Distinct TCR repertoire diversity, clonality and MHC-restriction in foetal and adult thymus

Abstract

Here we sequenced rearranged TCR{beta} and TCR chain sequences in CD4+CD8+ double positive (DP), CD4+CD8-single positive (SP4) and CD4-CD8+ (SP8) thymocyte populations from the foetus and young adult mouse. We found that life-stage had a greater impact on TCR{beta} and TCR gene segment usage than cell-type. Foetal repertoires showed bias towards 3TRAV and 5TRAJ rearrangements in all populations, whereas adult repertoires used more 5TRAV gene segments, suggesting that progressive TCR rearrangements occur less frequently in foetal DP cells. When we synchronised young adult DP thymocyte differentiation by hydrocortisone treatment the new recovering DP thymocyte population showed more foetal-like 3TRAV and 5TRAJ gene segment usage. In foetus we identified less influence of MHC-restriction on -chain and {beta}-chain combinatorial VxJ usage and CDR1xCDR2 (V region) usage in SP compared to adult, indicating weaker impact of MHC-restriction on the foetal TCR repertoire. The foetal TCR{beta} repertoire was less diverse, less evenly distributed, with fewer non-template insertions, and all foetal populations contained more clonotypic expansions than adult. The differences between the foetal and adult thymus TCR repertoires are consistent with the foetal thymus producing {beta}T-cells with properties and functions that are distinct from adult T-cells: their repertoire is less governed by MHC-restriction, with preference for particular gene segment usage, less diverse with more clonotypic expansions, and more closely encoded by genomic sequence.