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Single cell RNA and TCR sequencing reveals substantive similarities between synovial fluid and synovial tissue T-cells in inflammatory arthritis.

ABSTRACT: Objective: Synovial fluid (SF) derived T-cells are frequently studied as a proxy for investigating the synovial tissue (ST) T-cell infiltrate in inflammatory arthritis. However, since ST is the primary site of inflammatory activity, there is debate as to whether SF provides a true reflection of the ST T-cell population. Methods: In this study, we used single cell RNA sequencing paired with single cell TCR sequencing to directly compare memory T-cells from paired samples of SF and ST from 6 patients with inflammatory arthritis to investigate their similarity in terms of T-cell receptor (TCR) repertoire and T-cell subset composition. Results: The TCR repertoires of SF and ST T-cells were strikingly similar, particularly for CD8+ T-cells. A median of 49% of the total CD8+ TCR repertoire in SF was shared with ST, compared to 20% shared with blood and 47% of the ST CD8+ TCR repertoire was shared with SF compared to 25% with blood. Furthermore, once the effect of collagenase digestion on gene expression by ST T-cells had been accounted for, the frequencies of specific CD8+ and CD4+ T-cell subsets were, in general, very similar in SF and ST and were distinct from blood. Conclusion: Our results suggest that T-cells migrate and equilibrate between SF and ST and maintain similar phenotypes in both sites. We conclude that SF is an appropriate proxy for investigating the T-cell infiltrate in inflamed synovium using single cell RNA sequencing, particularly in terms of investigating the TCR repertoire.

ORGANISM(S): Homo sapiens

PROVIDER: GSE250242 | GEO | 2024/08/22

REPOSITORIES: GEO

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Project description:HLA-DR molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory arthritides, including in rheumatoid arthritis (RA) and Lyme arthritis (LA). In the current study, we identified HLA-DR-presented self-peptides (T cell epitopes) in ST, synovial fluid mononuclear cells (SF), and peripheral blood mononuclear cells (PB) from five patients with RA and eight with LA. Altogether, from 22 samples, 1,532 non-redundant HLA-DR-presented peptides were identified that were derived from 778 source proteins. Moreover, as the study progressed, application of newer, high sensitivity LC-MS instruments resulted in the identification of larger numbers of HLA-DR-presented peptides. Surprisingly, the source proteins for HLA-DR-presented peptides were as likely to have intracellular as extracellular locations. Although the number of peptides identified was greater in ST than in SF or PB, 68% of the peptides identified in SF were found in ST, and 55% of the peptides in PB were found in ST. Two RA patients had the same HLA-DR genotype (DRB1*0401 and 0101), and 44% of the peptides identified in these two patients were the same. In contrast, among the patients with RA or LA who had no shared HLA-DR alleles, only 6% of the peptides were the same. In the RA patients, HLA-DR-presented peptides were identified from source proteins that are thought to serve as potential autoantigens: collagen, enolase, fibrinogen, fibronectin, immunoglobulin and vimentin. Interestingly, peptides from these same source proteins were also commonly found in LA patients. However, citrullinated T cell epitopes were not identified in any patient. Thus, LC-MS/MS techniques are now sensitive enough to identify large numbers of T cell epitopes from tissue or fluids in individual patients. Importantly, analysis of SF or PB allowed us to identify a broader range of HLA-DR-presented self-peptides from individual patients and from patients seen earlier in the disease.

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Single cell RNA and TCR sequencing reveals substantive similarities between synovial fluid and synovial tissue T-cells in inflammatory arthritis.

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