# US 11,999,794 B2 · Human mesothelin chimeric antigen receptors and uses thereof

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- Number: US 11,999,794 B2
- Document ID: US11999794B2
- Status: Granted
- Kind: B2
- Application number: 16/750,951
- Filed: 2020-01-23
- Published: 2020-12-31
- Granted: 2024-06-04
- Earliest claimed: 2013-12-19
- Assignees: Novartis AG; The Trustees of the University of Pennsylvania
- Applicants: Novartis AG; The Trustees of the University of Pennsylvania
- Inventors: Gregory Beatty; Boris Engels; Neeraja Idamakanti; Carl H. June; Andreas Loew; Huijuan Song; Qilong Wu
- Web page: https://patentgrep.com/patent/US11999794B2

## CPC

- C07K 16/30: from tumour cells
- A61K 31/436: the heterocyclic ring system containing a six-membered ring having oxygen as a ring hetero atom, e.g. rapamycin
- A61K 38/1774: {Immunoglobulin superfamily (e.g. CD2, CD4, CD8, ICAM molecules, B7 molecules, Fc-receptors, MHC-molecules)}
- A61K 38/1793: {for cytokines; for lymphokines; for interferons}
- A61K 39/001168: {Mesothelin [MSLN]}
- A61K 39/39558: {against tumor tissues, cells, antigens}
- A61K 40/11: T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
- A61K 40/31: Chimeric antigen receptors [CAR]
- A61K 40/4211: {CD19 or B4}
- A61K 40/4255: {Mesothelin [MSLN]}
- A61K 48/0058: {Nucleic acids adapted for tissue specific expression, e.g. having tissue specific promoters as part of a contruct}
- A61P 1/00: Drugs for disorders of the alimentary tract or the digestive system
- A61P 1/18: for pancreatic disorders, e.g. pancreatic enzymes
- A61P 11/00: Drugs for disorders of the respiratory system
- A61P 13/10: of the bladder
- A61P 15/00: Drugs for genital or sexual disorders (for disorders of sex hormones A61P5/24); Contraceptives
- A61P 35/00: Antineoplastic agents
- A61P 35/04: specific for metastasis
- A61P 43/00: Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
- C07K 14/7051: {T-cell receptor (TcR)-CD3 complex}
- C07K 14/70517: {CD8}
- C07K 14/7151: {for tumor necrosis factor [TNF], for lymphotoxin [LT]}
- C07K 16/303: {Liver or Pancreas}
- C07K 16/3061: {Blood cells}
- C07K 16/3069: {Reproductive system, e.g. ovaria, uterus, testes, prostate}
- C12N 5/0638: {Cytotoxic T lymphocytes [CTL] or lymphokine activated killer cells [LAK]}
- C12N 15/85: for animal cells
- C12N 15/86: Viral vectors
- A61K 38/00: Medicinal preparations containing peptides (peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00)
- A61K 2039/505: {comprising antibodies}
- A61K 2039/5158: {Antigen-pulsed cells, e.g. T-cells}
- A61K 2239/31: characterized by the route of administration
- A61K 2239/38: characterised by the dose, timing or administration schedule
- A61K 2239/48: Blood cells, e.g. leukemia or lymphoma
- A61K 2239/54: Pancreas
- A61K 2239/59: Reproductive system, e.g. uterus, ovaries, cervix or testes
- C07K 2317/565: Complementarity determining region [CDR]
- C07K 2317/622: Single chain antibody (scFv)
- C07K 2317/73: Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
- C07K 2317/92: Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
- C07K 2319/00: Fusion polypeptide
- C07K 2319/02: containing a signal sequence
- C07K 2319/03: containing a transmembrane segment
- C07K 2319/74: containing a fusion for binding to a cell surface receptor
- C12N 2740/15041: Use of virus, viral particle or viral elements as a vector
- 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)

## Abstract

Provided are compositions and methods for treating diseases associated with expression of mesothelin. Also provided are a chimeric antigen receptor (CAR) specific to mesothelin, vectors encoding the same, and recombinant T cells comprising the mesothelin CAR. Further provided are methods of administering a genetically modified T cell expressing a CAR that comprises a mesothelin binding domain.

## Claims

### Claim 1

An immune effector cell comprising a nucleic acid molecule comprising a nucleic acid sequence encoding a chimeric antigen receptor (CAR) wherein the CAR comprises:
i) a human anti-mesothelin binding domain comprising:
(a) a light chain variable region comprising: a light chain complementary determining region 1 (LC CDR1) comprising the amino acid sequence of SEQ ID NO: 209; a light chain complementary determining region 2 (LC CDR2) comprising the amino acid sequence of SEQ ID NO: 233; and a light chain complementary-determining region 3 (LC CL)R3) comprising the amino acid sequence of SEQ ID NO: 257; and
(b) a heavy chain variable region comprising: a heavy chain complementary determining region 1 (HC CDR1) comprising the amino acid sequence of SEQ ID NO: 144; a heavy chain complementary determining region 2 (HC CDR2) comprising the amino acid sequence of SEQ ID NO: 162; and a heavy chain complementary determining region 3 (HC CDR3) comprising the amino acid sequence of SEQ. ID NO: 185;
ii) a transmembrane domain selected from the transmembrane domain of a protein selected from the group consisting of the alpha, beta or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and CD154;
iii) a costimulatory domain; and
iv) an intracellular signaling domain comprising the amino acid sequence of SEQ ID NO: 10;
wherein the isolated nucleic acid molecule does not comprise a nucleic acid sequence encoding an inducible promoter;
wherein the CAR is not a regulatable CAR; and
wherein the immune effector cell expresses a protein comprising a first polypeptide comprising an extracellular portion of PD1, PD-L1, CEACAM, LAG3, CTLA4, VISTA, CD160, BMA, LAIR1, TIM3, 2B4 or TIGIT and a second polypeptide comprising a costimulatory domain and/or a primary signaling domain.

### Claim 2 (depends on 1)

The immune effector cell of claim 1,
wherein the nucleic acid sequence encoding the CAR comprises the nucleic acid sequence of SEW NO: 121 or a sequence with 95-99% identity thereof.

### Claim 3 (depends on 1)

The immune effector cell of claim 1, wherein the nucleic acid sequence encoding the CAR comprises the nucleic acid sequence of SEQ ID NO: 121.

### Claim 4 (depends on 1)

The immune effector cell of claim 1, wherein the CAR comprises the amino acid sequence of SEQ ID NO: 73, or a sequence with 95-99% identity thereof.

### Claim 5 (depends on 1)

The immune effector cell of claim 1, wherein the CAR comprises the amino acid sequence of SEQ ID NO: 73.

### Claim 6 (depends on 1)

The immune effector cell of claim 1, wherein the CAR comprises a transmembrane domain comprising the amino acid sequence of SEQ ID NO: 6, or a transmembrane domain comprising an amino acid sequence with 95-99% identity to the amino acid sequence of SEQ NO: 6.

### Claim 7 (depends on 1)

The immune effector cell of claim 1, wherein the sequence encoding the transmembrane domain comprises the nucleic acid sequence of SEQ ID NO: 17; or a sequence with 95-99% identify to the nucleic acid sequence of SEQ. ID NO: 17.

### Claim 8 (depends on 1)

The immune effector cell of claim 1, wherein the costimulatory domain comprises the amino acid sequence of SEQ ID NO: 7, or a sequence with 95-99% identity to the amino acid sequence of SEQ ID NO: 7.

### Claim 9 (depends on 1)

The immune effector cell of claim 1, wherein the sequence encoding the costimulatory domain comprises the nucleic acid sequence of SEQ ID NO: 18, or a sequence with 95-99% identity to the nucleic acid sequence of SEQ ID NO: 18.

### Claim 10 (depends on 1)

The immune effector cell of claim 1, wherein the anti-mesothelin binding domain comprises the amino acid sequence of the light chain variable region of SEQ ID NO: 49; or an amino acid sequence with 95-99% identity to the amino acid sequence of the light chain variable region of SEQ ID NO: 49.

### Claim 11 (depends on 1)

The immune effector cell of claim 1, wherein the anti-mesothelin binding domain comprises the amino acid sequence of the heavy chain variable region of SEQ ID NO: 49; or an amino acid sequence with 95-99% identity to the amino acid sequence of the heavy chain variable region of SEQ ID NO: 49.

### Claim 12 (depends on 1)

The immune effector cell of claim 1, wherein the anti-mesothelin binding domain comprises the amino acid sequence of the light chain variable region of SEQ ID NO: 49; and the heavy chain variable region of SEQ ID NO: 49.

### Claim 13 (depends on 1)

The immune effector cell of claim 1, wherein the anti-mesothelin binding domain is a scFv.

### Claim 14 (depends on 1)

The immune effector cell of claim 1, wherein
(a) the anti-mesothelin binding domain comprises the sequence SEQ ID NO: 49, or a sequence with 95-99% identify to the amino acid sequence SEQ ID NO: 49; or
(b) the isolated nucleic acid sequence encoding the anti-mesothelin binding domain comprises the sequence of SEQ ID NO: 97, or a sequence with 95-99% identify to the nucleic acid sequence of SEQ ID NO: 97.

### Claim 15 (depends on 1)

The immune effector cell of claim 1, wherein the encoded anti-mesothelin binding domain is connected to the transmembrane domain by a hinge region, wherein
(a) the hinge region comprises the amino acid sequence of SEQ ID NO:2, or the hinge region comprises a sequence with 95-99% identity to the amino acid sequence of SEQ ID NO:2, or
(b) the hinge region comprises the amino acid sequence encoded by the nucleic acid sequence of SEQ ID NO:13, or the hinge region comprises an amino acid sequence encoded by a sequence with 95-99% identity to the nucleic acid sequence of SEQ ID NO:13;
(c) the hinge region comprises the amino acid sequence of SEQ ID NO: 36, or the hinge region comprises a sequence with 95-99% identity to the amino acid sequence of SEQ ID NO:36; or
(d) the hinge region comprises the amino acid sequence encoded by the nucleic acid sequence of SEQ ID NO: 37, or the hinge region comprises an amino acid sequence encoded by a sequence with 95-99% identity to the nucleic acid sequence of SEQ ID NO: 37.

### Claim 16 (depends on 1)

The immune effector cell of claim 1, wherein the costimulatory domain comprises a functional signaling domain derived from a protein selected from the group consisting of OX40, CD2, CD27, CD28, CD5, ICAM-1, LFA-1 (CD11a/CD18), ICOS (CD278), and 4-IBB (CD137).

### Claim 17 (depends on 1)

The immune effector cell of claim 1, wherein:
(a) the nucleic acid sequence encoding the costimulatory domain comprises the nucleic acid sequence of SEQ ID NO: 18, or a sequence with 95-99% identity thereof, and
(b) the nucleic acid sequence encoding the intracellular signaling comprises the nucleic acid sequence of SEQ ID NO: 21.

### Claim 18 (depends on 1)

The immune effector cell of claim 1, further comprising a leader sequence, wherein the leader sequence comprises the amino acid sequence of SEQ ID NO: 1.

### Claim 19 (depends on 1)

A method of treating a mammal having a disease or condition associated with cells that express mesothelin comprising administering to the mammal an effective amount of the immune effector cell of claim 1.

### Claim 20 (depends on 19)

The method of claim 19, wherein the disease is a cancer selected from the group consisting of mesothelioma, malignant pleural mesothelioma, non-small cell lung cancer, small cell lung cancer, squamous cell lung cancer, or large cell lung cancer, pancreatic cancer, pancreatic ductal adenocarcinoma, pancreatic metastatic cancer, ovarian cancer, colorectal cancer and bladder cancer, or any combination thereof.

### Claim 21 (depends on 19)

The method of claim 19, wherein the cell is a T cell or NK cell.