T Cell Receptor Gene Rearrangement Lineage Analysis Reveals Clues for the Origin of Highly Restricted Antigen-specific Repertoires

Due to ordered, stage-specific T cell receptor (TCR)-β and -α locus gene rearrangements and cell division during T cell development, a given, ancestral TCR-β locus VDJ rearrangement might be selected into the mature T cell repertoire as a small cohort of “half-sibling” progeny expressing identical TCR-β chains paired with different TCR-α chains. The low frequency of such a cohort relative to the total αβ TCR repertoire precludes their direct identification and characterization in normal mice. We considered it possible that positive selection constraints might limit the diversity of TCR-α chains selected to pair with β chains encoded by an ancestral VDJ-β rearrangement. If so, half-sibling T cells expressing structurally similar, but different TCR-α chains might recognize the same foreign antigen. By single cell polymerase chain reaction analysis of antigen-specific TCRs selected during a model anti-tumor response, we were able to identify clusters of T cells sharing identical VDJ-β rearrangements but expressing different TCR-α chains. The amplification of residual DJ-β rearrangements as clonal markers allowed us to track T cells expressing different TCR-α chains back to a common ancestral VDJ-β rearrangement. Thus, the diversity of TCR-α's selected as partners for a given VDJ-β rearrangement into the mature TCR repertoire may indeed be very limited.