# US 2020/0392201 A1 · Antigen Discovery for T Cell Receptors Isolated from Patient Tumors Recognizing Wild-Type Antigens and Potent Peptide Mimotopes

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- Number: US 2020/0392201 A1
- Document ID: US20200392201A1
- Status: Published application
- Kind: A1
- Application number: 16/983,937
- Filed: 2020-08-03
- Published: 2020-12-17
- Earliest claimed: 2017-03-24
- Assignees: The Board of Trustees of the Leland Stanford Junior University
- Applicants: The Board of Trustees of the Leland Stanford Junior University
- Inventors: MARVIN GEE; MARK M. DAVIS; ARNOLD HAN; KENAN CHRISTOPHER GARCIA
- Web page: https://patentgrep.com/patent/US20200392201A1

## CPC

- C07K 14/7051: {T-cell receptor (TcR)-CD3 complex}
- A61K 40/11: T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
- A61K 40/32: T-cell receptors [TCR]
- A61K 40/4201: {Neoantigens}
- A61K 40/4202: {Receptors, cell surface antigens or cell surface determinants}
- A61K 40/4272: {Melan-A/MART}
- A61P 35/00: Antineoplastic agents
- A61P 37/04: Immunostimulants
- C07K 14/16: HIV-1 {; HIV-2}
- C07K 14/70539: {MHC-molecules, e.g. HLA-molecules}
- C12N 15/01: Preparation of mutants without inserting foreign genetic material therein; Screening processes therefor
- C12N 15/1037: {Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display}
- C12N 15/1086: {Preparation or screening of expression libraries, e.g. reporter assays}
- C12N 15/63: Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N 15/85: for animal cells
- C12N 15/86: Viral vectors
- C40B 50/10: involving encoding steps
- G01N 33/505: {involving T-cells}
- G01N 33/5759: {involving compounds localised on the membrane of tumour or cancer cells}
- A61K 2239/50: Colon
- C07K 2319/21: containing a His-tag
- C07K 2319/50: containing protease site
- C07K 2319/74: containing a fusion for binding to a cell surface receptor
- C12N 15/905: {in yeast}
- C12N 2310/20: involving clustered regularly interspaced short palindromic repeats [CRISPR]
- G01N 2800/52: Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

Compositions and methods are provided for peptide sequences that are ligands for a T cell receptor (TCR) of interest, in a given MHC context.

## Claims

### Claim at position 1

-20. (canceled)

### Claim 21

A method of creating a cell library of candidate antigens of a T-cell receptor (TCR), the method comprising:
providing a population of cells;
introducing into the cells nucleic acids and a CRISPR system to create polypeptides comprising the candidate antigens, wherein the polypeptides are configured to be displayed on a surface of the cells; and
allowing the cells to express and display the candidate antigens on the surface of the cells.

### Claim 22 (depends on 21)

The method of claim 21, wherein the cells are yeast cells.

### Claim 23 (depends on 21)

The method of claim 21, wherein the polypeptides further comprise a tag.

### Claim 24 (depends on 21)

The method of claim 21, wherein the cells co-express the candidate antigens and MHC proteins, or portions thereof.

### Claim 25 (depends on 24)

The method of claim 24, wherein the cells co-express the candidate antigens and binding domains of the MHC proteins.

### Claim 26 (depends on 25)

The method of claim 25, wherein the binding domains comprise α1 and α2 domains of a Class I MHC protein and a β2 microglobulin.

### Claim 27 (depends on 24)

The method of claim 24, wherein the MHC proteins, or portions thereof, are complexed to the candidate antigens.

### Claim 28 (depends on 23)

The method of claim 23, wherein the tag is a barcode, and the method further comprises selecting a subset of the cells using the barcode.

### Claim 29 (depends on 21)

The method of claim 21, further comprising monitoring the cell library by detecting the tag.

### Claim 30 (depends on 21)

The method of claim 21, further comprising screening the cells displaying the candidate antigens and identifying candidate antigens that bind to the TCR.

### Claim 31 (depends on 30)

The method of claim 30, wherein the screening comprises combining a multimerized TCR with the cell library expressing the candidate antigens, and
selecting cells that bind to the multimerized TCR.

### Claim 32 (depends on 31)

The method of claim 31, further comprising isolating candidate antigens displayed on the cells that bind to the multimerized TCR.

### Claim 33 (depends on 21)

The method of claim 21, wherein one or more of the candidate antigens bind to an orphan TCR.

### Claim 34 (depends on 21)

The method of claim 21, wherein one or more of the candidate antigens are unknown antigens of the TCR.

### Claim 35 (depends on 21)

The method of claim 21, wherein the cell library comprises at least 108 different single chain polypeptides each comprising a candidate antigen and a binding domain of a MHC protein.

### Claim 36 (depends on 35)

The method of claim 35, wherein the MHC protein is an allele of HLA-A2.

### Claim 37 (depends on 36)

The method of claim 36, wherein the HLA-A2 allele comprises a Y84A amino acid substitution.

### Claim 38 (depends on 21)

The method of claim 21, wherein the cell library is a multiplexed cell library.

### Claim 39 (depends on 21)

The method of claim 21, wherein:
the cells are yeast cells;
the cells co-express the candidate antigens and binding domains of the MHC proteins, wherein the binding domains comprise α1 and α2 domains of a Class I MHC protein and a β2 microglobulin; and
wherein the binding domains are complexed to the candidate antigens.

### Claim 40 (depends on 39)

The method of claim 39, wherein the cell library comprises at least 108 different single chain polypeptides.