Dense genotyping of immune-related loci implicates host responses to microbial exposure in Behçet's disease susceptibility

Abstract

We analyzed 1,900 Turkish Behçet's disease cases and 1,779 controls genotyped with the Immunochip. The most significantly associated SNP was rs1050502, a tag SNP for HLA-B*51. In the Turkish discovery set, we identified three new risk loci, IL1A-IL1B, IRF8, and CEBPB-PTPN1, with genome-wide significance (P < 5 × 10^-8) by direct genotyping and ADO-EGR2 by imputation. We replicated the ADO-EGR2, IRF8, and CEBPB-PTPN1 loci by genotyping 969 Iranian cases and 826 controls. Imputed data in 608 Japanese cases and 737 controls further replicated ADO-EGR2 and IRF8, and meta-analysis additionally identified RIPK2 and LACC1. The disease-associated allele of rs4402765, the lead marker at IL1A-IL1B, was associated with both decreased IL-1α and increased IL-1β production. ABO non-secretor genotypes for two ancestry-specific FUT2 SNPs showed strong disease association (P = 5.89 × 10^-15). Our findings extend the list of susceptibility genes shared with Crohn's disease and leprosy and implicate mucosal factors and the innate immune response to microbial exposure in Behçet's disease susceptibility.

Figure 1. Association of Immunochip markers with Behçet’s disease in 1,900 cases and 1,779 controls from Turkey

The disease association P-value of the genotyped Immunochip markers is shown according to their genomic location. Three new loci exceeding genome-wide significance are identified by bold blue typeface. Four confirmed reported loci that exceed genome-wide significance are identified by bold black typeface. The solid line indicates the threshold for genome-wide significance (P=5×10⁻⁸) and the broken line indicates the threshold for suggestive disease association (P=5×10⁻⁵). Twenty novel loci outside of the MHC region with P<5×10⁻⁵ were selected for further analysis by imputation and/or additional genotyping. SNP locations are from build 37/hg19.

Figure 2. Expression analysis according to genotype of rs4402765, the lead SNP of the IL1A-IL1B locus

(a) Disease association plot of the IL1A region from this study. The solid line indicates the threshold for genome-wide significance (P=5×10⁻⁸). rs4402765 is the lead SNP of the IL1A region for Behçet’s disease susceptibility (P=2.22×10⁻⁹) discovered by imputation of direct Immunochip and additional fine-mapped marker genotypes. (b) IL1A mRNA expression association plot of the IL1A region in 856 lymphoblastoid cell lines from MuTHER project data. The solid line indicates the threshold for statistical significance (P=2.12×10⁻⁶). rs4402765 is the lead SNP for IL1A mRNA expression (β=−0.22, P=3.31×10⁻¹²). SNP locations in (a) and (b) are from build 37/hg19. (c) IL-1α protein production by zymosan stimulated healthy PBMCs with different rs4402765 genotypes (disease risk allele: C). (d) IL-1β protein production by zymosan stimulated healthy PBMCs with different rs4402765 genotypes (disease risk allele: C). Means (horizontal bars) and standard deviations (error bars) are marked. *P<0.05