Compositions and methods for t-cell receptor identification

A method for identifying a T-cell receptor (TCR), comprising:

• (a) providing a plurality of T cells expressing a plurality of TCRs, wherein each T cell of the plurality of T cells expresses a cognate pair of a TCR of the plurality of TCRs;
• (b) pairing a first polynucleotide encoding a first TCR chain of the cognate pair of the TCR of a given T cell of the plurality of T cells of (a) and a second polynucleotide encoding a second TCR chain of the cognate pair of the TCR of the given T cell of the plurality of T cells of (a), thereby generating a plurality of polynucleotide pairs;
• (c) delivering polynucleotides comprising the sequences of the plurality of polynucleotide pairs generated in (b) into a plurality of recipient cells, wherein each recipient cell comprises a polynucleotide comprising the sequence of at least one polynucleotide pair of the plurality of polynucleotide pairs;
• (d) expressing in the plurality of recipient cells the sequences of the plurality of polynucleotide pairs delivered into the plurality of recipient cells of (c);
• (e) determining a TCR repertoire of the plurality of recipient cells of (d) by sequencing and determining a frequency of a TCR in the TCR repertoire in the plurality of recipient cells of (d);
• (f) contacting the plurality of recipient cells of (d) with one or more antigens, thereby activating a marker in a subset of the plurality of recipient cells;
• (g) isolating the subset of the plurality of recipient cells of (f) based on the marker;
• (h) determining a TCR repertoire of the subset of the plurality of recipient cells of (g) by sequencing and determining a frequency of a TCR in the TCR repertoire in the subset of the plurality of recipient cells of (g);
• and
• (i) identifying a TCR having a frequency in the subset of the plurality of recipient cells of (g) that is higher than its frequency in the plurality of recipient cells of (d).