Different patterns of associations with anti-citrullinated protein antibody-positive and anti-citrullinated protein antibody-negative rheumatoid arthritis in the extended major histocompatibility complex region

Abstract

Objective: To identify additional variants in the major histocompatibility complex (MHC) region that independently contribute to risk in 2 disease subsets of rheumatoid arthritis (RA) defined according to the presence or absence of antibodies to citrullinated protein antigens (ACPAs).

Methods: In a multistep analytical strategy using unmatched as well as matched analyses to adjust for HLA-DRB1 genotype, we analyzed 2,221 single-nucleotide polymorphisms (SNPs) spanning 10.7 Mb, from 6p22.2 to 6p21.31, across the MHC. For ACPA-positive RA, we analyzed samples from the Swedish Epidemiological Investigation of Rheumatoid Arthritis (EIRA) and the North American Rheumatoid Arthritis Consortium (NARAC) studies (totaling 1,255 cases and 1,719 controls). For ACPA-negative RA, we used samples from the EIRA study (640 cases and 670 controls). Plink and SAS statistical packages were used to conduct all statistical analyses.

Results: A total of 299 SNPs reached locus-wide significance (P<2.3x10(-5)) for ACPA-positive RA, whereas surprisingly, no SNPs reached this significance for ACPA-negative RA. For ACPA-positive RA, we adjusted for known DRB1 risk alleles and identified additional independent associations with SNPs near HLA-DPB1 (rs3117213; odds ratio 1.42 [95% confidence interval 1.17-1.73], Pcombined=0.0003 for the strongest association).

Conclusion: There are distinct genetic patterns of MHC associations in the 2 disease subsets of RA defined according to ACPA status. HLA-DPB1 is an independent risk locus for ACPA-positive RA. We did not identify any associations with SNPs within the MHC for ACPA-negative RA.

Figure 1

Analytical approach used in our study of variants in the major histocompatibility complex region that contribute independently to risk in anti–citrullinated protein antibody (ACPA)–positive rheumatoid arthritis (RA) and ACPA-negative RA, as well as the number of single-nucleotide polymorphisms (SNPs) analyzed at each step. EIRA = Epidemiological Investigation of Rheumatoid Arthritis; NARAC = North American Rheumatoid Arthritis Consortium.

Figure 2

Single-nucleotide polymorphisms found to be significant (locus-wide significance defined as P < 2.3 × 10⁻⁵) in case–control association analyses, as determined by Armitage test for trend. Rheumatoid arthritis (RA) cases with anti–citrullinated protein antibody (ACPA) (A) and without ACPA (B) and control groups from the Epidemiological Investigation of Rheumatoid Arthritis population sample were analyzed.

Figure 3

Linkage disequilibrium structure for the 11 replicated single-nucleotide polymorphisms (SNPs) after adjustment for HLA–DRB1 in the Epidemiological Investigation of Rheumatoid Arthritis population sample. Correlation coefficients (r²; × 100) are shown in the individual boxes; white denotes r² = 0, black denotes r² =1, and various shades of gray denote 0 < r² < 1. SNP positions (in million bp) are indicated across the top. To illustrate the correlation between HLA–DRB1 and these SNPs, the position of HLA–DRB1 (rs660895) is also shown.