Genetic determinants and an epistasis of LILRA3 and HLA-B*52 in Takayasu arteritis

Abstract

Takayasu arteritis (TAK) is a systemic vasculitis with severe complications that affects the aorta and its large branches. HLA-B*52 is an established susceptibility locus to TAK. To date, there are still only a limited number of reports concerning non-HLA susceptibility loci to TAK. We conducted a genome-wide association study (GWAS) and a follow-up study in a total of 633 TAK cases and 5,928 controls. A total of 510,879 SNPs were genotyped, and 5,875,450 SNPs were imputed together with HLA-B*52. Functional annotation of significant loci, enhancer enrichment, and pathway analyses were conducted. We identified four unreported significant loci, namely rs2322599, rs103294, rs17133698, and rs1713450, in PTK2B, LILRA3/LILRB2, DUSP22, and KLHL33, respectively. Two additional significant loci unreported in non-European GWAS were identified, namely HSPA6/FCGR3A and chr21q.22. We found that a single variant associated with the expression of MICB, a ligand for natural killer (NK) cell receptor, could explain the entire association with the HLA-B region. Rs2322599 is strongly associated with the expression of PTK2B Rs103294 risk allele in LILRA3/LILRB2 is known to be a tagging SNP for the deletion of LILRA3, a soluble receptor of HLA class I molecules. We found a significant epistasis effect between HLA-B*52 and rs103294 (P = 1.2 × 10^-3). Enhancer enrichment analysis and pathway analysis suggested the involvement of NK cells (P = 8.8 × 10^-5, enhancer enrichment). In conclusion, four unreported TAK susceptibility loci and an epistasis effect between LILRA3 and HLA-B*52 were identified. HLA and non-HLA regions suggested a critical role for NK cells in TAK.

Keywords: HLA; Takayasu arteritis; autoimmunity; epistasis; genome-wide association study.

Fig. 1.

GWAS reveals susceptibility loci to TAK. Manhattan plot of GWAS is indicated. Genes in bold red and black indicate unreported susceptibility loci across populations and in Asian GWAS, respectively. PTPN2 reached GWAS significance, but this was not supported in replication.

Fig. 2.

Association between the HLA region and TAK susceptibility is explained by two variants in HLA class I, including HLA-B. (A) Sequential conditioning analyses in the HLA region. After condition on rs117298325, HLA-B associations disappeared and rs2523774 showed substantial evidence of association (Middle). After conditioning on the two SNPs, no markers showed association (Bottom). Color saturation indicates LD strength with the top SNPs measured by r². (B) Rs117298325 tags the two susceptibility HLA-B alleles, HLA-B*52 and B*67. OR, odds ratio with 95% CI. Haplotypic frequencies in cases and controls are indicated in the fifth and sixth columns. Ref, reference. (C) Rs117298325 risk allele (C allele) is associated with increased MICB expression in the Japanese eQTL data (35).

Fig. 3.

Rs103294 is associated with LILRA3 expression and shows a multiplicative interactive effect with HLA-B52. (A) Rs103294 risk allele (T allele) is associated with decreased expression of LILRA3 in the Japanese eQTL data (35). (B) An epistatic interactive effect is observed between TT genotype of rs103294 and HLA-B*52. TT genotype without HLA-B*52 did not show significant association with TAK susceptibility (P = 0.13; OR = 1.20; 95% CI = 0.95–1.53). Overall interactive and epistasis effects are evaluated by multiplicative interaction model in logistic regression (Methods). (C) Cell-specific enhancer enrichment analysis using non-HLA susceptibility SNPs to TAK revealed strongest signal in primary NK cells. We used the six loci in the present study and the two loci in our previous study. The vertical broken line indicates a significant level based on Bonferroni’s correction.