Diversity and Clonality of T Cell Receptor Repertoire and Antigen Specificities in Small Joints of Early Rheumatoid Arthritis

Abstract

Objective. CD4+ T cells are implicated in rheumatoid arthritis (RA) pathology from the strong association between RA and certain HLA class II gene variants. This study was undertaken to examine the synovial T cell receptor (TCR) repertoire, T cell phenotypes, and T cell specificities in small joints of RA patients at time of diagnosis before therapeutic intervention.Methods. Sixteen patients, of whom 11 patients were anti-citrullinated protein antibody (ACPA)-positive and 5 patients were ACPA-, underwent ultrasound-guided synovial biopsy of a small joint (n = 13) or arthroscopic synovial biopsy of a large joint (n = 3), followed by direct sorting of single T cells for paired sequencing of the αβ TCR together with flow cytometry analysis. TCRs from expanded CD4+ T cell clones of 4 patients carrying an HLA-DRB1*04:01 allele were artificially reexpressed to study antigen specificity.Results. T cell analysis demonstrated CD4+ dominance and the presence of peripheral helper T-like cells in both patient groups. We identified >4,000 unique TCR sequences, as well as 225 clonal expansions. Additionally, T cells with double α-chains were a recurring feature. We identified a biased gene usage of the V β chain segment TRBV20-1 in CD4+ cells from ACPA+ patients. In vitro stimulation of T cell lines expressing selected TCRs with an extensive panel of citrullinated and viral peptides identified several different virus-specific TCRs (e.g., human cytomegalovirus and human herpesvirus 2). Still, the majority of clones remained orphans with unknown specificity.Conclusion. Minimally invasive biopsies of the RA synovium allow for single-cell TCR sequencing and phenotyping. Clonally expanded, viral-reactive T cells account for part of the diverse CD4+ T cell repertoire. TRBV20-1 bias in ACPA+ patients suggests recognition of common antigens.

Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium

“…The presence of T cell cross-reactivity between virus and self has previously been associated with the capacity for driving autoimmunity, including in RA, yet the potential for virus- reactive T cells to contribute to synovial inflammation has remained uncertain (Wucherpfennig and Strominger 1995; Pender et al 2017; Ashton et al 2016; Lanz et al 2022). Our analyses identify multiple synovial T cell clones that match those previously identified to be viral-reactive, a result consistent with the recent demonstration of viral reactivity among TCRs from RA synovial CD4 T cells (Turcinov et al 2022). Our paired RNA-seq/TCR analysis enabled interrogation of the phenotypes of potentially viral-reactive CD8 T cells, yet no broad-scale difference in the cluster composition or clonal characteristics of these cells was apparent.…”

“…Studies tracking TCRs across tissues or longitudinally in RA patients have identified shared T cell clones in different joints (Musters et al 2018; Klarenbeek et al 2012), clonal expansion of specific cell subsets (Argyriou et al 2022), persistence of expanded clones over time (Ishigaki et al 2015), and overrepresented gene rearrangements that may suggest shared antigenic targets (Klarenbeek et al 2012; Chang et al 2019; X. Liu et al 2019); however, reactivity of expanded TCRs from RA synovial CD4 T cells to citrullinated peptides has been difficult to demonstrate (Turcinov et al 2022). Studies of BCR repertoires of RA patients have indicated somatic hypermutation in RA synovial B cells and identified potential specificities across B cells collected from synovial tissue or fluid (Scheel et al 2011; Corsiero et al 2016; Titcombe et al 2018; Hardt et al 2022).…”

Proinflammatory impact of putative viral-specific CD8+ T cells infiltrating new-onset seropositive rheumatoid arthritis synovium

“…We also identified MHC class II-restricted T cells with predicted viral-specific CDR3α and CDR3β, albeit at a much lower frequency, and only in the PB (Figure 4C). These findings are consistent with a previous publication that identified viral-reactive T cells within the CD4 + T cell repertoire 28 .…”

“…However, the degree of clonal dominance (exclusive expansion of a few clones) decreased with longer disease duration 25 suggesting that repertoire studies in early disease may yield the greatest insight to disease-relevant antigens and the role of T cells in early disease. Indeed, recent TCR repertoire studies identified a subset of clonally-expanded CD4 + T cells in early RA patients responding to viral antigens 28 . However, it is not known how virus-specific T cells contribute to early RA inflammation.…”

The Search for the Pathogenic T Cells in the Joint of Rheumatoid Arthritis: Which T-Cell Subset Drives Autoimmune Inflammation?

“…Recent studies reported antigen specificity of expanded T-cell clones in RA joints. Turcinov et al performed scRNAseq analysis on synovial T cells in treatment-naive RA [ 77 ]. A diverse TCR repertoire of CD4 T cells, including Tph cells, was observed, but several expanded clones could also be detected.…”