Association of valine and leucine at HLA-DRB1 position 11 with radiographic progression in rheumatoid arthritis, independent of the shared epitope alleles but not independent of anti-citrullinated protein antibodies

Abstract

Objective: For decades it has been known that the HLA-DRB1 shared epitope (SE) alleles are associated with an increased risk of development and progression of rheumatoid arthritis (RA). Recently, the following variations in the peptide-binding grooves of HLA molecules that predispose to RA development have been identified: Val and Leu at HLA-DRB1 position 11, Asp at HLA-B position 9, and Phe at HLA-DPB1 position 9. This study was undertaken to investigate whether these variants are also associated with radiographic progression in RA, independent of SE and anti-citrullinated protein antibody (ACPA) status.

Methods: A total of 4,911 radiograph sets from 1,878 RA patients included in the Leiden Early Arthritis Clinic (The Netherlands), Umeå (Sweden), Hospital Clinico San Carlos-Rheumatoid Arthritis (Spain), and National Data Bank for Rheumatic Diseases (US) cohorts were studied. HLA was imputed using single-nucleotide polymorphism data from an Immunochip, and the amino acids listed above were tested in relation to radiographic progression per cohort using an additive model. Results from the 4 cohorts were combined in inverse-variance weighted meta-analyses using a fixed-effects model. Analyses were conditioned on SE and ACPA status.

Results: Val and Leu at HLA-DRB1 position 11 were associated with more radiographic progression (meta-analysis P = 5.11 × 10(-7)); this effect was independent of SE status (meta-analysis P = 0.022) but not independent of ACPA status. Phe at HLA-DPB1 position 9 was associated with more severe radiographic progression (meta-analysis P = 0.024), though not independent of SE status. Asp at HLA-B position 9 was not associated with radiographic progression.

Conclusion: Val and Leu at HLA-DRB1 position 11 conferred a risk of a higher rate of radiographic progression independent of SE status but not independent of ACPA status. These findings support the relevance of these amino acids at position 11.

Figure 1

Frequencies of HLA–DRB1 shared epitope (SE) alleles and the amino acids at HLA–DRB1 position 11, HLA–B position 9, and HLA–DPB1 position 9. Frequencies are expressed as the percentage of a total of 3,756 alleles/amino acids. Of the 1,878 patients, 69.0% were positive for the HLA–DRB1 SE (at least 1 SE allele), 71.2% were positive for Val/Leu at HLA–DRB1 position 11 (at least 1 Val or Leu amino acid), 23.8% were positive for Asp at HLA–B position 9 (at least 1 Asp), and 93.0% were positive for Phe at HLA–DPB1 position 9 (at least 1 Phe). ACPA = anti–citrullinated protein antibody.

Figure 2

Associations of amino acids at HLA–DRB1, HLA–B, and HLA–DPB1 that are known to predispose to rheumatoid arthritis (RA) development with radiographic progression in RA. The yearly radiographic progression rates per risk amino acid in each individual cohort are shown. P values are from the fixed-effects meta-analyses evaluating the 4 cohorts, which consisted of a total of 1,878 patients and 4,911 sets of radiographs. Risk amino acids were defined according to the findings of Raychaudhuri et al (10). For the DRB1 shared epitope (SE), I² = 22.9%, P = 0.27, fixed-effects P = 6.41 × 10⁻⁷, and random-effects P = 2.01 × 10⁻⁴. For Val/Leu at DRB1 position 11, I² = 23.0%, P = 0.27, fixed-effects P = 5.11 × 10⁻⁷, and random-effects P = 2.19 × 10⁻⁴. For Val/Leu at DRB1 position 11 adjusted for SE status, I² = 37.3%, P = 0.19, fixed-effects P = 0.022, and random-effects P = 0.066. For Asp at B position 9, I² = 0.0%, P = 0.59, fixed-effects P = 0.43, and random-effects P = 0.43. For Phe at DPB1 position 9, I² = 0.0%, P = 0.85, fixed-effects P = 0.024, and random-effects P = 0.024. For Phe at DPB1 position 9 adjusted for SE status, I² = 0.0%, P = 0.90, fixed-effects P = 0.093, and random-effects P = 0.093. EAC = Early Arthritis Clinic; HCSC-RAC = Hospital Clinico San Carlos–Rheumatoid Arthritis Cohort; NDB = National Data Bank for Rheumatic Diseases; ES = effect size; 95% CI = 95% confidence interval.

Figure 3

Radiographic progression in rheumatoid arthritis patients in the Leiden Early Arthritis Clinic cohort per number of risk alleles or amino acids at HLA–DRB1, HLA–B, and HLA–DPB1. The median raw and unmodeled Sharp/van der Heijde scores (SHS) during 7 years of followup of 594 RA patients are shown. The P values obtained by multivariate normal regression analyses comparing the genotypes in relation to radiographic progression were P = 5.33 × 10⁻⁵ for the DRB1 shared epitope (SE) alleles, P = 4.94 × 10⁻⁵ for Val/Leu at DRB1 position 11, P = 0.044 for Ser at DRB1 position 11, P = 0.62 for Asp at HLA–B position 9, and P = 0.036 for Phe at DPB1 position 9.

Figure 4

Association of Ser at HLA–DRB1 position 11 with radiographic progression of rheumatoid arthritis in the total population and in the subgroup of patients who did not carry any predisposing Val or Leu amino acids. A, Yearly radiographic progression rates per Ser amino acid at HLA–DRB1 in the total population. Data are shown for each individual cohort and for the fixed-effects meta-analyses evaluating the 4 cohorts, consisting of a total of 1,878 patients and 4,911 sets of radiographs. I² = 0.0%, P = 0.40, fixed-effects P = 5.99 × 10⁻³, and random-effects P = 5.99 × 10⁻³. B, Yearly radiographic progression rates per Ser amino acid at HLA–DRB1 in the patients who did not carry any predisposing Val or Leu amino acids. To determine whether the observed association of Ser with radiographic progression was truly protective and not due to the concomitant absence of the predisposing amino acids Val and Leu, analyses were performed within the subgroup of patients not carrying Val and Leu (thus, patients with 2 copies of Ser, patients with 1 Ser and 1 neutral amino acid, and patients with 2 neutral amino acids were compared). Data are shown for each individual cohort and for the fixed-effects meta-analyses evaluating the 4 cohorts, consisting of a total of 541 patients and 1,477 sets of radiographs. I² = 9.5%, P = 0.35, fixed-effects P = 0.48, and random-effects P = 0.56. See Figure 2 for definitions.

Figure 5

Association of Val and Leu at HLA–DRB1 position 11 with radiographic progression in the subgroup of rheumatoid arthritis patients who did not carry any Ser at position 11 and with additional adjustment for shared epitope (SE) status. A, Yearly radiographic progression rates per Val or Leu amino acid at HLA–DRB1 position 11 in patients who did not carry any Ser at position 11. These analyses were performed to determine whether the observed association of Val and Leu with radiographic progression was truly predisposing and not due to the concomitant absence of Ser (thus, patients carrying 2 copies of Val or Leu, patients with 1 Val or Leu and 1 neutral amino acid, and patients with 2 neutral amino acids were compared). Data are shown for each individual cohort and for the fixed-effects meta-analyses evaluating a total of 781 patients and 1,747 sets of radiographs. I² = 0.0%, P = 0.92, fixed-effects P = 0.010, and random-effects P = 0.010. B, Yearly radiographic progression rates per Val or Leu amino acid at HLA–DRB1 position 11 in patients who did not carry any Ser at position 11, adjusted for SE status. I² = 0.0%, P = 0.90, fixed-effects P = 0.012, and random-effects P = 0.012. See Figure 2 for definitions.

Figure 6

Association of Leu and Ser at HLA–DRB1 position 11 and Asp at HLA–B position 9 with radiographic progression in anti–citrullinated protein antibody (ACPA)–negative RA. Data are shown for each individual cohort and for the fixed-effects meta-analyses evaluating the 4 cohorts, consisting of a total of 657 patients and 1,877 sets of radiographs. Risk amino acids were defined according to the findings of Han et al (11). A, Yearly radiographic progression rates per risk amino acid Leu or Ser at HLA–DRB1 position 11 in ACPA-negative patients. I² = 60.8%, P = 0.054, fixed-effects P = 0.18, and random-effects P = 0.59. B, Yearly radiographic progression rates per risk amino acid Asp at HLA–B position 9 in ACPA-negative patients. I² = 0.0%, P = 0.56, fixed-effects P = 0.28, random-effects P = 0.28. See Figure 2 for other definitions.