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

Biology Biology
Cell Atlas Cell Atlas
Genomics Genomics
Immunology Immunology
Technology Technology
Alex K. Shalek 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


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.