High throughput cloning of paired bipartite immunoreceptor polynucleotides and applications thereof

A method of identifying a target-reactive T-cell receptor (TCR), comprising:

• (a) providing a plurality of cells, wherein the plurality of cells expresses a plurality of TCRs, each cell of the plurality of cells expressing a TCR of the plurality of TCRs, wherein the plurality of TCRs comprises at least 50 different cognate pairs from a sample from a subject and comprises V regions from a plurality of V genes, wherein each cognate pair of the at least 50 different cognate pairs comprises a TCR alpha (TCRα) chain paired with a TCR beta (TCRβ) chain, and wherein the plurality of TCRs are exogenous to the plurality of cells;
• (b) contacting the plurality of cells from (a) with one or more target peptide antigens from the subject in complex with a major histocompatibility complex (MHC) molecule, wherein a cell of the plurality of cells expressing the target-reactive TCR binds to the one or more target peptide antigens in complex with the MHC molecule;
• and
• (c) selecting the cell of the plurality of cells from (b) that expresses the target-reactive TCR, thereby identifying the target-reactive TCR.