Genetic and clinical basis for two distinct subtypes of primary Sjögren's syndrome

Abstract

Objectives: Clinical presentation of primary Sjögren's syndrome (pSS) varies considerably. A shortage of evidence-based objective markers hinders efficient drug development and most clinical trials have failed to reach primary endpoints.

Methods: We performed a multicentre study to identify patient subgroups based on clinical, immunological and genetic features. Targeted DNA sequencing of 1853 autoimmune-related loci was performed. After quality control, 918 patients with pSS, 1264 controls and 107 045 single nucleotide variants remained for analysis. Replication was performed in 177 patients with pSS and 7672 controls.

Results: We found strong signals of association with pSS in the HLA region. Principal component analysis of clinical data distinguished two patient subgroups defined by the presence of SSA/SSB antibodies. We observed an unprecedented high risk of pSS for an association in the HLA-DQA1 locus of odds ratio 6.10 (95% CI: 4.93, 7.54, P=2.2×10-62) in the SSA/SSB-positive subgroup, while absent in the antibody negative group. Three independent signals within the MHC were observed. The two most significant variants in MHC class I and II respectively, identified patients with a higher risk of hypergammaglobulinaemia, leukopenia, anaemia, purpura, major salivary gland swelling and lymphadenopathy. Replication confirmed the association with both MHC class I and II signals confined to SSA/SSB antibody positive pSS.

Conclusion: Two subgroups of patients with pSS with distinct clinical manifestations can be defined by the presence or absence of SSA/SSB antibodies and genetic markers in the HLA locus. These subgroups should be considered in clinical follow-up, drug development and trial outcomes, for the benefit of both subgroups.

Keywords: Sjögren’s syndrome; autoantibodies; autoimmunity; gene polymorphism.

Fig. 1

Genetic association and subgroup analysis of primary Sjögren’s syndrome patients vs controls (A) Single variant association analysis between 918 pSS cases and 1264 healthy controls. Logistic regression with minor allele frequency ≥0.01 and three principal components as covariates. A total of 107 045 variants included after quality control. Red line indicates the experiment wide Bonferroni cutoff (P = 8.7 × 10⁻⁷); blue line represents the suggestive significance threshold (P = 1 × 10⁻⁵). (B) PCA of clinical data collected for 982 pSS cases. (C) Single variant association analysis between anti-SSA/SSB positive patients (dark blue in PCA plot) vs controls. (D) Single variant association analysis between anti-SSA and SSB negative patients (light blue in PCA plot) vs controls. PCA: principal component analysis.

Fig. 2

HLA associations with primary Sjögren’s syndrome Stepwise adjustment for the top associated variants. (A, B) Logistic regression analysis of all patients vs controls (A), or anti-SSA/SSB positive patients vs controls (B). Second panel after conditioning on rs6933289, bottom panel after conditioning on rs6933289 and rs7197, with rs3099839 top remaining variant in all cases vs controls, rs2523607 top remaining variant in anti-SSA/SSB positive vs controls. (C) Unadjusted P-values for all cases vs controls (blue), SSA/SSB positive vs controls (red), and SSA and SSB negative vs controls (grey). (D) Linkage disequilibrium (r²) between the variants. (E) Gene regions of the independent HLA variants: HLA-DQA1, HLA-DRA and the HLA-B/MICA/HCP5 locus.

Fig. 3

Correlations between clinical phenotypes and associated variants (A) Non-parametric correlations between associated genetic variants and clinical variables. The purple scale represents P-values for the correlation (darker represents more significant), and the blue–red scale represents the correlation coefficient, with darker blue representing stronger negative correlation, and deeper red representing stronger positive correlation. (B) Logistic regression of different clinical variables with risk allele count for the top associated independent genetic variants. Red lines represent significant positive associations, blue lines significant negative associations. Whiskers indicate 95% CI. OR: odds ratio.

Fig. 4

Comparison of effect sizes for associated variants in the HLA region Top variants from Lessard et al. [10] are shown as light grey circles and variants from Taylor et al. [13] are depicted as dark grey triangles. Red diamonds represent SSA and/or SSB positive primary Sjögren’s syndrome associations and blue diamonds represent the full primary Sjögren’s syndrome associations from the current study. Position on chromosome 6 is shown on the x-axis and ORs on the y-axis. The nearest genes are labelled below. OR: odds ratio.