title: Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells.
abstract: 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. We propose 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. We applied this method using rare Ag-specific T cells isolated from peripheral blood of a subject who cleared hepatitis C virus infection. We 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. We 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.
authors: Systems Medicine in Infectious Diseases, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia.
authors: Auda A
authors: AA
authors: Eltahla
authors: Systems Medicine in Infectious Diseases, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia.
authors: Simone
authors: S
authors: Rizzetto
authors: Systems Medicine in Infectious Diseases, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia.
authors: Mehdi R
authors: MR
authors: Pirozyan
authors: Systems Medicine in Infectious Diseases, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia.
authors: Brigid D
authors: BD
authors: Betz-Stablein
authors: Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia.
authors: Vanessa
authors: V
authors: Venturi
authors: Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
authors: Katherine
authors: K
authors: Kedzierska
authors: Systems Medicine in Infectious Diseases, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia.
authors: Andrew R
authors: AR
authors: Lloyd
authors: Systems Medicine in Infectious Diseases, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia.
authors: Rowena A
authors: RA
authors: Bull
authors: Systems Medicine in Infectious Diseases, Inflammation and Infection Research Centre, School of Medical Sciences, University of New South Wales, Sydney, Australia.
authors: Fabio
authors: F
authors: Luciani
mesh_terms: D000939:Epitopes / Q000235:genetics*; D018984:Epitopes, T-Lymphocyte / Q000276:immunology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D011948:Receptors, Antigen, T-Cell / Q000378:metabolism*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics; D017423:Sequence Analysis, RNA; D059010:Single-Cell Analysis / Q000379:methods*; D013601:T-Lymphocytes / Q000378:metabolism*; D059467:Transcriptome / Q000235:genetics*; D060152:V(D)J Recombination / Q000235:genetics
chemical_list: D000939:Epitopes; D018984:Epitopes, T-Lymphocyte; D011948:Receptors, Antigen, T-Cell; D016693:Receptors, Antigen, T-Cell, alpha-beta