The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share

Abstract

Exploiting genotyping, DNA sequencing, imputation and trans-ancestral mapping, we used Bayesian and frequentist approaches to model the IRF5-TNPO3 locus association, now implicated in two immunotherapies and seven autoimmune diseases. Specifically, in systemic lupus erythematosus (SLE), we resolved separate associations in the IRF5 promoter (all ancestries) and with an extended European haplotype. We captured 3230 IRF5-TNPO3 high-quality, common variants across 5 ethnicities in 8395 SLE cases and 7367 controls. The genetic effect from the IRF5 promoter can be explained by any one of four variants in 5.7 kb (P-valuemeta = 6 × 10(-49); OR = 1.38-1.97). The second genetic effect spanned an 85.5-kb, 24-variant haplotype that included the genes IRF5 and TNPO3 (P-valuesEU = 10(-27)-10(-32), OR = 1.7-1.81). Many variants at the IRF5 locus with previously assigned biological function are not members of either final credible set of potential causal variants identified herein. In addition to the known biologically functional variants, we demonstrated that the risk allele of rs4728142, a variant in the promoter among the lowest frequentist probability and highest Bayesian posterior probability, was correlated with IRF5 expression and differentially binds the transcription factor ZBTB3. Our analytical strategy provides a novel framework for future studies aimed at dissecting etiological genetic effects. Finally, both SLE elements of the statistical model appear to operate in Sjögren's syndrome and systemic sclerosis whereas only the IRF5-TNPO3 gene-spanning haplotype is associated with primary biliary cirrhosis, demonstrating the nuance of similarity and difference in autoimmune disease risk mechanisms at IRF5-TNPO3.

Figure 1.

Reported IRF5–TNPO3 associations. Disorders and immunotherapies purported to be associated with IRF5 and TNPO3. The most closely associated variant reported is identified. Disequilibrium as assessed by r² in European-Americans controls is presented. The positions presented are not on a nucleotide scale.

Figure 2.

IRF5- and TNPO3-imputed genetic variants demonstrate different patterns of lupus association in four distinct ethnicities. The association of genotyped and imputed variants in cohorts of SLE in European Americans (EU) (3936 cases and 3491 controls), AAs (AA) (1527 cases and 1811 controls), Asians and AS (1265 cases and 1260 controls) and HAs (HA) (1225 cases and 614 controls) was assessed in a logistic regression with an adjustment for admixture. While the association of SNPs in the promoter of IRF5 is present in all of the cohorts, the association of SNPs spanning the IRF5 and TNPO3 genes is only seen in the cohorts with European admixture.

Figure 3.

Trans-ancestral meta-analysis of genotyped and imputed variants. A meta-analysis of five ancestral cohorts contained 8395 SLE cases and 7367 controls identifies the IRF5–TNPO3 association and its boundaries. For each meta-analysis, the adjusted P-values from the step-wise regression of each ancestry were combined. Panels 1b and 1c present the association of each SNP in the region in a logistic regression adjusting for admixture covariants and rs4728142 (Panel 1a) in the IRF5 promoter and rs12534421 in a haplotype that spans IRF5 and TNPO3 (Panel 1c). After adjusting for these two variants and admixture, no other variant provides convincing evidence of association.

Figure 4.

The IRF5–TNPO3 association across other inflammatory diseases. Genomic position is given with Human Genome Build 37 coordinates. An analysis of European ancestry Sjögren's syndrome and systemic sclerosis using a different set of initially genotyped markers reproduces both components of the model we present herein for the European ancestry in SLE. For the IRF5–TNPO3 association with primary biliary cirrhosis, the IRF5 promoter association identified in SLE is absent, whereas the IRF5–TPO3 haplotype association is present. The full step-wise logistic regression analysis for Sjögren's syndrome, systemic sclerosis and primary biliary cirrhosis is presented in Supplementary Material, Figures S3, S4 and S5, respectively.

Figure 5.

Bayesian association plot showing the signal strength in the promoter of IRF5 (position < 128 585 000) and in the IRF5–TNPO3 gene-spanning region (position > 128 585 000) as the posterior probability of each SNP. Genomic position is given with Human Genome Build 37 coordinates; European American data are shown. Single-nucleotide polymorphisms are colored according to membership in credible sets: yellow diamonds, 95% credible set in the promoter region of IRF5; red diamonds, 95% credible set in the region spanning the IRF5 and TNPO3 genes; gray outline, neither set. The position of IRF5 and TNPO3 are labeled. Variants with larger posterior probabilities (>0.01) represent those most likely to be causal among the variants genotyped (yellow or red). Variants with relatively low posterior probabilities (<0.01) are unlikely to be causal (gray or black).

Figure 6.

Anti-ZBTB3 reduces the shifted band intensity at rs4728142 suggesting ZBTB3 binding. Labeled oligonucleotides corresponding to the non-risk (NR) and risk (R) variants at rs4728142. (A) Oligonucleotides NR and R at rs4728142 were used to probe nuclear extract from B cells. The four lanes shown are from the same blot. (B) Anti-ZBTB3 antibody was used to compete with the labeled oligonucleotides for binding of the nuclear extract. An oligonucleotide corresponding to the consensus ZBTB3 binding site was used as a positive control. The arrow indicates the specific band.