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Identification of Sjögren’s disease–associated T cell receptor motifs through deep sequencing
Ananth Aditya Jupudi, Michelle L. Joachims, Christina Lawrence, Charmaine Lopez-Davis, Bhuwan Khatri, Astrid Rasmussen, Kiely Grundahl, R. Hal Scofield, Judith A. James, Joel M. Guthridge, Christopher J. Lessard, Linda F. Thompson, A. Darise Farris
Ananth Aditya Jupudi, Michelle L. Joachims, Christina Lawrence, Charmaine Lopez-Davis, Bhuwan Khatri, Astrid Rasmussen, Kiely Grundahl, R. Hal Scofield, Judith A. James, Joel M. Guthridge, Christopher J. Lessard, Linda F. Thompson, A. Darise Farris
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Research Article Immunology

Identification of Sjögren’s disease–associated T cell receptor motifs through deep sequencing

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Abstract

CD4+ T cells predominate lymphocytic foci found in the salivary glands (SGs) of Sjögren’s disease (SjD) cases. Yet little is known about T cell receptor (TCR) repertoire features that distinguish cases from healthy controls (HCs), the relationship between SG and peripheral blood (PB) repertoires of cases, and antigens recognized by pathogenic T cell clones. We performed deep sequencing of bulk-sorted CD4+CD45RA– PB T cells from SjD cases and matched HCs, and single-cell TCR sequencing of the same T cell population from labial SG biopsies of these cases. We found that clonally expanded SG CD4+ T cells expressed complementarity-determining region 3 (CDR3) sequences that were also detected in multiple copies in the blood of the same individuals with SjD. SjD cases displayed a “private” and restricted PB TCR repertoire with reduced clonotype diversity. We identified SjD-associated TCR motifs with the same putative antigen specificity shared between SGs and PB of cases. Their abundances in PB correlated with reduced salivary flow, linking these T cells with pathogenic disease features. Finally, we discovered 2 Ro60 epitopes eliciting an HLA-restricted immune response from expanded SG T cell clones. The comprehensive characterization of SjD TCR repertoires enables the discovery of target antigens and therapeutic strategies.

Authors

Ananth Aditya Jupudi, Michelle L. Joachims, Christina Lawrence, Charmaine Lopez-Davis, Bhuwan Khatri, Astrid Rasmussen, Kiely Grundahl, R. Hal Scofield, Judith A. James, Joel M. Guthridge, Christopher J. Lessard, Linda F. Thompson, A. Darise Farris

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Figure 5

PB TCR repertoire of SjD cases contains disease-associated motifs not detected in SGs.

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PB TCR repertoire of SjD cases contains disease-associated motifs not de...
(A) Flowchart for establishing antigen-specificity-based PB TCR clusters associated with SjD. Filter 1: All PB specificity groups were subjected to GLIPH2-based filtration criteria, including TRBV gene enrichment, CDR3 length conservation, and clonal expansion score. Filter 2: The abundances of resulting clusters in SjD and HC repertoires were compared to determine those exclusively present or preferentially enriched in 3 or more cases. (B) Volcano plot comparing the frequency of PB CDR3β sequences constituting specificity groups passing filter 1 cutoff, between cases and HCs (2-sided Mann-Whitney U test). Significantly enriched motifs among cases (blue; Supplemental Table 6) and HCs (red) were determined by P value (negative log10-transformed P values on y axis) and mean rank difference (x axis). (C) The number of known TCR specificities against select pathogens display significantly increased prevalence in HCs compared with cases (paired t test; *P < 0.05). (D) PB abundance of the motifs RLAG%RTDT (top) and SLGGSS%ET (bottom) correlates with worsening disease measures. (E) PB abundance of the motifs RPRTG%DT (top) and S%LAGVSYNE (bottom) correlates with improving disease measures. (A–C) All comparisons were evaluated between cases (n = 17) and HCs (n = 17) with adequate PB TCR sampling (>25,000 unique clonotypes). (D and E) Two-tailed Spearman’s rank correlation test.

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