An African Ancestry-Specific Allele of CTLA4 Confers Protection against Rheumatoid Arthritis in African Americans

Cytotoxic T-lymphocyte associated protein 4 (CTLA4) is a negative regulator of T-cell proliferation. Polymorphisms in CTLA4 have been inconsistently associated with susceptibility to rheumatoid arthritis (RA) in populations of European ancestry but have not been examined in African Americans. The prevalence of RA in most populations of European and Asian ancestry is ∼1.0%; RA is purportedly less common in black Africans, with little known about its prevalence in African Americans. We sought to determine if CTLA4 polymorphisms are associated with RA in African Americans. We performed a 2-stage analysis of 12 haplotype tagging single nucleotide polymorphisms (SNPs) across CTLA4 in a total of 505 African American RA patients and 712 African American controls using Illumina and TaqMan platforms. The minor allele (G) of the rs231778 SNP was 0.054 in RA patients, compared to 0.209 in controls (4.462×10−26, Fisher's exact). The presence of the G allele was associated with a substantially reduced odds ratio (OR) of having RA (AG+GG genotypes vs. AA genotype, OR 0.19, 95% CI: 0.13–0.26, p = 2.4×10−28, Fisher's exact), suggesting a protective effect. This SNP is polymorphic in the African population (minor allele frequency [MAF] 0.09 in the Yoruba population), but is very rare in other groups (MAF = 0.002 in 530 Caucasians genotyped for this study). Markers associated with RA in populations of European ancestry (rs3087243 [+60C/T] and rs231775 [+49A/G]) were not replicated in African Americans. We found no confounding of association for rs231778 after stratifying for the HLA-DRB1 shared epitope, presence of anti-cyclic citrullinated peptide antibody, or degree of admixture from the European population. An African ancestry-specific genetic variant of CTLA4 appears to be associated with protection from RA in African Americans. This finding may explain, in part, the relatively low prevalence of RA in black African populations

Odds ratios for the protective effect of the rs231778 G allele in African Americans with RA.

<p>Analysis compares number of patients and controls for genotype AA vs those with either AG or GG in a 2×2 Fisher's exact test. OR – odds ratio; CI – confidence interval.</p

Mean percentage of European ancestry segregated by genotype of rs231778.

<p>This table provides data for the 347 samples with complete admixture and rs231778 genotyping data. Standard error is provided in parenthesis. Brackets indicate frequency counts used in determining association of the rs231778 G allele with rheumatoid arthritis among 366 samples, as described in the text.</p

Minor allele frequency (MAF) of rs231778 segregated by HLA-DRB1 shared epitope status.

<p>This table combines samples from both CLEAR I and CLEAR II and only incorporates data where HLA-DRB1 shared epitope (SE) status has been determined. The ‘N’ listed below each MAF represents the number of ‘G’ alleles over the total number of alleles for each number of SE alleles present. SE – <i>HLA-DRB1</i> shared epitope.</p

Association with rheumatoid arthritis at rs231778 in African Americans.

<p>Values indicate number of samples with allele frequency in parentheses. Analysis compares number of patients and controls for each genotype (AA vs AG vs GG) in a 3×2 Fisher's exact test.</p

Only SNPs genotyped in this study are listed by name.

<p>SNPs in linkage disequilibrium with SNPs genotyped in this study are shown in brown. SNPs in gray were not genotyped or haplotype tagged due to low minor allele frequency (MAF). SNP - Single Nucleotide Polymorphism. 5251* is not yet registered in dbSNP as described in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000424#s2" target="_blank">methods</a>.</p

This plot, generated from HaploView v3.31 (Broad Institute), shows the r² values between SNPs genotyped in <i>CTLA4</i>.

<p>Darker boxes represent stronger r² values. 5251* is not yet registered in dbSNP as described in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000424#s2" target="_blank">methods</a>.</p

Minor allele frequencies of CTLA4 SNPs for African American RA patients and controls.

<p>This table represents combined data from CLEAR I and CLEAR II. rs3087243 (+60C/T) has been associated with RA in Caucasians, and rs231775 (+49A/G) has been associated with other autoimmune conditions. Position is the physical location of each polymorphism relative to the start codon (position = 0) in dbSNP build 129. CCP refers to anti-cyclic citrullinated antibody status. SE refers to presence of HLA-DRB1 shared epitope. Public databases include allele frequencies from HapMap or SeattleSNP. rs231776 was not in Hardy-Weinberg Equilibrium. *5251 is not currently listed in dbSNP as described in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000424#s2" target="_blank">methods</a>.</p