TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits

Abstract

Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3 x 10(-21)), A928V (rs35018800, OR = 0.53, P = 1.2 x 10(-9)), and I684S (rs12720356, OR = 0.86, P = 4.6 x 10(-7)). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6 x 10(-18)), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P(omnibus) = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.

Fig 1. Results from stepwise conditional analysis of the TYK2 locus.

We fine-mapped the TYK2 locus using Immunochip data available for 7,222 ACPA+ RA cases and 15,870 controls (MAF>0). (A) In the meta-analysis, the best signal of association was at the TYK2 missense variant P1104A (rs34536443).(B) Conditional on P1104A, the best signal of association was at the TYK2 missense variant A928V (rs35018800). (C) Conditional on P1104A and A928V variants, the best signal of association is at the TYK2 missense variant I684S (rs12720356). (D) Conditional on the 3 RA-protective variants in TYK2, we observed no additional signal of association at the locus (best signal is rs3176768, P = 0.01). P-values from meta-analyses of logistic regressions results from 6 Immunochip collections are shown. The three TYK2 missense variants predicted to be damaging and independently associated with RA risk are highlighted in green.

Fig 2. Contribution of 3 independent TYK2 protein-coding variants to protection from RA.

(A) Three variants with MAF>0.5% predicted to be damaging and protecting from RA (P1104A, A928V and I684S) were identified using Immunochip data for 7,222 ACPA+ RA cases and 15,870 controls of European ancestry. (B) The three variants were genotyped in an independent dataset on the Exomechip (4,726 RA cases, 13,683 controls). (C) The three variants genotypes were also available from exon sequencing of TYK2 in 1,118 RA cases, 1,118 matched controls of European ancestry. Frequencies of the independent haplotypes and odds ratios (OR) relative to the most frequent haplotype are shown. Minor alleles of the variants are highlighted in red. H, haplotypes; F, haplotype frequency; 1, P1104A; 2, A928V; 3, I684S.

Fig 3. TYK2 protein-coding variants identified by exon-sequencing of RA cases and controls.

Using dense genotyping, we demonstrate that three TYK2 protein-coding variants predicted to be damaging, P1104A, A928V, and I684S, protect against RA (highlighted in red). By exon-sequencing in 1,118 RA cases and 1,118 controls, we identified 23 additional missense variants predicted to be damaging (PolyPhen-2 and SIFT), with no strong evidence of association to RA in gene-based association tests. The TYK2 coding exons, the protein domains, and the minor allele count (MAC) of the rare variants (MAC<5) in cases and controls are shown.

Fig 4. Association of the three RA-associated TYK2 missense variants with SLE and IBD.

We used Exomechip data from 3,053 SLE cases and 13,687 controls (A) and 1,346 IBD cases and 13,687 controls (B) to built haplotypes using the RA-associated TYK2 variants P1104A, A928V and I684S. In the haplotype model, we also included the TYK2 SNP V362F, which has previously been reported to be associated with SLE (highlighted in gray). Frequencies of the independent haplotypes and odds ratios (OR) relative to the most frequent haplotype are shown. Minor alleles of the variants are highlighted in red. H, haplotypes; F, haplotype frequency; 1, P1104A; 2, A928V; 3, I684S; 4, V362F.

Fig 5. Investigation of pleiotropic effects of RA-protecting TYK2 variants using electronic medical records.

We first tested association of the P1104A (A) and I684S (B) variants to 502 PheWAS phenotypes with frequency>1% in two independent EMR collections including 3,005 and 26,372 individuals of European ancestry, respectively. Pvalues of each PheWAS phenotype in meta-analysis of the two EMR collections are shown. We also tested association of the TYK2 P1104A and I684S variants with low-density lipoproteins (LDL) levels (C), and white blood cell counts (WBC) (D). Effect sizes and confidence intervals in each EMR collection are shown. Pvalues from meta-analysis of the two EMR collections are indicated. Association results from SNPs previously reported to be associated with each quantitative trait (indicated by their respective rsIDs) are also shown.