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

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 3

TCR motifs are commonly enriched in the PB and SGs of SjD cases.

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TCR motifs are commonly enriched in the PB and SGs of SjD cases. (A) Flo...
(A) Flowchart for the selection of antigen-specificity-based TCR clusters shared between SG and PB TCRs. (B) Stacked Venn diagrams show the number of TCR specificity groups detected in SGs only (yellow), SGs and PB of SjD cases only (orange), SGs of cases and PB of HCs only (brick red), or SGs of cases and PB of both cases and HCs (gray). Likelihood of SG TCR motif detection in the PB of cases compared to HCs was measured by 2-sided Fisher’s exact test. (C) Volcano plot comparing the PB abundances of CDR3β sequences constituting individual SG PB shared specificity groups, between SjD cases (n = 17) and HCs (n = 17) with adequate PB clonotype sampling (2-sided Mann-Whitney U test). TCR motifs significantly enriched among cases (blue) and HCs (red) were determined by P value (negative log10-transformed P values on y axis) and mean rank difference (x axis). (D) The number of SG PB shared motifs comprising glandular and circulating TCRs detected in the same SjD case among those with adequate sampling in both SGs and PB (n = 10) negatively correlates with whole unstimulated salivary flow (WUSF). (E) No correlation was seen between the number of motifs found in the SGs and PB of the same SjD individual and age. (C–E) Adequate sampling thresholds (per individual) for PB: >25,000 unique clonotypes; SG: >40 TCRβ+ cells. (D and E) Two-tailed Spearman’s rank correlation test.