Identification of antigen-specific B cell receptors

• US 10,428,325 B1
• Filed: 09/20/2017
• Issued: 10/01/2019
• Est. Priority Date: 09/21/2016
• Status: Active Grant

• Current Assignee: Adaptive Biotechnologies Corp.
• Original Assignee: Adaptive Biotechnologies Corp.
• Inventors: Klinger, Mark
• Primary Examiner(s): Boesen, Christian C
• Application Number:
  US15/710,390
• Time in Patent Office: 741 Days
• Field of Search: None
• CPC Class Codes: C07K 16/00 Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies antibodies with enzymatic activity, e.g. abzymes C12N9/0002
• CPC Class Codes: C12N 15/1037 Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding

Abstract

Compositions and methods are disclosed for identifying B-cell receptor sequences that bind to corresponding antigens. The disclosed methods and related embodiments permit the identification paired relationships between rearranged gene segments of B-cell receptors with unique antigens.

Claims

1. A method for identifying antigen-specific B-cell receptor (BCR) sequences comprising:

(A) incubating a plurality of B-cells with an antigen library displayed by an organism capable of displaying antigens;

(B) distributing the B-cells bound to antigens of the antigen library into a plurality of aliquots;

(C) isolating nucleic acids from B-cells bound to antigens of the antigen library and from the organism displaying said antigens;

(D) sequencing the following elements from each of the aliquots;

(i) B-cell heavy chain sequence,

(ii) B-cell light chain sequence, and

(iii) a nucleotide sequence encoding the antigen bound to the BCR; and

(E) identifying the sequenced elements of (D) that occur together in more than one aliquot thereby identifying antigen-specific BCR sequences.

2. The method of claim 1, wherein (A) is immediately followed by enriching for B-cells bound to species of the antigen library.

3. The method of claim 2, wherein enriching for B-cells bound to species of the antigen library comprises flow cytometry.

4. The method of claim 1, wherein (C) is immediately followed by generating a library of amplicons by performing multiplex PCR on the isolated nucleic acids.

5. The method of claim 1, wherein the plurality of B-cells are isolated from a human.

6. The method of claim 1, wherein a plurality of B-cells comprises at least 10⁴ cells.

7. The method of claim 1, wherein said antigen library is a phage display library, a bacterial surface display library, or a yeast surface display library.

8. The method of claim 7, wherein said antigen library is a phage display library, and wherein the phage is selected from the group consisting of T7, M13, fd, f1, T4, and Lambda.

9. The method of claim 1, wherein said antigen library comprises antigens selected from the group consisting of bacterial antigens, viral antigens, fungal antigens, protist antigens, plant antigens, vertebrate antigens, mammalian antigens, and any combination thereof.

10. The method of claim 1, wherein the antigen library comprises a whole-genome library of an organism.

11. The method of claim 10, wherein the organism is a mammalian pathogen.

12. The method of claim 11, wherein the mammalian pathogen is a human pathogen.

13. The method of claim 1, wherein the B-cells express BCRs on the cell surface.

14. The method of claim 1, wherein the antigen library comprises a plurality of antigens, and wherein the nucleotide sequence encoding each antigen is flanked by a synthetic polynucleotide sequence.

15. The method of claim 14, wherein the synthetic polynucleotide sequence comprises at least one barcode sequence.

16. The method of claim 14, wherein the synthetic polynucleotide sequence comprises at least one universal adaptor sequence flanking the antigen.

17. The method of claim 14, wherein the synthetic polynucleotide comprises at least one universal adaptor sequence, a sequencing platform tag sequence, and at least one barcode sequence.

18. The method of claim 1, wherein the nucleotide sequence encoding the antigen is a cDNA.

19. The method of claim 1, further comprising:

(i) for each aliquot, reverse transcribing mRNA comprising rearranged CDR3 regions of the B-cells using oligonucleotide reverse transcription primers that direct incorporation of an oligonucleotide barcode and a universal adapter resulting in cDNA from each of the light and heavy chain sequences comprising a barcode and a universal adaptor, such that amplicons in an aliquot comprises the same unique barcode;

(ii) amplifying the cDNA using amplification primers to obtain amplification products;

(iii) quantitatively sequencing the amplification products of (ii) to obtain a data set of sequences that includes the B-cell light and heavy chain sequences and associated barcodes for each aliquot;

(iv) sorting amplification products based on the unique barcode to identify light and heavy chain sequences that were amplified from the same aliquot and determining an aliquot occupancy pattern for each unique light and heavy chain sequence; and

(v) identifying light and heavy chain sequences as paired immune receptor chains based on whether the sequences occur together or do not occur together in a plurality of aliquots based on a statistical probability of observing said aliquot occupancy pattern.

20. The method of claim 19, wherein each of the oligonucleotide reverse transcription primers that are contacted with the contents of a single aliquot share a common barcode sequence.

21. The method of claim 19, wherein the amplification primers further comprise an additional barcode, an n6 spacer, and/or a sequencing oligonucleotide.

22. The method of claim 19, wherein the amplification primers specifically hybridize to the universal adapter added to the cDNA in step (ii).

23. The method of claim 19, wherein the reverse transcription primers specifically hybridize to V, J, or C segments of each rearranged DNA sequence encoding a light chain and heavy chain polypeptide.

24. The method of claim 23 further comprising clustering the sorted amplification products in step (iv) based on the V, J, and/or C segments of each rearranged DNA sequence.

25. A method for identifying antigen-specific B-cell receptor (BCR) sequences comprising:

(A) incubating a plurality of B-cells with a phage antigen display library;

(B) distributing the B-cells bound to antigens of the antigen library into a plurality of aliquots;

(C) isolating mRNA from B-cells bound to antigens of the antigen library and nucleic acids from the phage;

(D) for each aliquot, reverse transcribing mRNA comprising rearranged CDR3 regions of the B-cells using oligonucleotide reverse transcription primers that direct incorporation of an oligonucleotide barcode and a universal adapter resulting in cDNA from each of the light and heavy chain sequences comprising a barcode and a universal adaptor, wherein each of the oligonucleotide reverse transcription primers that are contacted with the contents of a single aliquot share a common barcode sequence;

(E) amplifying the light and heavy chain cDNA sequences using amplification primers to obtain amplification products;

(F) quantitatively sequencing the amplification products of (E) to obtain a data set of sequences that includes the B-cell light and heavy chain sequences and associated barcodes for each aliquot;

(G) sorting amplification products based on the unique barcode to identify light and heavy chain sequences that were amplified from the same aliquot and determining an aliquot occupancy pattern for each unique light and heavy chain sequence;

(H) identifying light and heavy chain sequences as paired immune receptor chains based on whether the sequences occur together or do not occur together in a plurality of aliquots based on a statistical probability of observing said aliquot occupancy pattern;

(I) generating a library of amplicons by performing PCR on the isolated nucleic acids from the phage, followed by sequencing the library of amplicons; and

(J) identifying the paired immune receptor chains in (H) and the nucleic acids in (I) based on whether the sequences occur together or do not occur together in a plurality of aliquots.

26. The method of claim 25, wherein the amplification primers further comprise an additional barcode, an n6 spacer, and/or a sequencing oligonucleotide.

27. The method of claim 25, wherein the amplification primers specifically hybridize to the universal adapter added to the cDNA in (E).

28. The method of claim 25, wherein the reverse transcription primers specifically hybridize to V, J, or C segments of each rearranged DNA sequence encoding a light chain and heavy chain polypeptide.

29. The method of claim 25 further comprising clustering the sorted amplification products in (G) based on the V, J, and/or C segments of each rearranged DNA sequence.

30. The method of claim 25, wherein the isolated nucleic acids from the phage comprise RNA, step (I) is immediately preceded by reverse transcribing RNA comprising antigens of the antigen display library.