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

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

Tu AA1,2, Gierahn TM1, Monian B1,3, Morgan DM1,3, Mehta NK1,2, Ruiter B4,5, Shreffler WG4,5,6, Shalek AK7,8,9,10, Love JC11,12,13,14.

Author information

1
Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
2
Department of Biological Engineering, MIT, Cambridge, MA, USA.
3
Department of Chemical Engineering, MIT, Cambridge, MA, USA.
4
Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
5
Harvard Medical School, Boston, MA, USA.
6
Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA.
7
Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. shalek@mit.edu.
8
Institute for Medical Engineering & Science and Department of Chemistry, MIT, Cambridge, MA, USA. shalek@mit.edu.
9
Broad Institute of MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu.
10
Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu.
11
Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. clove@mit.edu.
12
Department of Chemical Engineering, MIT, Cambridge, MA, USA. clove@mit.edu.
13
Broad Institute of MIT and Harvard, Cambridge, MA, USA. clove@mit.edu.
14
Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. clove@mit.edu.

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.

PMID:
31745340
DOI:
10.1038/s41590-019-0544-5

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