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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 4

PB TCRs of SjD cases display reduced diversity, clonotypes with higher abundance, and a relatively private repertoire compared with HCs.

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PB TCRs of SjD cases display reduced diversity, clonotypes with higher a...
(A) Distribution of TCRβ clonotype abundance across SjD cases and HCs. (B) Number of TCRβ clonotypes detected in the PB of SjD cases (blue) and HCs (red). (C) Number of TCR-encoding cDNA molecules detected in cases (blue) and HCs (red). (D–F) Comparison of TCRβ diversity between cases (blue) and HCs (red) measured by (D) chao1 estimator (species richness) and Efron-Thisted method, (E) D50 diversity index, and (F) Shannon-Weiner diversity index. (G) Proportion of repertoire space occupied by PB TCRs of rare (0 < x < 0.001%), small (0.001% < x < 0.025%), moderate (0.025% < x < 0.25%), and large (x > 0.25%) clonal abundance groups in SjD cases and HCs. (H) Distribution of effect sizes (β3, left) and corresponding P values (right), of the estimated change in pGen of CDR3β clonotypes against increase in their mean abundances, between SjD and HC repertoires (interaction term). Distributions are shown for 10,000 different subsamples comprising 10,000 CDR3β sequences each, from both cases and HCs. Positive β3 values (99.98%) reflect increase in the pGen of HC clonotypes over that of cases, with increasing mean clonotype abundance. Red dashed line (left) shows mean β3 across all subsamples (0.29). Red solid line (right) indicates iterations with P < 0.05 (96.62%). (B–G) Two-sided Mann-Whitney U test; data shown as mean ± SD. All comparisons were evaluated between cases (n = 17) and HCs (n = 17) with adequate PB TCR sampling (>25,000 unique clonotypes). *P < 0.05, **P < 0.01, ***P < 0.001. NS, not significant.

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