The Thymic Microenvironment Shapes Age‐Related Qualitative Changes in the TCR Repertoire

ABSTRACT Ageing impairs immune function, increasing susceptibility to infection, autoimmunity and inflammation. The thymus undergoes involution during childhood, and thymocyte and thymic epithelial cell (TEC) numbers decline. Given that adaptive immunity depends on T‐cells recognising diverse antigens via their unique T‐cell receptor (TCR), the precise age‐related changes in TCR repertoire composition are key to understand immunity. To investigate the influence of age on the thymic TCR repertoire we sequenced TCRα and TCRβ transcripts from developmentally defined thymocyte populations from 4‐week, 12‐month and 18‐month‐old mice, and from thymocytes recovering from hydrocortisone‐treatment, and athymic recipients of RAG1‐deficient thymus transplants. The 18‐month thymus selected TCR repertoires with distinctive patterns of VxJ and CDR3 k‐mer usage compared to young thymus, indicating it had a qualitatively different repertoire with different specificity. It also selected a less diverse TCRβ repertoire with more expanded clones than young thymus. On recovery from hydrocortisone‐treatment, both 4‐week and 12‐month thymus showed bias towards foetal‐like 3′TRAVx5′TRAJ rearrangements, but 12‐month thymus also produced less diverse and evenly distributed TCRβ repertoires, with increased expansion of TCRβ clones at the CD4 − CD8 − CD25 + CD44 − intracellularTCRβ + stage, increased TRBJ‐1‐cluster usage and distinctive patterns of combinatorial VxJ usage. Transplantation of athymic nude recipients with old RAG1‐deficient thymus generated less diverse, less evenly distributed TCR repertoires with different combinatorial VxJ usage than those generated by young transplants. Taken together our experiments show that the old thymus generates qualitatively different TCR repertoires than young thymus and the non‐lymphoid compartment of the thymus contributes strongly to these changes and to age‐associated decline in TCR repertoire diversity.