To couple TCR CDR3 identification with gene expression phenotyping in individual cells, Tu and Gierahn et al. developed a PCR strategy to amplify 3’-barcoded individual whole cell transcriptomes, followed by TCR gene enrichment and amplification prior to targeted Illumina sequencing of the 3’-barcode and the CDR3. In ~20% of the cells, both CDR3s could be identified and matched to the barcoded mRNA phenotype. Application to a mouse model antigen immunization revealed clonotypic effects on CD8+ T cell phenotype; application to human CD4+ T cells from patients with peanut allergy revealed expanded clonotypes with a TH2 phenotype.
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.
Author Info: (1) Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. Department of Biological Engineering, MIT, Cambridge, MA, USA. (2) Koch Institute for Integrative Cance
Author Info: (1) Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. Department of Biological Engineering, MIT, Cambridge, MA, USA. (2) Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. (3) Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. Department of Chemical Engineering, MIT, Cambridge, MA, USA. (4) Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. Department of Chemical Engineering, MIT, Cambridge, MA, USA. (5) Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. Department of Biological Engineering, MIT, Cambridge, MA, USA. (6) Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA. Harvard Medical School, Boston, MA, USA. (7) Center for Immunology & Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA. Harvard Medical School, Boston, MA, USA. Food Allergy Center, Massachusetts General Hospital, Boston, MA, USA. (8) Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. shalek@mit.edu. Institute for Medical Engineering & Science and Department of Chemistry, MIT, Cambridge, MA, USA. shalek@mit.edu. Broad Institute of MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu. Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. shalek@mit.edu. (9) Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA. clove@mit.edu. Department of Chemical Engineering, MIT, Cambridge, MA, USA. clove@mit.edu. Broad Institute of MIT and Harvard, Cambridge, MA, USA. clove@mit.edu. Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. clove@mit.edu.
