Systems and methods for simultaneous detection of antigens and antigen specific antibodies

1 . A method for simultaneous detection of an antigen and an antibody that specifically binds said antigen, comprising:

labeling a plurality of antigens with unique antigen barcodes, wherein the plurality of antigens comprises multiple different antigenic proteins;

providing a plurality of barcode-labeled antigens to a population of B-cells;

allowing the plurality of barcode-labeled antigens to bind to the population of B-cells;

washing unbound barcode-labeled antigens from the population of B-cells;

separating the population of B-cells into single cell emulsions;

introducing into each single cell emulsion a unique cell barcode-labeled bead;

tagging cellular transcripts and the unique antigen barcodes with a bead-delivered cell barcodes;

pooling all tagged transcripts and the unique antigen barcodes that have been tagged with the bead-delivered cell barcodes;

preparing a cDNA library from the pooled tagged transcripts and the unique antigen barcodes that have been tagged with the bead-delivered cell barcodes;

performing PCR amplification reactions to produce a plurality of amplicons, wherein the amplicons comprise: 1) the bead-delivered cell barcode and the unique antigen barcode, and 2) the bead-delivered cell barcode and i) an immunoglobulin heavy chain (VDJ) sequence, or ii) an immunoglobulin light chain (VJ) sequence; and

sequencing the plurality of amplicons;

to identify the unique antigen barcodes and the immunoglobulin heavy chain or light chain sequences with the bead-delivered cell barcode.

2 . The method of claim 1 , wherein the barcode-labeled antigens are labeled with a first barcode comprising a DNA sequence or an RNA sequence.

3 . The method of claim 1 , wherein the cell barcode-labeled beads are labeled with a second barcode comprising a DNA sequence or an RNA sequence.

4 . The method of claim 1 , wherein the barcode-labeled antigens comprise an antigen from a pathogen or an animal.

5 . The method of claim 4 , wherein the antigen from a pathogen comprises an antigen from a virus.

6 . The method of claim 5 , wherein the antigen from a virus comprises an antigen from human immunodeficiency virus (HIV), an antigen from influenza virus, or an antigen from respiratory syncytial virus (RSV).

7 . The method of claim 6 , wherein the antigen from HIV comprises HIV-1 Env.

8 . The method of claim 6 , wherein the antigen from influenza virus comprises hemagglutinin (HA).

9 . The method of claim 6 , wherein the antigen from RSV comprises an RSV F protein.

10 . The method of claim 4 , wherein the antigen from an animal comprises an antigen from a human.

11 . The method of claim 10 , wherein the antigen from a human comprises a vascular endothelial growth factor (VEGF) protein.

12 . The method of claim 1 , wherein the population of B-cells comprise a memory B-cell, a plasma cell, a naïve B cell, an activated B-cell, or a B-cell line.

13 . The method of claim 12 , wherein the B-cell line comprises VRC01, PGT128, PGT145, VRC34, 10E8, 447-52D, Fe53, or CH65.

14 . The method of claim 1 , wherein the plurality of antigens comprise a panel of epitope knock-outs.

15 . The method of claim 1 , wherein the plurality of antigens comprise a panel of antigen variants or mutations for epitope mapping.