Deep sequencing of the TCR-β repertoire of human forkhead box protein 3 (FoxP3) and FoxP3 T cells suggests that they are completely distinct and non-overlapping.

Maintenance of peripheral tolerance requires a balance between autoreactive conventional T cells (T ) and thymically derived forkhead box protein 3 (FoxP3) regulatory T cells (tT ). Considerable controversy exists regarding the similarities/differences in T cell receptor (TCR) repertoires expressed by T and tT . We generated highly purified populations of human adult and cord blood T and tT based on the differential expression of CD25 and CD127. The purity of the sorted populations was validated by intracellular staining for FoxP3 and Helios. We also purified an overlap group of CD4 T cells from adult donors to ensure that considerable numbers of shared clonotypes could be detected when present. We used deep sequencing of entire TCR-β CDR3 sequences to analyse the TCR repertoire of T and tT . Our studies suggest that both neonatal and adult human T and tT cells are, in fact, entirely distinct CD4 T cell lineages.