Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells

Abstract

The adaptive immune system uses several strategies to generate a repertoire of T-and B-cell antigen receptors with sufficient diversity to recognize the universe of potential pathogens. In ␣␤ T cells, which primarily recognize peptide antigens presented by major histocompatibility complex molecules, most of this receptor diversity is contained within the third complementarity-determining region (CDR3) of the T-cell receptor (TCR) ␣ and ␤ chains. Although it has been estimated that the adaptive immune system can generate up to 10 16 distinct ␣␤ pairs, direct assessment of TCR CDR3 diversity has not proved amenable to standard capillary electrophoresis-based DNA sequencing. We developed a novel experimental and computational approach to measure TCR CDR3 diversity based on single-molecule DNA sequencing, and used this approach to determine the CDR3 sequence in millions of rearranged TCR␤ genes from T cells of 2 adults. We find that total TCR␤ receptor diversity is at least 4-fold higher than previous estimates, and the diversity in the subset of CD45RO ؉ antigen-experienced ␣␤ T cells is at least 10-fold higher than previous estimates. These methods should prove valuable for assessment of ␣␤ T-cell repertoire diversity after hematopoietic cell transplantation, in states of congenital or acquired immunodeficiency, and during normal aging. (Blood. 2009;114:4099-4107)

Predicting the spectrum of TCR repertoire sharing with a data‐driven model of recombination

“…In this hypothesis, shared TCRs are simply those that have a higher‐than‐average generation probability and are thus more abundant in the unselected repertoire 13. The advent of high‐throughput sequencing of TCR repertoires14, 15, 16, 17 has largely confirmed this view through the analysis of shared TCR sequences between unrelated humans,18, 19, 20 monozygous human twins,21, 22 and mice 23. However, despite recent efforts to characterize the landscape of public TCRs,24 the contributions of V(D)J generation biases and convergent recombination relative to convergent selection remain to be elucidated and quantified.…”

The Hayflick Limit May Determine the Effective Clonal Diversity of Naive T Cells

“…We propose that over time this dynamic will cause a chain reaction of cell loss, which will suddenly drive most T cell clones to extinction. In the following, we will demonstrate, using stochastic numerical simulations based on experimental data (18,21,22,28,29,31,38,(42)(43)(44)(45)(46)(47)(48), that this model provides a plausible explanation for the sharp decline of effective clonal diversity observed in elderly humans.…”

Half of the T‐cell repertoire combinatorial diversity is genetically determined in humans and humanized mice

“…In theory, these sequential processes occurring during T-cell differentiation in the thymus could These are not the final page numbers Correspondence: Dr. Gilles Marodon e-mail: gilles.marodon@upmc.fr generate up to 10 15 different TCRs, a number far in excess of the number of T-cells in the body. The 'real' size of the repertoire is probably much lower though, with recent estimations of unique TCR b chains ranging from 10 6 to 4.10 6 in humans [1,2].…”

“…In this line, an interesting study recently proposed a numerical model of mouse TCR Va/Ja gene accessibility that pointed out unbalanced V-J associations resulting from preferential access to gene rearrangements [6]. Despite studies using high-throughput sequencing of TCR b chains [2,[7][8][9], a global view on the distribution of V-J rearrangement combinations of the TCR b chain in humans was lacking. Here, we have reanalyzed T-cell repertoire data that we generated in humanized NOD.SCID.gc À/À (NSG) mice [5] with the aim to determine the extent of the overlap between the T-cell repertoire of humans and humanized mice at the level of V-J rearrangements.…”

“…42: 760-770 760 generate up to 10 15 different TCRs, a number far in excess of the number of T-cells in the body. The 'real' size of the repertoire is probably much lower though, with recent estimations of unique TCR b chains ranging from 10 6 to 4.10 6 in humans [1,2]. Mice reconstituted with a human immune system generated from hematopoietic precursors represent a new animal model for human immunology studies.…”