# US 11,026,969 B2 · High affinity T cell receptors and uses thereof

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- Number: US 11,026,969 B2
- Document ID: US11026969B2
- Status: Granted
- Kind: B2
- Application number: 16/064,161
- Filed: 2016-12-23
- Published: 2018-12-27
- Granted: 2021-06-08
- Earliest claimed: 2015-12-23
- Assignees: Fred Hutchinson Cancer Research Center; Adaptive Biotechnologies Corporation
- Applicants: Fred Hutchinson Cancer Research Center; Adaptive Biotechnologies Corporation
- Inventors: Thomas M. Schmitt; Philip D. Greenberg; Aude G. Chapuis; Harlan S. Robins; Anna M. Sherwood
- Web page: https://patentgrep.com/patent/US11026969B2

## CPC

- A61K 35/12: Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells (vaccines or medicinal preparations containing antigens or antibodies A61K39/00)
- A61K 9/0019: {Injectable compositions; Intramuscular, intravenous, arterial, subcutaneous administration; Compositions to be administered through the skin in an invasive manner (non-active ingredients are additionally classified in A61K47/00)}
- A61K 38/20: Interleukins [IL]
- 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 40/4243: {Wilms tumor 1 [WT1]}
- A61K 40/4255: {Mesothelin [MSLN]}
- A61P 35/00: Antineoplastic agents
- A61P 35/02: specific for leukemia
- C07K 14/435: from animals; from humans
- C07K 14/5443: {IL-15}
- C07K 14/55: IL-2
- C07K 14/705: Receptors; Cell surface antigens; Cell surface determinants {(tumour specific antigens C07K14/4748)}
- C07K 14/7051: {T-cell receptor (TcR)-CD3 complex}
- A61K 45/06: Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
- A61K 2300/00: Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00
- 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
- 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 disclosure provides TCRs with high or enhanced affinity against various tumor associated antigens (including human Wilms tumor protein 1 (WT 1) epitopes and mesothelin epitopes), T cells expressing such high affinity antigen specific TCRs, nucleic acids encoding the same, and compositions for use in treating diseases or disorders in which cells overexpress one or more of these antigens, such as in cancer.

## Claims

### Claim 1

A binding protein, comprising:
(a) a T cell receptor (TCR) α-chain variable (Vα) domain having a CDR3 amino acid sequence shown in any one of SEQ ID NOS.:93-102, and a TCR β-chain variable (Vβ) domain; or
(b) a Vαdomain of (a) and a Vβdomain having a CDR3 amino acid sequence shown in any one of SEQ ID NOS.:105-114;
wherein the binding protein is capable of specifically binding to a WT-1 peptide:HLA complex on a cell surface independent of CD8 or in the absence of CD8.

### Claim 2 (depends on 1)

The binding protein according to claim 1, wherein the binding protein is capable of specifically binding to a VLDFAPPGA (SEQ ID NO.:117):human leukocyte antigen (HLA) complex with a Kd less than or equal to about 10−8M.

### Claim 3 (depends on 1)

The binding protein according to claim 1, wherein the binding protein comprises a Vαdomain that is at least about 90% identical to an amino acid sequence as set forth in any one of SEQ ID NOS.:19, 26, 33, 40, 47, 54, 63, 70, 77 and 84, and comprises a Vβdomain that is at least about 90% identical to the amino acid sequence as set forth in any one of SEQ ID NOS.:22, 29, 36, 43, 50, 57, 66, 73, 80 and 87, provided that (a) at least three or four of the CDRs have no change in sequence, wherein the CDRs that do have sequence changes have only up to two amino acid substitutions, up to a contiguous five amino acid deletion, or a combination thereof, and (b) the binding protein remains capable of specifically binding to a WT-1 peptide:HLA cell surface complex independent, or in the absence, of CD8.

### Claim 4 (depends on 1)

The binding protein according to claim 1, wherein the binding protein specifically binds to a VLDFAPPGA (SEQ ID NO.:117):HLA-A*201 complex.

### Claim 5 (depends on 1)

The binding protein according to claim 1, wherein the Vαdomain comprises or consists of an amino acid sequence as set forth in SEQ ID NO.:19, 26, 33, 40, 47, 54, 63, 70, 77, or 84; and/or the Vβdomain comprises or consists of an amino acid sequence as set forth in SEQ ID NO.:22, 29, 36, 43, 50, 57, 66, 73, 80, or 87.

### Claim 6 (depends on 1)

The binding protein according to claim 1, wherein the binding protein comprises:
(a) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:20, and a TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:23; or
(b) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:27, and the TCR β-chain comprising or consists of the amino acid sequence as set forth in SEQ ID NO:30; or
(c) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO:34, and the TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:37; or
(d) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:41, and the TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:44; or
(e) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:48, and the TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:51; or
(f) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:55, and the TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:60, or
(g) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:64, and the TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:67; or
(h) a TCR α-chain comprisng or consisting of the amino acid sequence as set forth in SEQ ID NO.:71, and the TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:74; or
(i) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:78, and the TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:81: or
(j) a TCR α-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO:85, and the TCR β-chain comprising or consisting of the amino acid sequence as set forth in SEQ ID NO.:88.

### Claim 7 (depends on 1)

The binding protein according to claim 1, wherein the binding protein is a T cell receptor (TCR), an antigen-binding fragment of a TCR, or a chimeric antigen receptor.

### Claim 8 (depends on 1)

A composition comprising a binding protein according to claim 1 and a pharmaceutically acceptable carrier, diluent, or excipient.

### Claim 9 (depends on 1)

An isolated polynucleotide encoding a binding protein according to claim 1.

### Claim 10 (depends on 9)

An expression vector, comprising a polynucleotide of claim 9 operably linked to an expression control sequence.

### Claim 11 (depends on 10)

The expression vector according to claim 10, wherein the vector is capable of delivering the polynucleotide to a host cell, wherein the host cell is a hematopoietic progenitor cell or a human immune system cell.

### Claim 12 (depends on 9)

A recombinant host cell, comprising a heterologous polynucleotide according to claim 9, wherein the recombinant host cell expresses on its cell surface a binding protein encoded by the heterologous polynucleotide.

### Claim 13 (depends on 12)

The recombinant host cell according to claim 12, wherein the heterologous polynucleotide encodes a Vαdomain comprising or consisting of a nucleotide sequence as set forth in any one of SEQ ID NOS.:150, 151, 160, 161, 170, 171, 180, 181, 190, 191 200, 201, 214, 215, 224, 225, 234, 235, 244 and 245; and/or encodes a Vβdomain comprising or consisting of a nucleotide sequence as set forth in any one SEQ ID NOS.:154, 155, 164, 165, 174, 175, 184, 185, 194, 204, 205, 218, 219, 228, 229, 238, 239, 248 and 249.

### Claim 14 (depends on 12)

The recombinant host cell according to claim 12, wherein a polynucleotide encodes:
(a) a TCR α-chain comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:152 or 153, and-the a TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:156 or 157; or
(b) a TCR α-chain comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:162 or 163, and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:166 or 167; or
(c) a TCR α-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:172 or 173, and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ NO.:176 or 177; or
(d) a TCR α-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO:182 or 183, and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:186 or 187; or
(e) a TCR α-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:192 or 193, and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:196 or 197; or
(f) a TCR α-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:202 or 203, and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO:210 or 211; or
(g) a TCR α-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:216 or 217, and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO:220 or 221; or
(h) a TCR α-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:226 or 227, and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:230 or 231; or
(i) a TCR α-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:236 or 237 and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:240 or 241; or
(j) a TCR α-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:246 or 247 and the TCR β-chain encoding polynucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO.:250 or 251.

### Claim 15 (depends on 12)

An adoptive immunotherapy method for treating a condition characterized by WT-1 overexpression in cells of a subject having a hyperproliferative disorder, comprising administering to the subject an effective amount of recombinant host cell according to any one of claim 12.

### Claim 16 (depends on 15)

The method according to claim 15, wherein the host cell is a hematopoietic progenitor cell or a human immune system cell, optionally wherein the immune system cell is a CD4+T cell, a CD8+T cell, a CD4− CD8−double negative T cell, a γδ T cell, a natural killer cell, a dendritic cell, or any combination thereof.

### Claim 17 (depends on 1)

A method for treating a hyperproliferative disorder, comprising administering to human subject in need thereof a composition comprising a binding protein specific for human Wilms tumor protein 1 (WT-1) according to claim 1.