Genetic Association of a Gain-of-Function IFNGR1 Polymorphism and the Intergenic Region LNCAROD/DKK1 With Behçet's Disease

Abstract

Objective: Behçet's disease is a complex systemic inflammatory vasculitis of incompletely understood etiology. This study was undertaken to investigate genetic associations with Behçet's disease in a diverse multiethnic population.

Methods: A total of 9,444 patients and controls from 7 different populations were included in this study. Genotyping was performed using an Infinium ImmunoArray-24 v.1.0 or v.2.0 BeadChip. Analysis of expression data from stimulated monocytes, and epigenetic and chromatin interaction analyses were performed.

Results: We identified 2 novel genetic susceptibility loci for Behçet's disease, including a risk locus in IFNGR1 (rs4896243) (odds ratio [OR] 1.25; P = 2.42 × 10^-9 ) and within the intergenic region LNCAROD/DKK1 (rs1660760) (OR 0.78; P = 2.75 × 10^-8 ). The risk variants in IFNGR1 significantly increased IFNGR1 messenger RNA expression in lipopolysaccharide-stimulated monocytes. In addition, our results replicated the association (P < 5 × 10^-8 ) of 6 previously identified susceptibility loci in Behçet's disease: IL10, IL23R, IL12A-AS1, CCR3, ADO, and LACC1, reinforcing the notion that these loci are strong genetic factors in Behçet's disease shared across ancestries. We also identified >30 genetic susceptibility loci with a suggestive level of association (P < 5 × 10^-5 ), which will require replication. Finally, functional annotation of genetic susceptibility loci in Behçet's disease revealed their possible regulatory roles and suggested potential causal genes and molecular mechanisms that could be further investigated.

Conclusion: We performed the largest genetic association study in Behçet's disease to date. Our findings reveal novel putative functional variants associated with the disease and replicate and extend the genetic associations in other loci across multiple ancestries.

Figure 1.. Manhattan plot showing the results of a meta-analysis of Behçet’s disease cases and controls included in this study.

The -log₁₀ p value for each genetic variant analyzed is plotted against its physical chromosomal position. The red and blue lines represent the genome-wide level of significance (p value < 5 × 10⁻⁸) and the suggestive level of significance (p value < 5 × 10⁻⁵), respectively.

Figure 2.. Expression quantitative trait loci (eQTL) associations between two IFNGR1-variants (rs1327474 and rs4896243) and IFNGR1 transcript in 2-hour lipopolysaccharide (LPS) stimulated monocytes.

The risk alleles (C) for both SNPs correlate with significantly higher expression levels of IFNGR1 (one-way ANOVA p value= 1.08 × 10⁻⁴ and 8.25 × 10⁻⁵, respectively). Differences between genotypes were assessed using Tukey’s multiple comparisons test; rs1327474 (CC vs. CT, p = 4.40 × 10⁻²; CC vs. TT, p = 5.98 × 10⁻⁵; CT vs. TT = 2.10 × 10⁻²), rs4896243 (CC vs. CT, p = 6.15 × 10⁻³; CC vs. TT, p = 5.74 × 10⁻⁵; CT vs. TT = 1.02 × 10⁻¹).