The Peanut-Specific TCR Repertoire: A Statistical Approach to Define Homology Among CDR3β Sequences in Peanut-Allergic Individuals

Abstract

The induction and persistence of peanut allergies is fundamentally dependent on T cells’ ability to recognize allergenic antigens. Peanut-specificity of a T cell is conferred by its TCR and more specifically, the CDR3 of the β-chain. In this study, we elucidated 7345 putatively peanut-specific CDR3βs from 27 peanut-allergic individuals by applying a novel statistical approach to an existing TCRβseq data set that consisted of in vitro peanut-activated and memory resting T cell sequences. These putatively-specific sequences displayed enhanced homology and reduced diversity as compared to randomly sampled CDR3βs, which is consistent with independently published antigen-specific populations. Motif analysis revealed 149 unique motifs that were both highly enriched and public within the psCDR3s. Given peanut is a polyantigenic stimulant, we illustrated the local homology of the psCDR3s with a network analysis that clustered sequences based on the presence of either an enriched motif, a low Levenshtein distance (distance = 1), or evidence of convergent recombination as defined by multiple nucleotide rearrangements that corresponded to the same amino acid sequence. This network was broken into 990 distinct neighborhoods that were individually probed for their tendency to represent Teff or Treg sequences. Using bulk Teff and Treg data from 9 of the 27 individuals in this study, we discovered 253 Teff- and 74 Treg-exclusive neighborhoods, suggesting differences in antigen-recognition across the phenotypic compartments. The analysis approach described here can be a template for future studies aimed at understanding TCR repertoires where epitope and/or HLA genotype information is unknown and has the potential to define antigen-specific repertoire features that could be used as biomarkers of disease.