Analysis of the TCR α-chain rearrangement profile in human T lymphocytes

Abstract

The size of the available human αβ T cell repertoire is difficult to determine and is open to debate. Empirical analysis of TCR β-chain diversity reveals ∼10 6 different β chains in peripheral blood. Due in part to locus complexity, comparable information for TCRα is lacking. Rather, current estimates for human TCRα diversity, and hence, total repertoire diversity, are based on theoretical analyses that assume equal probabilities of rearrangement between any Vα gene and Jα gene. Here, we report on a systematic locus-wide rearrangement analysis of the TCR α-chain in human T cells. We first demonstrate that the V-Jα recombination in the thymus is not random but depends on the reciprocal Vα and Jα position within the locus. Characterization of the frequency of gene usage combined with identification of five previously unrecognized pseudogenes enables us to empirically estimate the human TCRα combinatorial repertoire. The number of V-Jα combinations achieved is ∼44–56% of the total combinatorial possibilities, significantly lower than theoretical estimates. We also demonstrate that TCR α-chain diversity in peripheral T lymphocytes mimics the same general patterns of rearrangement as observed in the thymus, and these patterns appear conserved among different individuals. This unexpected observation indicates that, unlike the TCRβ locus, the human TCR α-chain repertoire is primarily predetermined by genetic recombination and its size is restricted by limits on the combinatorial repertoire rather than post-thymic selection.