TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures

Nat Immunol. 2019 Dec;20(12):1692-1699. doi: 10.1038/s41590-019-0544-5. Epub 2019 Nov 19.


High-throughput 3' single-cell RNA-sequencing (scRNA-seq) allows cost-effective, detailed characterization of individual immune cells from tissues. Current techniques, however, are limited in their ability to elucidate essential immune cell features, including variable sequences of T cell antigen receptors (TCRs) that confer antigen specificity. Here, we present a strategy that enables simultaneous analysis of TCR sequences and corresponding full transcriptomes from 3'-barcoded scRNA-seq samples. This approach is compatible with common 3' scRNA-seq methods, and adaptable to processed samples post hoc. We applied the technique to identify transcriptional signatures associated with T cells sharing common TCRs from immunized mice and from patients with food allergy. We observed preferential phenotypes among subsets of expanded clonotypes, including type 2 helper CD4+ T cell (TH2) states associated with food allergy. These results demonstrate the utility of our method when studying diseases in which clonotype-driven responses are critical to understanding the underlying biology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 2S Albumins, Plant / immunology
  • Animals
  • Antigens, Plant / immunology
  • CD8-Positive T-Lymphocytes / immunology*
  • Cells, Cultured
  • Complementarity Determining Regions / genetics
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Immunization
  • Immunoglobulin E / metabolism
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Papillomavirus E7 Proteins / immunology
  • Peanut Hypersensitivity / immunology*
  • Receptors, Antigen, T-Cell, alpha-beta / genetics*
  • Single-Cell Analysis
  • T-Cell Antigen Receptor Specificity / genetics
  • Th2 Cells / immunology*
  • Transcriptome


  • 2S Albumins, Plant
  • Antigens, Plant
  • Ara h 2 allergen, Arachis hypogaea
  • Complementarity Determining Regions
  • Papillomavirus E7 Proteins
  • Receptors, Antigen, T-Cell, alpha-beta
  • oncogene protein E7, Human papillomavirus type 16
  • Immunoglobulin E