Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells

Immunol Cell Biol. 2016 Jul;94(6):604-11. doi: 10.1038/icb.2016.16. Epub 2016 Feb 10.


Heterogeneity of T cells is a hallmark of a successful adaptive immune response, harnessing the vast diversity of antigen-specific T cells into a coordinated evolution of effector and memory outcomes. The T cell receptor (TCR) repertoire is highly diverse to account for the highly heterogeneous antigenic world. During the response to a virus multiple individual clones of antigen specific CD8+ (Ag-specific) T cells can be identified against a single epitope and multiple epitopes are recognised. Advances in single-cell technologies have provided the potential to study Ag-specific T cell heterogeneity at both surface phenotype and transcriptome levels, thereby allowing investigation of the diversity within the same apparent sub-population. We propose a new method (VDJPuzzle) to reconstruct the native TCRαβ from single cell RNA-seq data of Ag-specific T cells and then to link these with the gene expression profile of individual cells. We applied this method using rare Ag-specific T cells isolated from peripheral blood of a subject who cleared hepatitis C virus infection. We successfully reconstructed productive TCRαβ in 56 of a total of 63 cells (89%), with double α and double β in 18, and 7% respectively, and double TCRαβ in 2 cells. The method was validated via standard single cell PCR sequencing of the TCR. We demonstrate that single-cell transcriptome analysis can successfully distinguish Ag-specific T cell populations sorted directly from resting memory cells in peripheral blood and sorted after ex vivo stimulation. This approach allows a detailed analysis of the TCR diversity and its relationship with the transcriptional profile of different clones.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Epitopes / genetics*
  • Epitopes, T-Lymphocyte / immunology
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Humans
  • Receptors, Antigen, T-Cell / metabolism*
  • Receptors, Antigen, T-Cell, alpha-beta / genetics
  • Sequence Analysis, RNA
  • Single-Cell Analysis / methods*
  • T-Lymphocytes / metabolism*
  • Transcriptome / genetics*
  • V(D)J Recombination / genetics


  • Epitopes
  • Epitopes, T-Lymphocyte
  • Receptors, Antigen, T-Cell
  • Receptors, Antigen, T-Cell, alpha-beta