Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus

Abstract

Systemic lupus erythematosus is a complex and potentially fatal autoimmune disease, characterized by autoantibody production and multi-organ damage. By a genome-wide association study (320 patients and 1,500 controls) and subsequent replication altogether involving a total of 3,300 Asian SLE patients from Hong Kong, Mainland China, and Thailand, as well as 4,200 ethnically and geographically matched controls, genetic variants in ETS1 and WDFY4 were found to be associated with SLE (ETS1: rs1128334, P = 2.33x10(-11), OR = 1.29; WDFY4: rs7097397, P = 8.15x10(-12), OR = 1.30). ETS1 encodes for a transcription factor known to be involved in a wide range of immune functions, including Th17 cell development and terminal differentiation of B lymphocytes. SNP rs1128334 is located in the 3'-UTR of ETS1, and allelic expression analysis from peripheral blood mononuclear cells showed significantly lower expression level from the risk allele. WDFY4 is a conserved protein with unknown function, but is predominantly expressed in primary and secondary immune tissues, and rs7097397 in WDFY4 changes an arginine residue to glutamine (R1816Q) in this protein. Our study also confirmed association of the HLA locus, STAT4, TNFSF4, BLK, BANK1, IRF5, and TNFAIP3 with SLE in Asians. These new genetic findings may help us to gain a better understanding of the disease and the functions of the genes involved.

Figure 1. Principal component analysis of Chinese samples collected in Hong Kong, Taiwan, and Beijing.

The red dots denote SLE patient samples collected in Hong Kong used in our GWAS study and the blue dots are unaffected samples from Beijing (A), Taiwan (B), and Hong Kong (C). The data on Taiwan samples was received from deCODE Genetics; the data on Han Chinese in Beijing is available from HapMap. The data on Hong Kong controls were from other studies in the University of Hong Kong that were genotyped by the same platform. Repeat of Eigenstrat analysis for 20 times using randomly chosen 100,000 SNPs each time from all the available SNPs produced similar results.

Figure 2. Confirmation of association of HLA locus, and TNFSF4, STAT4, TNFAIP3, IRF5, BLK with SLE.

Shown are association results comparing SLE patients with controls collected in Hong Kong analyzed by Plink (−log₁₀(P-value) of SNPs). The best SNP in Chromosome 11 is around ETS1 gene (rs6590330), which is in high LD with rs1128334. And the best SNP in Chromosome 10 is in WDFY4 (rs877819).

Figure 3. Quantile-Quantile plot of expected (x-axis) and observed (y-axis) −log₁₀(P value) distribution in our GWAS analysis.

(A) Considering all the available SNPs. (B) SNPs in and around HLA locus, and TNFSF4, STAT4, TNFAIP3, IRF5, BLK, as well as BANK1 were excluded from analysis.

Figure 4. Linkage disequilibrium and sequence conservation of SNPs in ETS1.

Shown are LD for significant SNPs in and around ETS1 detected by GWAS (A), and replicated SNPs in the 3′-UTR and downstream of the gene (B), and sequence conservation for sequences around SNP rs1128334 among different species (C).

Figure 5. Allelic expression of ETS1 on SNP rs1128334 in PBMC of healthy individuals.

PBMC cDNA processed from 33 healthy individuals heterozygous on rs1128334 were used for allelic expression detection of ETS1 by pyrosequencing. (A) A case example of detection on the “A” allele and the “G” allele from both DNA and cDNA samples from the same individual. (B) The ratio of G/A allelic detection for both DNA and cDNA samples. The median G/A ratio for DNA is 1.09 (95% CI: 1.08–1.11) and the median G/A ratio for cDNA expression is 1.32 (95% CI: 1.21–1.43), P<0.0001 by paired student's t test.

Figure 6. LD among WDFY4 SNPs examined in this study (A) and sequence conservation of the three nonsynonymous variations among various species (B).

Figure 7. Involvement of ETS1 in Th17 cell and B lymphocyte development and autoimmunity.