# US 2023/0054958 A1 · Ctl peptide epitopes and antigen-specific t cells, methods for their discovery, and uses thereof

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- Number: US 2023/0054958 A1
- Document ID: US20230054958A1
- Status: Published application
- Kind: A1
- Application number: 17/935,211
- Filed: 2022-09-26
- Published: 2023-02-23
- Earliest claimed: 2013-11-15
- Assignees: Oslo Universitetssykehus Hf
- Applicants: Oslo universitetssykehus HF
- Inventors: Johanna OLWEUS; Shraddha KUMARI
- Web page: https://patentgrep.com/patent/US20230054958A1

## CPC

- G01N 33/56977: {HLA or MHC typing}
- A61K 39/0011: {Cancer antigens}
- A61K 39/39: characterised by the immunostimulating additives, e.g. chemical adjuvants
- C07K 14/70503: {Immunoglobulin superfamily}
- C07K 14/70539: {MHC-molecules, e.g. HLA-molecules}
- G01N 33/505: {involving T-cells}
- A61K 2039/5158: {Antigen-pulsed cells, e.g. T-cells}
- A61K 2039/55527: {Interleukins}
- A61K 2039/572: {cytotoxic response}
- G01N 2333/70539: MHC-molecules, e.g. HLA-molecules
- 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)
- 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)
- 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)

## Abstract

The present invention relates to CTL peptide epitopes, high-throughput methods for their identification, and their uses. In particular, the present invention relates to peptide epitopes for cancer immunotherapy and Hepatitis C Virus vaccines. The present invention also relates to methods and systems for identifying antigen-specific CTLs.

## Claims

### Claim 1

A method of screening for novel T cell epitopes and T cell receptors binding to said novel epitopes, comprising:
a) expressing a polypeptide comprising one or more candidate foreign-antigens in an antigen presenting cell that expresses a defined HLA molecule by introducing a nucleic acid construct encoding said polypeptide into said antigen presenting cell;
b) utilizing an affinity-based algorithmic prediction to identify a plurality of peptides from said polypeptide that are predicted to bind to said defined HLA molecule to provide predicted peptides;
c) synthesizing said predicted peptides and contacting said defined HLA molecule with said synthesized predicted peptides to allow those peptides among said synthesized predicted peptides that exhibit binding to said defined HLA molecule to generate predicted peptide:defined HLA molecule complexes;
d) forming a plurality of labelled complexes of said synthesized predicted peptide:defined HLA molecules from those predicted peptides that bind to said defined HLA molecules to provide a plurality of labelled predicted peptide:defined HLA molecule multimer complexes;
e) obtaining donor T cells from a donor, wherein T cells are not tolerant to said predicted peptide:defined HLA molecule multimer complexes;
f) contacting said antigen-presenting cells with said donor T cells to provide induced T cells; and
g) identifying one or more of said plurality of said labelled predicted peptide:defined HLA molecule multimer complexes binding to said donor T cells to identify multimer complexes containing novel epitopes that simultaneously bind said defined HLA molecule and T-cell receptors on said induced T cells based on detection of said label.

### Claim 3 (depends on 1)

The method of claim 1, wherein said defined HLA molecule is naturally expressed in said antigen presenting cell.

### Claim 4 (depends on 1)

The method of claim 1, wherein said defined HLA molecule is exogenously expressed in said antigen presenting cell.

### Claim 5 (depends on 1)

The method of claim 1, wherein said candidate antigen is foreign to said T cells and said defined HLA molecule is expressed by said T cells.

### Claim 6 (depends on 1)

The method of claim 1, wherein said defined HLA molecule is HLA-A*02:01.

### Claim 7 (depends on 1)

The method of claim 1, wherein said nucleic acid construct is an mRNA construct.

### Claim 8 (depends on 1)

The method of claim 1, wherein said nucleic acid construct is part of a viral vector.

### Claim 9 (depends on 1)

The method of claim 1, wherein said candidate antigen is screened for expression in disease-affected cells prior to said expressing.

### Claim 10 (depends on 1)

The method of claim 1, wherein said forming comprises UV-induced ligand exchange and multimerization.

### Claim 11 (depends on 1)

The method of claim 1, wherein said donor T cells binding said predicted peptide:defined HLA molecule complexes express a T-cell receptor that binds to said complex and wherein the method further comprises the step of cloning said T-cell receptor from one of said identified T-cells and modifying cells from a subject to express said T-cell receptor to provide modified cells.

### Claim 12 (depends on 1)

The method of claim 1, wherein said nucleic acid construct is a DNA construct.