Autoreactive T cell receptors with shared germline-like α chains in type 1 diabetes
Peter S. Linsley, Fariba Barahmand-pour-Whitman, Elisa Balmas, Hannah A. DeBerg, Kaitlin J. Flynn, Alex K. Hu, Mario G. Rosasco, Janice Chen, Colin O’Rourke, Elisavet Serti, Vivian H. Gersuk, Keshav Motwani, Howard R. Seay, Todd M. Brusko, William W. Kwok, Cate Speake, Carla J. Greenbaum, Gerald T. Nepom, Karen Cerosaletti
Peter S. Linsley, Fariba Barahmand-pour-Whitman, Elisa Balmas, Hannah A. DeBerg, Kaitlin J. Flynn, Alex K. Hu, Mario G. Rosasco, Janice Chen, Colin O’Rourke, Elisavet Serti, Vivian H. Gersuk, Keshav Motwani, Howard R. Seay, Todd M. Brusko, William W. Kwok, Cate Speake, Carla J. Greenbaum, Gerald T. Nepom, Karen Cerosaletti
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Research Article

Autoreactive T cell receptors with shared germline-like α chains in type 1 diabetes

Abstract

Human islet antigen reactive CD4+ memory T cells (IAR T cells) play a key role in the pathogenesis of autoimmune type 1 diabetes (T1D). Using single-cell RNA sequencing (scRNA-Seq) to identify T cell receptors (TCRs) in IAR T cells, we have identified a class of TCRs that share TCRα chains between individuals (“public” chains). We isolated IAR T cells from blood of healthy, new-onset T1D and established T1D donors using multiplexed CD154 enrichment and identified paired TCRα/β sequences from 2767 individual cells. More than a quarter of cells shared TCR junctions between 2 or more cells (“expanded”), and 29/47 (~62%) of expanded TCRs tested showed specificity for islet antigen epitopes. Public TCRs sharing TCRα junctions were most prominent in new-onset T1D. Public TCR sequences were more germline like than expanded unique, or “private,” TCRs, and had shorter junction sequences, suggestive of fewer random nucleotide insertions. Public TCRα junctions were often paired with mismatched TCRβ junctions in TCRs; remarkably, a subset of these TCRs exhibited cross-reactivity toward distinct islet antigen peptides. Our findings demonstrate a prevalent population of IAR T cells with diverse specificities determined by TCRs with restricted TCRα junctions and germline-constrained antigen recognition properties. Since these “innate-like” TCRs differ from previously described immunodominant TCRβ chains in autoimmunity, they have implications for fundamental studies of disease mechanisms. Self-reactive restricted TCRα chains and their associated epitopes should be considered in fundamental and translational investigations of TCRs in T1D.

Authors

Peter S. Linsley, Fariba Barahmand-pour-Whitman, Elisa Balmas, Hannah A. DeBerg, Kaitlin J. Flynn, Alex K. Hu, Mario G. Rosasco, Janice Chen, Colin O’Rourke, Elisavet Serti, Vivian H. Gersuk, Keshav Motwani, Howard R. Seay, Todd M. Brusko, William W. Kwok, Cate Speake, Carla J. Greenbaum, Gerald T. Nepom, Karen Cerosaletti

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Figure 3

Public and private TCRs have different properties.

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Public and private TCRs have different properties. (A) Frequency of priv...
(A) Frequency of private junctions was higher than public junctions. Frequencies of public (n = 270) and private (n = 1130) junctions (Supplemental Table 3, public/private TCRs) were compared. Public and private TRA or TRB junctions were combined, and the percentage of junctions in each class was calculated. Violin plots show the probability density of all data without summary statistics. The significance of differences between groups was determined using a 2-sided unpaired Wilcoxon’s signed rank test. *****, FDR < 1 × 10–5. (B) Private TRB junctions were longer than public junctions. Shown are the distributions of amino acid sequence lengths for all unique public and private TRA and TRB junctions (Supplemental Table 3, public/private TCRs) (n = 237 and 227 unique junctions for TRA and TRB chains, respectively). *, FDR < 0.05; NS, not significant. (C) Public TRA and TRB junctions were more germline like than private TRA chains. Shown are V(D)J generation probability values (pgen) for public (n = 270) and private (n = 1130) junctions (Supplemental Table 3, public/private TCRs), calculated using IGoR (50) software. Higher (less negative) pgen values indicate more germline-like V(D)J recombination compared to lower values. The significance of pgen differences between groups was determined using Wilcoxon’s signed rank tests. ***, FDR < 1 × 10–3; *, FDR < 0.05. (D) Public TRB chains show a higher fraction of TRB matches with sequences from pancreatic organ donors. Unique public and private TRB junctions (n = 78 and 149, respectively) (Supplemental Table 3, public/private TCRs) were tested for overlap with nPOD TRB junction sequences from spleen and lymph node (n = 2322 unique junctions). The significance of differences in frequencies of junction matches of public TRB chains with nPOD sequences was assessed by Fisher’s exact test. ***, P < 1 × 10–3. (E) Public TRA junctions show more perfect matches than private junctions with VDJdb junctions. Shown are the fractions of unique public and private TRA and TRB junctions (Supplemental Table 3, public/private TCRs) (n = 237 and 227 unique junctions for TRA and TRB chains, respectively) that overlap with VDJdb junctions (n = 47,069 unique junctions). 15/72 unique public TRA junctions had perfect matches with VDJdb sequences versus 9/165 public TRA junctions. **, FDR < 1 × 10–2.