Alpha/Beta Mouse TCR Sequencing of CD4+ thymic regulatory and conventional T-cells

Thymic regulatory T cells (tTreg) are critical in maintenance of normal T cell immunity and tolerance. The role of TCR in tTreg cell selection remains incompletely understood. Here we assessed TCRa and TCRb sequences of tTreg and conventional thymic CD4+ T (Tconv) cells by high throughput sequencing. We identified ab TCR sequences that were unique to either tTreg or Tconv cells and found that these were distinct as recognized by machine learning (ML) algorithm and by preferentially used amino acid trimers in ab CDR3 of tTreg cells. In addition, a proportion of ab TCR sequences expressed by tTreg were also found in Tconv cells, and ML classified the great majority of these shared ab TCR sequences as characteristic of Tconv and not tTreg cells. These findings identify two populations of tTreg, one in which Treg fate is associated with unique properties of the TCR, and another with TCR properties characteristic of Tconv cells for which tTreg fate is determined by factors beyond TCR sequence. 3 individual Rag2GFP-Foxp3-RFP mice with Alpha-Beta TCR sequencing data. 3 individual TCRdCreER ZsGreen Foxp3 RAF samples with Alpha-Beta TCR sequencing data (each samples were pooled from 3 mice). 3 individual TCRα +/- TCRβ Tg mice with Alpha TCR Sequencing data. The raw data for this study has been deposited into NCI SRA (BioProject ID: PRJNA541952; SRA Accession: SRP197126).