Droplet-based mRNA sequencing of fixed and permeabilized cells by CLInt-seq allows for antigen-specific TCR cloning

Proc Natl Acad Sci U S A. 2021 Jan 19;118(3):e2021190118. doi: 10.1073/pnas.2021190118.


T cell receptors (TCRs) are generated by somatic recombination of V/D/J segments to produce up to 1015 unique sequences. Highly sensitive and specific techniques are required to isolate and identify the rare TCR sequences that respond to antigens of interest. Here, we describe the use of mRNA sequencing via cross-linker regulated intracellular phenotype (CLInt-Seq) for efficient recovery of antigen-specific TCRs in cells stained for combinations of intracellular proteins such as cytokines or transcription factors. This method enables high-throughput identification and isolation of low-frequency TCRs specific for any antigen. As a proof of principle, intracellular staining for TNFα and IFNγ identified cytomegalovirus (CMV)- and Epstein-Barr virus (EBV)-reactive TCRs with efficiencies similar to state-of-the-art peptide-MHC multimer methodology. In a separate experiment, regulatory T cells were profiled based on intracellular FOXP3 staining, demonstrating the ability to examine phenotypes based on transcription factors. We further optimized the intracellular staining conditions to use a chemically cleavable primary amine cross-linker compatible with current single-cell sequencing technology. CLInt-Seq for TNFα and IFNγ performed similarly to isolation with multimer staining for EBV-reactive TCRs. We anticipate CLInt-Seq will enable droplet-based single-cell mRNA analysis from any tissue where minor populations need to be isolated by intracellular markers.

Keywords: T cell receptor; T cells; TCR; mRNA sequencing; single-cell sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • CD8-Positive T-Lymphocytes / immunology
  • CD8-Positive T-Lymphocytes / virology
  • Cloning, Molecular
  • Cytomegalovirus / immunology
  • Cytomegalovirus / pathogenicity
  • Epitopes / immunology
  • Epstein-Barr Virus Infections / genetics
  • Epstein-Barr Virus Infections / immunology
  • Epstein-Barr Virus Infections / virology
  • Forkhead Transcription Factors / genetics*
  • Herpesvirus 4, Human / immunology
  • Herpesvirus 4, Human / pathogenicity
  • Humans
  • Interferon-gamma / genetics*
  • RNA, Messenger / genetics
  • RNA-Seq
  • Receptors, Antigen, T-Cell / genetics
  • Receptors, Antigen, T-Cell / immunology
  • Single-Cell Analysis
  • T-Lymphocytes, Regulatory / immunology
  • Tumor Necrosis Factor-alpha / genetics*
  • V(D)J Recombination / genetics*
  • V(D)J Recombination / immunology


  • Epitopes
  • FOXP3 protein, human
  • Forkhead Transcription Factors
  • IFNG protein, human
  • RNA, Messenger
  • Receptors, Antigen, T-Cell
  • Tumor Necrosis Factor-alpha
  • Interferon-gamma