High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets

Abstract

Developing T cells face a series of cell fate choices in the thymus and in the periphery. The role of the individual T cell receptor (TCR) in determining decisions of cell fate remains unresolved. The stochastic/selection model postulates that the initial fate of the cell is independent of TCR specificity, with survival dependent on additional TCR/coreceptor "rescue" signals. The "instructive" model holds that cell fate is initiated by the interaction of the TCR with a cognate peptide-MHC complex. T cells are then segregated on the basis of TCR specificity with the aid of critical coreceptors and signal modulators [Chan S, Correia-Neves M, Benoist C, Mathis (1998) Immunol Rev 165: 195-207]. The former would predict a random representation of individual TCR across divergent T cell lineages whereas the latter would predict minimal overlap between divergent T cell subsets. To address this issue, we have used high-throughput sequencing to evaluate the TCR distribution among key T cell developmental and effector subsets from a single donor. We found numerous examples of individual subsets sharing identical TCR sequence, supporting a model of a stochastic process of cell fate determination coupled with dynamic patterns of clonal expansion of T cells bearing the same TCR sequence among both CD4(+) and CD8+ populations.

Fig. 1.

Abundance of CDR3 sequences versus cumulative frequency for TCRα (Left) and TCRβ (Right). Red: Tr; pink: Th1; green: Th2; cyan: Tc; gray: Tn+t; black: Ta; blue: Tm; and orange: pan T. As the total number of CDR3 sequences for different subsets of T cells are different, uniform sampling procedure was applied to each subset of T cells to bring the same number of TCRα or TCRβ CDR3, respectively.

Fig. 2.

(A–M) The 100 most abundant TCRβ CDR3 sequences of a particular subset (labeled at the top left corner of each box) common to those in subsets of T cells of either different developing stages (gray: Tn+t; dark grey: Ta; and black: Tm) or different fates (red: Tr; green: Th1; blue: Th2; and brown: Tc). The numbers of CDR3 sequences that are unique to each subset are shown in the nonoverlapping sections. The number of CDR3 sequences that are common to any two, three, and four of these subsets are indicated in the relevant overlapping areas. The number of CDR3 sequences that are not found in those examined subsets is labeled at the bottom left corner of each box.