Transcriptomic profiling of Sjögren's disease salivary glands identifies signatures associated with both follicular and extrafollicular responses linked to rheumatoid factor and anti-La/SSB seropositivity

Abstract

Objectives: This study aims to identify salivary gland (SG) transcriptomic signatures associated with peripheral and histological biomarkers of disease activity and lymphoma risk factors to inform on Sjögren's disease (SjD) stratification.

Methods: Bulk RNA-sequencing of labial SG from exploratory Queen Mary University of London (QMUL) cohort (SjD [n = 55] and non specific-chronic-sialadenitis [sicca, n = 44]) and trial for anti-B-cell therapy in Sjogren's syndrome (TRACTISS)validation cohort (SjD, n = 29) analysed integrating transcriptomic, clinical, serological, and histological data.

Results: Unsupervised gene clustering confirmed clear transcriptome segregation between sicca and SjD. The most differentially expressed genes were either common to all SjD's versus sicca or specific to SjD's glands with lymphocytic infiltrates with features of ectopic lymphoid structures (ELS). In SjD, principal component analysis identified a significant proportion of variability associated with rheumatoid factor (RF)-seropositivity, exceeding that associated with SG-ELS and anti-Ro/Sjögren's syndrome antigen-A (SSA) seropositivity. Transcriptomes of SjD-SG with ELS from patients with positivity for either RF, anti-Ro/SSA, and anti-La/SSB showed mainly genes associated with germinal centre formation. Conversely, SG without ELS from patients with either RF or double anti-Ro (SSA)/anti-La (SSB) seropositivity (unlike patients with seronegative or single anti-Ro/SSA seropositivity) displayed a unique extrafollicular B-cell gene set associated with type-I interferon (IFN), through the retinoic acid-inducible gene-I (RIG-1) endogenous RNAs (including viral) sensing pathway and E3-ubiquitin ligases. The identified IFN genes showed strong positive correlations with serum RF levels in 2 independent cohorts (QMUL and TRACTISS).

Conclusions: Comprehensive SG bulk-RNA sequencing provided the first transcriptomic evidence of distinct RF and anti-La/SSB-driven SG transcriptomic signatures in patients with SjD with and without ELS. These findings suggest that both classical follicular and extrafollicular viral-associated responses contribute to the selection of autoreactive B-cells in the glands of patients with SjD.