Researchers devise a new method to study T cell heterogeneity from single cell RNA-seq data

Heterogeneity of T cells is a hallmark of a successful adaptive immune response, harnessing the vast diversity of antigen-specific T cells into a coordinated evolution of effector and memory outcomes. The T cell receptor (TCR) repertoire is highly diverse to account for the highly heterogeneous antigenic world. During the response to a virus multiple individual clones of antigen specific CD8+ (Ag-specific) T cells can be identified against a single epitope and multiple epitopes are recognised. Advances in single-cell technologies have provided the potential to study Ag-specific T cell heterogeneity at both surface phenotype and transcriptome levels, thereby allowing investigation of the diversity within the same apparent sub-population.

Researchers at the UNSW, Australia have developed  a new method (VDJPuzzle) to reconstruct the native TCRαβ from single cell RNA-seq data of Ag-specific T cells and then to link these with the gene expression profile of individual cells. The researchers applied this method using rare Ag-specific T cells isolated from peripheral blood of a subject who cleared hepatitis C virus infection. They successfully reconstructed productive TCRαβ in 56 of a total of 63 cells (89%), with double α and double β in 18%, and 7% respectively, and double TCRαβ in 2 cells. The method was validated via standard single cell PCR sequencing of the TCR.

VDJPuzzle workflow and results.

rna-seq

A. Schematic of the VDJPuzzle workflow. B. PCA showing the four cells bearing the most common TCRαβ (triangle).

These data demonstrate that single-cell transcriptome analysis can successfully distinguish Ag-specific T cell populations sorted directly from resting memory cells in peripheral blood and sorted after ex vivo stimulation. This approach allows a detailed analysis of the TCR diversity and its relationship with the transcriptional profile of different clones.

Availability – VDJPuzzle is freely available at: https://github.com/Simo-88/VDJPuzzle

Eltahla AA, Rizzetto S, Rasoli M, Betz-Stablein BD, Venturi V, Kedzierska K, Lloyd AR, Bull RA, Luciani F. (2016) Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells. Immunol Cell Biol [Epub ahead of print]. [abstract]

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