Single-Cell Analysis Of T-Cell Receptor Alpha Beta Repertoire

The unbiased, paired analysis of T-cell receptor (TCR) alpha- and beta-chain usage at the single-cell level provides a valuable window of understanding into the TCR repertoire and the nature of the immune response. Earlier technologies for TCR repertoire analysis were often limited to examining TCR complementarity-determining region 3 (CDR3) beta expression or required in vitro cloning procedures that can artificially skew the TCR repertoire from its in vivo state. We describe here a direct ex vivo, single-cell-based strategy for the clonotypic analysis of TCR alpha beta repertoires that utilizes multiplexed panels of TCR alpha and TCR beta-specific primers in a nested PCR to amplify expressed transcripts from individual, epitope-specific T cells. This strategy yields the paired TCR alpha beta sequences of any given population of alpha beta T cells of interest.