Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis

Abstract

Objective: To identify genetic determinants of granulomatosis with polyangiitis (Wegener's) (GPA).

Methods: We carried out a genome-wide association study (GWAS) of 492 GPA cases and 1,506 healthy controls (white subjects of European descent), followed by replication analysis of the most strongly associated signals in an independent cohort of 528 GPA cases and 1,228 controls.

Results: Genome-wide significant associations were identified in 32 single-nucleotide polymorphic (SNP) markers across the HLA region, the majority of which were located in the HLA-DPB1 and HLA-DPA1 genes encoding the class II major histocompatibility complex (MHC) DPβ chain 1 and DPα chain 1 proteins, respectively. Peak association signals in these 2 genes, emanating from SNPs rs9277554 (for DPβ chain 1) and rs9277341 (DPα chain 1) were strongly replicated in an independent cohort (in the combined analysis of the initial cohort and the replication cohort, P = 1.92 × 10(-50) and 2.18 × 10(-39) , respectively). Imputation of classic HLA alleles and conditional analyses revealed that the SNP association signal was fully accounted for by the classic HLA-DPB1*04 allele. An independent single SNP, rs26595, near SEMA6A (the gene for semaphorin 6A) on chromosome 5, was also associated with GPA, reaching genome-wide significance in a combined analysis of the GWAS and replication cohorts (P = 2.09 × 10(-8) ).

Conclusion: We identified the SEMA6A and HLA-DP loci as significant contributors to risk for GPA, with the HLA-DPB1*04 allele almost completely accounting for the MHC association. These two associations confirm the critical role of immunogenetic factors in the development of GPA.

Figure 1

Results of the granulomatosis with polyangiitis (Wegener’s) genome-wide association screen. The −log₁₀ P values for association of 287,802 single-nucleotide polymorphisms (SNPs) in 1,962 subjects are shown based on chromosomal locations. The y-axis represents the level of significance (determined using Plink) for each SNP on each chromosome shown along the x-axis. Dashed line shows the threshold for significance of the genome-wide association (P < 5 × 10⁻⁸). Circles with dots indicate the SNPs most significantly associated with disease, in the major histocompatibility complex (MHC) region genes HLA–DPB1 and HLA–DPA1 (encoding class II MHC DP β chain 1 and α chain 1, respectively) and in the non-MHC region genes DCTD (encoding deoxycytidylate deaminase), COBL (encoding protein cordon bleu), CCDC86 (encoding coiled-coil domain-containing protein 86), and WSCD1 (encoding water-soluble carbodiimide domain-containing protein 1). Color figure can be viewed in the online issue, which is available at http:onlinelibrary.wiley.com/doi/10.1002/acr.38036/abstract.

Figure 2

Association plots from genome-wide analyses across the major histocompatibility complex (MHC) region. A, The -log₁₀ P values of 283 genotyped single-nucleotide polymorphisms (SNPs) across the class II MHC region are plotted against their physical position on chromosome 6 (chr6). LocusZoom software was used for analysis. Estimated recombination rates from the HapMap phase II Centre d’ Étude du Polymorphisme Humain study population of Utah residents with ancestry from northern and western Europe (CEU) population show the local linkage disequilibrium (LD) structure. Colors in the upper panel indicate the extent of LD with the top HLA–DPB1 SNP (rs9277554) (♦), according to a scale of r²= 0 to r²= 1 based on pairwise r² values from HapMap CEU. The HLA–DPA1 rs9277341 is indicated by an arrow. The lower panel shows gene annotation data from the University of California at Santa Cruz genome browser. B, The-log₁₀ P values of 1,160 genotyped SNPs and 7,261 imputed SNPs, 424 classic HLA alleles, and 1,276 corresponding amino acid polymorphisms across the MHC region are plotted against their physical position on chromosome 6. Dotted line shows the threshold for significance of the genome-wide association (P < 5 × 10⁻⁸).

Figure 3. cctf

Association plot and LD structure of the disease-associated region surrounding SEMA6A. The -log₁₀P values of 135 genotyped SNPs and 3,880 imputed SNPs surrounding SEMA6A are plotted against their physical position on chromosome 5. LocusZoom software was used for analysis. Estimated recombination rates from the HapMap phase II CEU population show the local LD structure. Colors in the upper panel indicate the extent of LD with the top SNP (rs26595), according to a scale of r²= 0 to r²= 1 based on pairwise r² values from HapMap CEU. The lower panel shows gene annotation data from the University of California at Santa Cruz genome browser. GWAS = genome-wide association study (see Figure 2 for other definitions). Color figure can be viewed in the online issue, which is available at http:onlinelibrary.wiley.com/doi/10.1002/acr.38036/abstract.