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US-20260125740-A1 - PRIMERS FOR IMMUNE REPERTOIRE PROFILING

US20260125740A1US 20260125740 A1US20260125740 A1US 20260125740A1US-20260125740-A1

Abstract

Disclosed herein include systems, methods, compositions, and kits for immune repertoire profiling. There are provided, in some embodiments, primer panels enabling the determination of the nucleotide sequence of the complete variable region of nucleic acids encoding mouse B cell receptor (BCR) and T cell receptor (TCR) polypeptides. In some embodiments, the method comprises single cell transcriptomic analysis.

Inventors

  • Devon Jensen
  • Katherine Lazaruk
  • Dennis Prosen
  • Ricelle A. Acob
  • Kai Liu

Assignees

  • BECTON, DICKINSON AND COMPANY

Dates

Publication Date
20260507
Application Date
20250708

Claims (20)

  1. 1 .- 76 . (canceled)
  2. 77 . A composition for the identification and quantification of a T Cell Receptor (TCR) repertoire in a sample, comprising: one or more primers capable of hybridizing to a constant domain of a T Cell Receptor Alpha Chain, wherein the one or more primers comprises any one of the sequences of SEQ ID NOS: 5 and 32, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 5 and 32; one or more primers capable of hybridizing to a constant domain of a T Cell Receptor Beta Chain, wherein the one or more primers comprises any one of the sequences of SEQ ID NOS: 6 and 33, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 6 and 33; one or more primers capable of hybridizing to a constant domain of a T Cell Receptor Delta Chain, wherein the one or more primers comprises any one of the sequences of SEQ ID NOS: 7 and 34, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 7 and 34; and/or one or more primers capable of hybridizing to a constant domain of a T Cell Receptor Gamma Chain, wherein the one or more primers comprises any one of the sequences of SEQ ID NOS: 8-9 and 35-36, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 8-9 and 35-36.
  3. 78 . The composition of claim 77 , comprising: one or more primers capable of hybridizing to a constant domain of a T Cell Receptor Alpha Chain, wherein the one or more primers comprises a sequence of SEQ ID NO: 1, or a sequence that exhibits at least about 85% identity to SEQ ID NO: 1; one or more primers capable of hybridizing to a constant domain of a T Cell Receptor Beta Chain, wherein the one or more primers comprises a sequence of SEQ ID NO: 2, or a sequence that exhibits at least about 85% identity to SEQ ID NO: 2; one or more primers capable of hybridizing to a constant domain of a T Cell Receptor Delta Chain, wherein the one or more primers comprises a sequence of SEQ ID NO: 3, or a sequence that exhibits at least about 85% identity to SEQ ID NO: 3; and/or one or more primers capable of hybridizing to a constant domain of a T Cell Receptor Gamma Chain, wherein the one or more primers comprises a sequence of SEQ ID NO: 4, or a sequence that exhibits at least about 85% identity to SEQ ID NO: 4.
  4. 79 . The composition of claim 77 , wherein the constant domain of the T Cell Receptor Gamma Chain comprises T Cell Receptor Gamma Constant 1 (TRGC1), T Cell Receptor Gamma Constant 2 (TRGC2), T Cell Receptor Gamma Constant 4 (TRGC4), or any combination thereof.
  5. 80 . The composition of claim 77 , wherein the constant domain of a T Cell Receptor Alpha Chain comprises T Cell Receptor Alpha Constant (TRAC).
  6. 81 . The composition of claim 77 , wherein the constant domain of a T Cell Receptor Beta Chain comprises T Cell Receptor Beta Constant (TRBC).
  7. 82 . The composition of claim 77 , wherein the constant domain of a T Cell Receptor Delta Chain comprises T Cell Receptor Delta Constant (TRDC).
  8. 83 . The composition of claim 77 , wherein the constant domain of a T Cell Receptor Alpha Chain comprises the constant domain of a mouse T Cell Receptor Alpha Chain, wherein the constant domain of a T Cell Receptor Beta Chain comprises the constant domain of a mouse T Cell Receptor Beta Chain, wherein the constant domain of a T Cell Receptor Gamma Chain comprises the constant domain of a mouse T Cell Receptor Gamma Chain, and wherein the constant domain of a T Cell Receptor Delta Chain comprises the constant domain of a mouse T Cell Receptor Delta Chain.
  9. 84 . A kit, comprising: the composition of claim 77 ; and a plurality of oligonucleotide barcodes, wherein each of the plurality of oligonucleotide barcodes comprises a molecular label and a target-binding region, and wherein at least 10 of the plurality of oligonucleotide barcodes comprise different molecular label sequences.
  10. 85 . The kit of claim 84 , comprising a reverse transcriptase.
  11. 86 . The kit of claim 85 , wherein the reverse transcriptase comprises a murine leukemia virus (MLV) reverse transcriptase or a Moloney murine leukemia virus (MMLV) reverse transcriptase.
  12. 87 . The kit of claim 84 , comprising a DNA polymerase lacking at least one of 5′ to 3′ exonuclease activity and 3′ to 5′ exonuclease activity.
  13. 88 . The kit of claim 87 , wherein the DNA polymerase comprises a Klenow Fragment.
  14. 89 . The kit of claim 84 , comprising a template switching oligonucleotide comprising the target-binding region, or a portion thereof.
  15. 90 . The kit of claim 89 , wherein the template switch oligonucleotide comprises one or more 3′ ribonucleotides.
  16. 91 . The kit of claim 90 , wherein the template switch oligonucleotide comprises three 3′ ribonucleotides, and wherein the 3′ ribonucleotides comprise guanine.
  17. 92 . The kit of claim 84 , comprising a buffer, a cartridge, one or more reagents for a reverse transcription reaction, one or more reagents for an amplification reaction, or a combination thereof.
  18. 93 . The kit of claim 84 , comprising one or more of ethylene glycol, polyethylene glycol, 1,2-propanediol, dimethyl sulfoxide (DMSO), glycerol, formamide, 7-deaza-GTP, acetamide, tetramethylammonium chloride salt, betaine, or any combination thereof.
  19. 94 . The kit of claim 84 , wherein the target-binding region comprises a gene-specific sequence, an oligo(dT) sequence, a random multimer, or any combination thereof.
  20. 95 . The kit of claim 84 , wherein: at least one of the plurality of oligonucleotide barcodes is immobilized or partially immobilized on a synthetic particle; and/or at least one of the plurality of oligonucleotide barcodes is enclosed or partially enclosed in a synthetic particle.

Description

RELATED APPLICATIONS This application is a continuation of the U.S. patent application Ser. No. 18/190,465, filed Mar. 27, 2023, which is a divisional application of the U.S. patent application Ser. No. 17/320,052, filed May 13, 2021, which claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Patent Application Ser. No. 63/025,079, filed May 14, 2020, the content of these related applications are incorporated herein by reference in its entirety for all purposes. REFERENCE TO SEQUENCE LISTING The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled 68EB-298732-US3, created Mar. 21, 2023, which is 46,881 bytes in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety. BACKGROUND Field The present disclosure relates generally to the field of molecular biology, and for particular to multiomics analyses using molecular barcoding. Description of the Related Art Methods and techniques of molecular barcoding are useful for single cell transcriptomics analysis, including deciphering gene expression profiles to determine the states of cells using, for example, reverse transcription, polymerase chain reaction (PCR) amplification, and next generation sequencing (NGS). Molecular barcoding is also useful for single cell proteomics analysis. There is a need for methods and compositions (e.g., primer panels) for the determination of the nucleotide sequence of the complete variable region of nucleic acids encoding BCR and TCR immune receptor polypeptides in high-throughput sequencing single cell multiomics assays. SUMMARY Disclosed herein include compositions for the identification and quantification of a B Cell Receptor (BCR) repertoire in a sample. In some embodiments, the composition comprises: one or more primers capable of hybridizing to a constant domain of an immunoglobulin heavy chain, wherein the one or more primers comprises any one of the sequences of SEQ ID NOS: 10-17, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 10-17; and one or more primers capable of hybridizing to a constant domain of an immunoglobulin light chain, wherein the one or more primers comprises any one of the sequences of SEQ ID NOS: 18-20, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 18-20. Disclosed herein include compositions for the identification and quantification of a B Cell Receptor (BCR) repertoire in a sample. In some embodiments, the composition comprises: one or more primers capable of hybridizing to a constant domain of an immunoglobulin heavy chain, wherein the one or more primers comprises any one of the sequences of SEQ ID NOS: 21-28 and 37-44, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 21-28 and 37-44; and one or more primers capable of hybridizing to a constant domain of an immunoglobulin light chain, wherein the one or more primers comprises any one of the sequences of SEQ ID NOS: 29-31 and 45-47, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 29-31 and 45-47. Disclosed herein include compositions for the identification and quantification of a B Cell Receptor (BCR) repertoire in a sample. In some embodiments, the composition comprises: one or more first primers capable of hybridizing to a constant domain of an immunoglobulin heavy chain, wherein the one or more first primers comprises any one of the sequences of SEQ ID NOS: 10-17, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 10-17; one or more first primers capable of hybridizing to a constant domain of an immunoglobulin light chain, wherein the one or more first primers comprises any one of the sequences of SEQ ID NOS: 18-20, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 18-20; one or more second primers capable of hybridizing to a constant domain of an immunoglobulin heavy chain, wherein the one or more second primers comprises any one of the sequences of SEQ ID NOS: 21-28 and 37-44, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 21-28 and 37-44; and one or more second primers capable of hybridizing to a constant domain of an immunoglobulin light chain, wherein the one or more second primers comprises any one of the sequences of SEQ ID NOS: 29-31 and 45-47, or a sequence that exhibits at least about 85% identity to any one of the sequences of SEQ ID NOS: 29-31 and 45-47. In some embodiments, the immunoglobulin light chain comprises a kappa chain and/or a lambda chain. In some embodiments, the constant domain of an immunoglobulin heavy chain comprises Immunoglobulin Heavy Constant Alpha (IGHA), Immunoglobulin Heavy Constant Delta (IGHD), Immunogl