 0 to 100, corresponding to P value of 1 down to 10−120). B: The scan is from the adjusted associations for three residues (α44, β57, β135) (y-axis is scaled from 0 to 10, corresponding to P value of 1 down to 10−10). C: XY display of computed logarithmic P values from marginal and conditional association analyses. Comparisons of P values from adjusted and unadjusted analyses on all 104 residues.
- Figure 2
A fan representation of hierarchically organized DQ haplotypes following the phylogenic analysis of AA sequences of all unique DQ haplotypes. Among seven clusters, DQ2 and DQ8/9 clusters correspond with two DQ haplotype clusters that include both risk (font colored green), resistant (font colored red), and neutral (font colored black) haplotypes, in addition to uncommon DQ haplotypes (with <3 copies of alleles in the study).
- Figure 3
A: Depiction of the crystal structure of the HLA-DQ8–insulin B11–23/24Gly complex (from 1jk8.pdb) highlighting the AA residues shown by HOH analysis to be involved in T1D pathogenesis via this MHC II allele. The orientation of the molecule is with its long axis nearly parallel to the plane of the paper/screen. The cognate TCR would bind on the righthand side of the molecule, recognizing simultaneously peptide residues as well as HLA-DQ8 residues from the α1β1 antigen–binding domain. The HLA-DQ8–insulin peptide complex is depicted in its secondary structure formation (α-helix in red, β-sheet in turquoise, β-turn in green, and random coil or any other form, such as polyproline II helix of the antigenic peptide backbone, in gray). The AA residues in question are depicted in stick form (atom color convention: carbon, gray; oxygen, red; nitrogen, blue; sulfur, yellow; hydrogen, white). Three anchor residues of the antigenic peptide (p1Glu, p4Tyr, and p9Glu) are shown in space-filling form and the same atomic color conventions, only for orientation purposes in order to appreciate the position and role of the identified residues from the HLA-DQ8–insulin peptide complex. The sequence β105–β112 did not diffract satisfactorily and was not depicted in the originally reported structure. The gap is not clearly seen in this orientation. We also depict the N-terminal residues of the two DQ chains, α2Val and β3Ser, as well as the two C-terminal residues of the two DQ chains: α181Glu and β192Ser. B: Depiction of the crystal structure of the HLA-DQ2–gliadin α1 complex (from 6mfg.pdb) highlighting the AA residues shown by HOH analysis to be involved in T1D pathogenesis via this MHC II allele. A similar orientation and the same color and depiction conventions for secondary structures and individual AA renderings hold, as in A. Three anchor residues of the antigenic peptide (p1Pro, p4Gln, and p9Tyr) are again shown, only for orientation purposes. As in the structure of HLA-DQ8 (A), the sequence β105–β113 did not diffract satisfactorily and was not depicted in the originally reported structure. We label here residues β104Ser and β114Asn in order to identify the break in the β-chain. We also depict the C-terminal residues of the two DQ chains: α181Glu and β190Ala. The gliadin α1 peptide contains several prolines, a property unique to various gluten peptides and not encountered in any of the thus far identified DQ2-restricted antigenic peptides deemed to be involved in T1D pathogenesis.
Tables
- Table 1
A total of 45 unique DQA1-DQB1 haplotypes are observed among control subjects and patients, and their association results are shown
Data are n (%) unless otherwise indicated. Association results are shown as haplotypic frequency and percentage (%) among control subjects, those among patients, estimated ORs, z scores, and P values. The 45 unique haplotypes are observed in 636 control subjects (resulting in 1,272 haplotypes) and 962 patients (1,924 haplotypes). Risk and protective haplotypes are highlighted red and green, respectively, at the significance level of 5%.
- Table 2
Direct comparisons of allelic sequences within mixture 1 and 2 results in identification of 12 and 25 AAs that differentiate between risk and protective alleles in, respectively, DQ8/9 and DQ2 mixtures of haplotypes
Estimated haplotype frequencies (%) among control subjects, those among patients, estimated ORs, z scores, and P values are listed. Risk and protective haplotypes are highlighted green and red, respectively, at the significance level of 5%. Neutrally associated haplotypes with more than three subjects are in black font, while neutrally associated haplotypes with fewer than three subjects are colored gray. The AA β26 has a variant G only on the rare DQ haplotype and is thus excluded from further analysis. Similarly, the AA α(−13) has a variant T-associated haplotype and is also excluded.
- Table 3
T1D associations with individual AAs within clusters of, respectively, DQ8/9 and DQ2 haplotypes
Among polymorphic AAs in respective clusters, 2 out of 11 AAs in the DQ8/9 haplotype cluster show no association (Fisher exact P value >0.05, highlighted in yellow), and 7 out of 12 AAs in the DQ2 haplotype cluster show no association (Fisher exact P value >0.05) with T1D. Within respective clusters, the computed Fisher exact calculations indicate whether the residue has differential associations between AAs (Fisher exact P value <0.01, highlighted in yellow). Ten AAs, represented by two AAs, are found to have significant differential associations in the DQ8/9 cluster, in which (α22, α23, α44, α49, α51, α53, α54, α73) are in complete LD in the DQ8/9 cluster. Seventeen AAs in the DQ2 cluster, represented by two AAs (α44, β135), have differential T1D associations, in which (α22, α44, α49, α51) are in complete LD and so are (α31, α37, α47, α48, α50, α72, α158, α160, α172, α212, β135). Four shared AAs (α22, α44, α49, α51) are indicative of associations of AAs among carriers of DQ8/9 or those of DQ2. Frequencies (%) of AAs among control subjects are listed within two DQ haplotype clusters, and so are estimated ORs, z scores, and P values. Fisher exact P values measure the significance of AA association with T1D within each DQ cluster.
* There are thirteen residues on the α-chain together with β135 here that are in perfect LD with each other and are listed in Supplementary Table 1. Risk and protective haplotypes are highlighted green and red, respectively, at the significance level of 5%.
- Table 4
Haplotypic association results with selected AAs from both α-chain and β-chain
Estimated haplotype frequency (%) (out of 636 control subjects and 962 patients), estimated ORs, haplotype score, and P values from association analysis with T1D (in case-control study), with GADA level among patients, and with IA-2A level among patients. For given haplotypes, one or more DQA1-DQB1 haplotypes may be merged into haplotype groups. Estimated haplotype frequencies (%) among those with positive autoantibody, estimated ORs, z scores, and P value are listed: A) three motifs with effectively two AAs (α44, β57) among carriers of DQ8/9 haplotypes, B) three motifs with effectively two AAs (α44, β135) among carriers of DQ2, and C) six motifs with three AAs (α44, β57, β135) among carriers of DQ8/9 or DQ2. AAs (α44, α22, α23, α49, α51, α53, α54, α73, α184) in DQ8/9 mixture are in complete LD and can be represented by α44, and AAs (α22, α49, α51) are in complete LD in DQ2 mixture, and their polymorphisms are captured by α44. Further, (β135, α31, α37, α47, α48, α50, α72, α104, α153, α158, α160, α172, α212) are in complete LD with each other and thus represented by β135. Hence, three AAs (α44, β57, β135) capture all polymorphisms of their motifs in both DQ2 and DQ8/9 mixtures. Haplotype groups include haplotypes that share the same DQ motifs. DQ2.5 refers to DQA1*05:01-DQB1*02:01 (blue), and DQ8.1 includes either DQA1*03:01-DQB1*03:02 or DQA1*03:02-DQB1*03:02 (red). Risk and protective haplotypes are highlighted green and red, respectively, at the significance level of 5%. pos, positive.
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