Healthy human T-cell receptor β-chain repertoire: Quantitative analysis and evidence for Jβ-related effects on CDR3 structure and diversity

Abstract

Analysis of TCR repertoire usage and clonality is of potential value in understanding the pathogenesis of a number of human immune-mediated diseases. In diseases that are likely to be dependent on antigen-driven T cells, it has been suggested that particular TCR junctional region or CDR3 sequences may be critical. Rigorous methods for TCR analysis which are both quantitative and qualitative are therefore required. Of those commonly available, only anchor and inverse PCR are capable of giving high-quality information on V, D, N, and J region usage, but it has not been established whether both methods are quantitatively or analytically equivalent. We show here that both methods detected considerable variability in the usage of Vβ and Jβ segments in the peripheral blood repertoire of a normal individual. No preferential V-J pairing could be demonstrated. An ex cess usage of Jβ2 family members was indicated by both methods, although the relative usage of different Jβ2 families differed between the two techniques. The predominantly used Vβ usage showed that for some families, estimates of their frequency in the repertoire differed significantly between the anchor and inverse libraries. When sampling relatively few clones the variation between Vβ families estimated using the two methods can be considerable. This is likely to be a result of sampling error from a large gene family. Large-scale screening of several thousand clones is recommended to confirm the absolute values obtained from sequencing. Variation in CDR3 length appeared to be normally distributed, suggesting that a statistically optimal junctional region length may have been selected for contact with antigen. CDR3 length distribution differs significantly between receptors, which have rearranged to Jβ1 versus Jβ2 families, with the Jβ2-associated CDR3 on average between 0.5 and 1.2 of an amino acid longer. Thus the TCR β junctional region repertoire of humans is subject to structural constraints associated with Jβ usage. It will be important to establish whether variation in CDR3 length and Jβ usage exists between subsets of human T cells in order to interpret TCR repertoire data from disease and control tissues.