Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCRβ rearranges after αβ and γδ T cell commitment

Abstract

T lymphocytes respond to a broad array of pathogens with the combinatorial diversity of the T cell receptor (TCR). This adaptive response is possible because of the unique structure of the TCR, which is composed of two chains, either αβ or γδ, that undergo genetic rearrangement in the thymus. αβ and γδ T cells are functionally distinct within the host but are derived from a common multipotent precursor. The canonical model for T cell lineage commitment assumes that the γ, δ, and β chains rearrange before αβ or γδ T cell commitment. To test the standard model in humans, we used high-throughput sequencing to catalog millions of TCRγ and TCRβ chains from peripheral blood αβ and γδ T cells from three unrelated individuals. Almost all sampled αβ and γδ T cells had rearranged TCRγ sequences. Although sampled αβ T cells had a diverse repertoire of rearranged TCRβ chains, less than 4% of γδ T cells in peripheral blood had a rearranged TCRβ chain. Our data suggest that TCRγ rearranges in all T lymphocytes, consistent with TCRγ rearranging before T cell lineage commitment. However, rearrangement of the TCRβ locus appears to be restricted after T cell precursors commit to the αβ T cell lineage. Indeed, in T cell leukemias and lymphomas, TCRγ is almost always rearranged and TCRβ is only rearranged in a subset of cancers. Because high-throughput sequencing of TCRs is translated into the clinic for monitoring minimal residual for leukemia/lymphoma, our data suggest the sequencing target should be TCRγ.

Fig. 1. Frequency of the 25 most common TCR sequences

For each sample we plot the proportion of productive sequences accounted for by the 25 most numerous productive TCR sequences.(1A) TCRγ chains amplified from γδ T cells and αβ T cells and (1B) TCRβ chains amplified from αβ T cells.

Fig. 2. Shared nucleotide identical TCRγ CDR3 sequences

Nine nucleotide identical TCRγ CDR3 sequences amplified from γδ T cells are shared by all three individuals. For each shared sequence, the copy count detected for each individual is indicated on the Y-axis.

Fig. 3. Average V-J gene utilization of sequenced TCRγ and TCRβ sequences across three samples

Average V-J utilization of gene segments in TCRγ CDR3 sequences amplified from γδ T cells (3A), TCRγ CDR3 sequences amplified from αβ T cells (3B), and TCRβ sequences amplified from αβ T cells (3C).

Fig. 4. Average copy number, by V-J pairing, of unique out-of-frame TCRγ sequences

Average copy number, by VJ gene segment usage, of unique out-of- frame TCRγ sequences amplified from αβ T cells.