T cell receptor diversity in the human thymus

Abstract

A diverse T cell receptor (TCR) repertoire is essential for adaptive immune responses and is generated by somatic recombination of TCRα and TCRβ gene segments in the thymus. Previous estimates of the total TCR diversity have studied the circulating mature repertoire, identifying 1 to 3×10(6) unique TCRβ and 0.5×10(6) TCRα sequences. Here we provide the first estimate of the total TCR diversity generated in the human thymus, an organ which in principle can be sampled in its entirety. High-throughput sequencing of samples from four pediatric donors detected up to 10.3×10(6) unique TCRβ sequences and 3.7×10(6) TCRα sequences, the highest directly observed diversity so far for either chain. To obtain an estimate of the total diversity we then used three different estimators, preseq and DivE, which measure the saturation of rarefaction curves, and Chao2, which measures the size of the overlap between samples. Our results provide an estimate of a thymic repertoire consisting of 40 to 70×10(6) unique TCRβ sequences and 60 to 100×10(6) TCRα sequences. The thymic repertoire is thus extremely diverse. Moreover, extrapolation of the data and comparison with earlier estimates of peripheral diversity also suggest that the thymic repertoire is transient, with different clones produced at different times.

Cross-reactive public TCR sequences undergo positive selection in the human thymic repertoire

“…The first such study estimated that normal human blood contains 3 × 10 6 to 4 × 10 6 unique TCR β chains (2), while a later study provided a minimal estimate of 100 × 10 6 unique TCRβ sequences in naive CD4 + and CD8 + T cell repertoires of young adults (3). Another study estimated that there are 40 × 10 6 to 70 × 10 6 unique TCRβ sequences and 60 × 10 6 to 100 × 10 6 TCRα sequences in human pediatric thymi (4). However, a surpris-ing degree of repertoire overlap has been observed between individuals in studies of peripheral T cells (5).…”

Identifying the inheritable component of human thymic T cell repertoire generation in monozygous twins

“…In contrast, for α repertoire the sharing in the repeat samples from Twin B was similar to the sharing between Twin A and Twin B. This may be due to the higher diversity of TCR‐α than TCR‐β repertoire in the thymus . Interindividual comparison of the TCR‐α repertoire showed a small but consistently higher sharing for twin samples compared with unrelated samples in both nonproductive and inframe nucleotide sequences and amino acid chains (Fig.…”

Comprehensive profiling of TCRβ repertoire in a non-model species (the bank vole) using high-throughput sequencing

“…They allow to estimate, from given samples, how many unobserved species (or in this case–clonotypes) are present in an individual. Following other authors 5,45 we used a non-parametric, incidence-based estimator Chao2 46 to estimate the lower boundary of TCRβ repertoire size. The mean of the lower-bound estimate was 2.1 ×10 5 (range 1.7–2.3 ×10 5 ) different nucleotide CDR3 sequences (Supplementary Table S3), which indicates that in four samples we directly observed up to 86% splenic TCRβ CDR3 sequences.…”

“…To estimate the lower bound of individual TCRβ diversity (repertoire size) we chose a non-parametric, incidence-based Chao2 estimator 46 . Chao2 does not require assumption of a priori clonotype distributions, and it had been previously applied to TCR repertoire estimation 5,45 . In contrast to abundance-based estimators, which use absolute counts of T cells bearing the given CDR3 (clonotype), Chao2 uses presence–absence data across replicates.…”