TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

  • Biology
  • Cell Atlas
  • Genomics
  • Immunology
  • R&D
  • Technology
  • Alex K. Shalek
  • Tu et al.▾
    Tu, A.A., Gierahn, T.M., Monian, B., Morgan, D.M., Mehta, N.K., Ruiter, B., Shreffler, W.G., Shalek A.K., Love, J.C.
  • Nature Immunology , Volume 20
  • November, 2019
Biology
Cell Atlas
Genomics
Immunology
R&D
Technology
Alex K. Shalek

Abstract

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. The protocol can be found here.

TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures