Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection

To prevent autoimmunity, thymocytes expressing self-reactive T cell receptors (TCRs) are negatively selected, however, divergence into tolerogenic, agonist selected lineages represent an alternative fate. As thymocyte development, selection, and lineage choices are dependent on spatial context and cell-to-cell interactions, we have performed Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) and spatial transcriptomics on paediatric human thymu s. Thymocytes expressing markers of strong TCR signalling diverged from the conventional developmental trajectory prior to CD4(+) or CD8(+) lineage commitment, while markers of different agonist selected T cell populations (CD8 alpha alpha(I), CD8 alpha alpha(II), T-(agonist), T-reg(diff), and T-reg) exhibited variable timing of induction. Expression profiles of chemokines and co-stimulatory molecules, together with spatial localisation, supported that dendritic cells, B cells, and stromal cells contribute to agonist selection, with different subsets influencing thymocytes at specific developmental stages within distinct spatial niches. Understanding factors influencing agonist T cells is needed to benefit from their immunoregulatory effects in clinical use.

Automated summary

To prevent autoimmune reactions, thymocytes expressing self-reactive T cell receptors (TCRs) are eliminated, but they may diverge into tolerogenic, agonist selected lineages. In this study, Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) and spatial transcriptomics were performed on pediatric human thymus to investigate thymocyte development and agonist selection. It was found that thymocytes expressing markers of strong TCR signaling followed a different developmental trajectory, while different agonist selected T cell populations exhibited variable timing of induction. Dendritic cells, B cells, and stromal cells were identified as contributors to agonist selection, influencing thymocytes at specific developmental stages within distinct spatial niches.