High-throughput and high-dimensional single-cell analysis of antigen-specific CD8+ T cells

Nat Immunol. 2021 Dec;22(12):1590-1598. doi: 10.1038/s41590-021-01073-2. Epub 2021 Nov 22.

Abstract

Although critical to T cell function, antigen specificity is often omitted in high-throughput multiomics-based T cell profiling due to technical challenges. We describe a high-dimensional, tetramer-associated T cell antigen receptor (TCR) sequencing (TetTCR-SeqHD) method to simultaneously profile cognate antigen specificities, TCR sequences, targeted gene expression and surface-protein expression from tens of thousands of single cells. Using human polyclonal CD8+ T cells with known antigen specificity and TCR sequences, we demonstrate over 98% precision for detecting the correct antigen specificity. We also evaluate gene expression and phenotypic differences among antigen-specific CD8+ T cells and characterize phenotype signatures of influenza- and Epstein-Barr virus-specific CD8+ T cells that are unique to their pathogen targets. Moreover, with the high-throughput capacity of profiling hundreds of antigens simultaneously, we apply TetTCR-SeqHD to identify antigens that preferentially enrich cognate CD8+ T cells in patients with type 1 diabetes compared to healthy controls and discover a TCR that cross-reacts with diabetes-related and microbiome antigens. TetTCR-SeqHD is a powerful approach for profiling T cell responses in humans and mice.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Technical Report

MeSH terms

  • Antigens / immunology*
  • Antigens / metabolism
  • Antigens, Viral / immunology
  • Antigens, Viral / metabolism
  • Autoantigens / immunology
  • Autoantigens / metabolism
  • Autoimmunity
  • CD8-Positive T-Lymphocytes / immunology*
  • CD8-Positive T-Lymphocytes / metabolism
  • CD8-Positive T-Lymphocytes / virology
  • Case-Control Studies
  • Cell Separation
  • Cells, Cultured
  • Diabetes Mellitus, Type 1 / genetics
  • Diabetes Mellitus, Type 1 / immunology
  • Diabetes Mellitus, Type 1 / metabolism
  • Herpesvirus 4, Human / immunology
  • Herpesvirus 4, Human / pathogenicity
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Orthomyxoviridae / immunology
  • Orthomyxoviridae / pathogenicity
  • Phenotype
  • Receptors, Antigen, T-Cell / genetics*
  • Receptors, Antigen, T-Cell / immunology
  • Receptors, Antigen, T-Cell / metabolism
  • Single-Cell Analysis*

Substances

  • Antigens
  • Antigens, Viral
  • Autoantigens
  • Receptors, Antigen, T-Cell