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

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 Crosslinker 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 and Epstein-Barr virus 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 crosslinker compatible with current single-cell sequencing technology. CLInt-Seq for TNFα and IFNγ staining followed by single-cell sequencing performed similarly to isolation with multimer staining for Epstein-Barr virus 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. We developed a new technique for cloning T cell receptors, based on IC staining, and compare this technique to state of the art methods such as pMHC multimer selection.