Association of two independent functional risk haplotypes in TNIP1 with systemic lupus erythematosus

Abstract

Objective: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by autoantibody production and altered type I interferon expression. Genetic surveys and genome-wide association studies have identified >30 SLE susceptibility genes. One of these genes, TNIP1, encodes the ABIN1 protein. ABIN1 functions in the immune system by restricting NF-κB signaling. The present study was undertaken to investigate the genetic factors that influence association with SLE in genes that regulate the NF-κB pathway.

Methods: We analyzed a dense set of genetic markers spanning TNIP1 and TAX1BP1, as well as the TNIP1 homolog TNIP2, in case-control populations of diverse ethnic origins. TNIP1, TNIP2, and TAX1BP1 were fine-mapped in a total of 8,372 SLE cases and 7,492 healthy controls from European-ancestry, African American, Hispanic, East Asian, and African American Gullah populations. Levels of TNIP1 messenger RNA (mRNA) and ABIN1 protein in Epstein-Barr virus-transformed human B cell lines were analyzed by quantitative reverse transcription-polymerase chain reaction and Western blotting, respectively.

Results: We found significant associations between SLE and genetic variants within TNIP1, but not in TNIP2 or TAX1BP1. After resequencing and imputation, we identified 2 independent risk haplotypes within TNIP1 in individuals of European ancestry that were also present in African American and Hispanic populations. Levels of TNIP1 mRNA and ABIN1 protein were reduced among subjects with these haplotypes, suggesting that they harbor hypomorphic functional variants that influence susceptibility to SLE by restricting ABIN1 expression.

Conclusion: Our results confirm the association signals between SLE and TNIP1 variants in multiple populations and provide new insight into the mechanism by which TNIP1 variants may contribute to SLE pathogenesis.

Figure 1

SNPs in and around the TNIP1 region associated with SLE in (A) European-ancestry (B) African-American, (C) Hispanic, and (D) East Asian populations. Genotyped SNPs are represented by triangles and imputed SNPs are shown in circles. The red solid line refers to the Bonferroni threshold of significance. The color of each triangle or circles represents the level of linkage disequilibrium (LD) between each SNP and the most significant SNP.

Figure 2

TNIP1 haplotypes and linkage disequilibrium (LD) for SLE-associated variants that surpassed the Bonferroni correction threshold of P < 3.21 × 10⁻⁴ in European-ancestry population. Haplotypes are shown at a frequency > 3%. The group of variants unique to H1, H2, or shared by H1 and H2 haplotypes, are colored in blue, red, and green, respectively. In the haplotype block, white boxes represent the major alleles and colored boxes represent the minor alleles (colored according to their group). Pairwise LD relationships (r²) are shown below the haplotype block with different color intensities according to degree of correlation between two variants.

Figure 3

Effect of the risk haplotypes on (A) TNIP1 mRNA and (B) ABIN1 protein expression. On the X-axis, the three different haplotypes are displayed corresponding to the non-risk, H1, and H2 haplotypes. On the Y-axis is the level of normalized expression for each assay. Each data point represents the expression level of TNIP1 mRNA or ABIN1 protein for one individual. Significant differences from the mean expression of the non-risk haplotype were determined using an unpaired t-test.