Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs

Abstract

Gluten-specific CD4+ T cells are drivers of celiac disease (CeD). Previous studies of gluten-specific T-cell receptor (TCR) repertoires have found public TCRs shared across multiple individuals, biased usage of particular V-genes and conserved CDR3 motifs. The CDR3 motifs within the gluten-specific TCR repertoire, however, have not been systematically investigated. In the current study, we analyzed the largest TCR database of gluten-specific CD4+ T cells studied so far consisting of TCRs of 3122 clonotypes from 63 CeD patients. We established a TCR database from CD4+ T cells isolated with a mix of HLA-DQ2.5:gluten tetramers representing four immunodominant gluten epitopes. In an unbiased fashion we searched by hierarchical clustering for common CDR3 motifs among 2764 clonotypes. We identified multiple CDR3α, CDR3β, and paired CDR3α:CDR3β motif candidates. Among these, a previously known conserved CDR3β R-motif used by TRAV26-1/TRBV7-2 TCRs specific for the DQ2.5-glia-α2 epitope was the most prominent motif. Furthermore, we identified the epitope specificity of altogether 16 new CDR3α:CDR3β motifs by comparing with TCR sequences of 231 T-cell clones with known specificity and TCR sequences of cells sorted with single HLA-DQ2.5:gluten tetramers. We identified 325 public TCRα and TCRβ sequences of which 145, 102 and 78 belonged to TCRα, TCRβ and paired TCRαβ sequences, respectively. While the number of public sequences was depended on the number of clonotypes in each patient, we found that the proportion of public clonotypes from the gluten-specific TCR repertoire of given CeD patients appeared to be stable (median 37%). Taken together, we here demonstrate that the TCR repertoire of CD4+ T cells specific to immunodominant gluten epitopes in CeD is diverse, yet there is clearly biased V-gene usage, presence of public TCRs and existence of conserved motifs of which R-motif is the most prominent.

TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences

“…In the future, our work could be extended to consider family-wise or false discovery error rates, as has been done for RNA sequencing [ 31 , 35 ]. Such an extension would allow for the quantification of detection power to entire sets of TCRs, which is especially relevant when considering ‘public’ TCR sets that are shared across many individuals [ 6 , 16 , 41 ]. Finally, our read count model could also be used to generate synthetic TCR sequencing repertoires.…”

Immunosenescence and Autoimmunity: Exploiting the T-Cell Receptor Repertoire to Investigate the Impact of Aging on Multiple Sclerosis

“…On the other hand, the current knowledge about immunosenescence and TCR repertoire dynamics in autoimmune and T-cell mediated diseases is still quite fragmented. In RA ( 15 , 36 – 39 ), CD ( 49 – 53 ) and T1D ( 59 – 61 ) patients, different compartments (blood, synovia, gut, pancreatic draining lymph nodes) share TCRβ clones and show reduced TCR repertoire diversity. Furthermore, immunosenescence seems to be accelerated in RA patients ( 15 , 42 – 44 ), and T1D severity is aggravated in older patients ( 58 ); however, most of these studies are not centered on an age-related perspective, stressing for further insights.…”

“…HTS on single-cell gut IELs TCRγδ showed that CD patients, either under GFD or not, have a biased TRDV pattern compared to healthy controls, a private CDR3δ repertoire, whereas CDR3γ clones are shared between CD and controls ( 52 ). A recent investigation leveraging a large TCRαβ dataset of data from 63 CD patients ( 53 ) identified a number of 325 public TCRαβ clones in gluten-specific CD4+ T cells across patient; furthermore, they observed a biased V-gene usage and conserved CDR3α:CDR3β motifs across CD repertoires. Taken together, these findings indicate that TCR repertoire shares common features across CD patients that may be linked to disease pathogenesis and progression; however, the association between TCR repertoire dynamics, T-cell senescence and aging in CD is still not deeply investigated.…”

Phenotype‐Based Isolation of Antigen‐Specific CD4+ T Cells in Autoimmunity: A Study of Celiac Disease

“…Two of these 12 shared sequences were found in the collection of public, gluten-specific TCR sequences. Six of the 12 shared TCR sequences were represented among the generated O, [25] ; 13 AV41_AVEGGSNYKLT_AJ53 O, [25] ; 10 BV7-2_ASSIRATDTQY_BJ2-3 R1 O, [25] ; 9 BV7-3_ASSIRSTDTQY_BJ2-3 NR1 O, [25] ; 14 BV20-1_SASRTSGRAGDEQF_BJ2-1 O, [26] The grey filling represents patients that express the indicated public TCR sequences. Some sequences were expressed by T cell clones (TCCs) that were tested for gluten reactivity.…”