Figure 1. Study design.

(a) We first examined the structure of the T cell receptor (TCR) sequence to define 1080 sequence features. Depicted is a T cell receptor (TCR) β chain in complex with antigenic peptide (red) and human MHC II molecules (brown). The TCR is colored by region: V-region (including CDR1β and CDR2β loops) in green, CDR3β middle region (CDR3βmr) in orange, and J-region in pink. We used mutual information analysis and mixed effects model comparisons to select 606 nonredundant TCR features that best explained variance in T cell state. We fit mixed effects logistic regression models for 70% of the data in the discovery and replication cohorts separately, and combined the effect sizes for each TCR feature across the two cohorts by meta-analysis. TiRP was calibrated to include only 208 of the 606 TCR features that had Bonferroni-significant meta-analytic P values. (b) We then applied TiRP to the TCRs to tumor-infiltrating CD4⁺ cells in order to study mixed clones: groups of T_regs and T_convs with the same TRB and TRA sequences observed in the same individual. These mixed clones likely represent lineages of T cells that have undergone a peripheral conversion between the regulatory and conventional phenotypes. Such clones may include induced or iT_regs (T_conv cells that have acquired a regulatory phenotype), exT_regs (T_reg cells that have lost the regulatory phenotype), or both. (c) Finally, we investigated the drivers of TiRP by separately examining the two elements of the human T_reg TCR ligand: the self-peptide and the human MHC II molecule.

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