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

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. Single-cell RNA-Sequencing of murine samples via Seq-Well. Mouse 1-4 was sorted against HPV-E7 peptide (RAHYNIVTF) MHC-tetramer. OT1 (spiked into wild-type BL6 murine T cells) samples were enriched for T cells using magnetic beads enrichment, without MHC-tetramer sorting. See DOI: 10.1038/s41590-019-0544-5.