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NZ747154B2 - Transfected t-cells and t-cell receptors for use in immunotherapy against cancers - Google Patents
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NZ747154B2 - Transfected t-cells and t-cell receptors for use in immunotherapy against cancers - Google Patents

Transfected t-cells and t-cell receptors for use in immunotherapy against cancers Download PDF

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NZ747154B2
NZ747154B2 NZ747154A NZ74715417A NZ747154B2 NZ 747154 B2 NZ747154 B2 NZ 747154B2 NZ 747154 A NZ747154 A NZ 747154A NZ 74715417 A NZ74715417 A NZ 74715417A NZ 747154 B2 NZ747154 B2 NZ 747154B2
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tcr
seq
cell
amino acid
chain
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NZ747154A
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NZ747154A (en
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Leonie Alten
Sebastian Bunk
Dominik Maurer
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Immatics Biotechnologies Gmbh
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Publication of NZ747154A publication Critical patent/NZ747154A/en
Publication of NZ747154B2 publication Critical patent/NZ747154B2/en

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    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/14Blood; Artificial blood
    • A61K35/17Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66Microorganisms or materials therefrom
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00Medicinal preparations containing peptides
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00Drugs for immunological or allergic disorders
    • A61P37/02Immunomodulators
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    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
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    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503Immunoglobulin superfamily
    • C07K14/7051T-cell receptor (TcR)-CD3 complex
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
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    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2510/00Genetically modified cells
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06Animal cells or tissues; Human cells or tissues
    • C12N5/0602Vertebrate cells
    • C12N5/0634Cells from the blood or the immune system
    • C12N5/0636T lymphocytes

Abstract

The present description relates to T-cell receptors (TCRs) binding to tumor-associated antigens (TAAs) for targeting cancer cells, T-cells expressing same, methods for producing same, and methods for treating cancers using same. In particular, the present description relates to TCRs and their variants that bind to HLA class I or II molecules with a peptide, such as MAG-003 have the amino acid sequence of KVLEHVVRV (SEQ ID NO:1). The present description further relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present description relates to the immunotherapy of cancer. The present description furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or to stimulate T-cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules. ts that bind to HLA class I or II molecules with a peptide, such as MAG-003 have the amino acid sequence of KVLEHVVRV (SEQ ID NO:1). The present description further relates to peptides, proteins, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present description relates to the immunotherapy of cancer. The present description furthermore relates to tumor-associated T-cell peptide epitopes, alone or in combination with other tumor-associated peptides that can for example serve as active pharmaceutical ingredients of vaccine compositions that stimulate anti-tumor immune responses, or to stimulate T-cells ex vivo and transfer into patients. Peptides bound to molecules of the major histocompatibility complex (MHC), or peptides as such, can also be targets of antibodies, soluble T-cell receptors, and other binding molecules.

Description

TRANSFECTED T-CELLS AND T-CELL RECEPTORS FOR USE IN THERAPYAGAINST CANCERS OUND T-cell based immunotherapy targets peptide epitopes derived from tumor-associated or tu- mor-specific proteins, which are presented by molecules of the major histocompatibility complex (MHC). These tumor associated antigens (TAAs) can be peptides derived from all n classes, such as s, receptors, transcription s, etc. which are expressed and, as compared to unaltered cells of the same origin, usually up-regulated in cells of the respective tumor.
Specific elements of the cellular immune response are capable of specifically recognizing and destroying tumor cells. The isolation of T-cells from tumor-infiltrating cell populations or from peripheral blood suggests that such cells play an important role in natural immune defense against cancer. CD8-positive T-cells in particular, which recognize class I molecules of the major histocompatibility complex bea1ing peptides of usually 8 to 10 amino acid residues derived from proteins or defect ribosomal products (DRIPS) located in the cytosol, play an important role in this response. The MHC-molecules of the human are also designat- ed as human yte-antigens (HLA).
MAGEA4 is a member of the MAGEA gene family. Expression of the MAGEA4 protein and mRNA has been linked to the development and prognosis of various cancers. 3 pep- tide, i.e., KVLEHVVRV (SEQ ID NO:1), is an HLA—A*0201—restricted cytotoxic T lymphocyte (CTL) epitope of MAGEA4 (amino acids 286-294). (Jia et al. 2010; Wu et al. 2011), the con- tents of which are hereby incorporated by reference in their entirety. MAG—003 elicits pep- tide-specific CTLs both in vitro from 0201—positive PBMCs and in HLA—A*0201/Kb transgenic mice. MAG—003-induced CTLs lyse -cells in an HLA—A*0201-restricted fashion, demonstrating that MAG—003 is an HLA—A*0201-restricted CTL epitope.
There are two classes of MHC-molecules, MHC class I and MHC class II. xes of e and MHC class I are recognized by CD8-positive T-cells bearing the riate T-cell receptor (TCR), whereas complexes of peptide and MHC class II molecules are recognized by CD4-positive-helper-T-cells bearing the appropriate TCR. Since both types of response, CD8 and CD4 dependent, contribute jointly and synergistically to the anti—tumor effect, the identi- fication and characterization of tumor-associated antigens and corresponding T cell receptors is important in the development of cancer immunotherapies such as vaccines and cell thera- p1es.
In the MHC class I dependent immune reaction, peptides not only have to be able to bind to certain MHC class I molecules expressed by tumor cells, they subsequently also have to be recognized by T—cells g specific T—cell receptors (TCR). ore, TAAs are a starting point for the development of a T-cell based therapy including but not limited to tumor vac- cines and cell therapies.
In the case of targeting e-MHC by specific TCRs (e.g., soluble TCRs or cell-surface TCRs) and antibodies or other binding molecules (complexes) according to the description, the immunogenicity of the underlying peptides is secondary. In these cases, the presentation is a determining factor.
While advances have been made in the development of molecular-targeting drugs for cancer therapy, there s a need in the art to develop new anti-cancer agents that specifically target molecules highly specific to cancer cells. The present description addresses that need by providing novel MAG-003 TCRs, c acids, vectors and host cells which specifically bind MAG-003; and methods of using such les in the treatment of cancer.
SUMMARY The present description relates to T—cell receptors (TCRs) comprising an alpha chain and/or a beta chain ("alpha/beta TCRs"). In another embodiment, the present description relates to TCRs comprising a gamma chain and/or delta chain ("gamma/delta TCRs").
The present description further relates to TCRs, dual TCR subunits (alone or in combi- nation), and subdomains f, soluble TCRs ), for example, e alpha/beta di- meric TCRs having at least one disulfide inter-chain bond between constant domain residues that are not present in native TCRs, and cloned TCRs, said TCRs engineered into autologous or allogeneic T—cells or T-cell progenitor cells, and methods of making same, as well as other cells bearing said TCR.
The present description further relates to a TCR that specifically binds to a MAG-003 pep- tide-HLA molecule x, wherein the 3 peptide is selected from KVLEHVVRV (SEQ ID NO:1) and ts thereof, such as those shown in SEQ ID N022 to SEQ ID NO:24.
In an ment the HLA molecule is HLA—A*02.
The t description further relates to TCRs comprising, a TCR alpha variable domain that has at least 75%, 80%, 90%, 95%, 98%, or 99% sequence identity, preferably 90% se- quence identity, to a TCR alpha variable domain shown in Table 2; and the TCR beta variable domain has at least at least 75%, 80%, 90%, 95%, 98%, or 99% sequence identity, preferably 90% sequence identity, to a TCR beta variable domain shown in Table 2.
In an embodiment, the TCR alpha variable domain has at least one mutation relative to a TCR alpha domain shown in Table 2; and/or the TCR beta variable domain has at least one mutation relative to a TCR alpha domain shown in Table 2. In an ment, a TCR com- prising at least one mutation in the TCR alpha variable domain and/or TCR beta variable domain has a binding affinity for, and/or a binding half-life for, a MAG-003 peptide-HLA molecule complex, which is at least double that of a TCR comprising the unmutated TCR al- pha domain and/or unmutated TCR beta variable domain.
The TCR alpha chains of the t description may further comprise a TCR alpha nt domain that has at least 70%, 75%, 80%, 90%, 95%, 98%, or 99% sequence ty to a TCR alpha constant domain shown in Table 2. The TCR beta chains of the present description may further comprise a TCR beta constant domain that has at least 70%, 75%, 80%, 90%, 95%, 98%, or 99% sequence identity to a TCR beta constant domain shown in Table 2.
The TCR alpha chains of the present description may further comprise a TCR alpha trans- membrane domain and/or a TCR alpha intracellular domain. The TCR beta chains of the present ption may further comprise a TCR beta transmembrane domain and/or a TCR beta intracellular domain.
The description r relates to TCR alpha chains sing one or more alpha chain complementarity determining regions (CDRs) disclosed in Table 2, and variants thereof hav— ing one, two, three or four substitutions relative to the CDRs shown in Table 2. Further described are TCR alpha chains comprising at least one CDR selected from a CDR1, CDR2 and CDR3 shown in Table 2. Further described are TCR alpha chains comprising an alpha chain CDR3 shown in Table 2.
The description further relates to TCR beta chains sing one or more beta chain com- plementarity determining regions (CDRs) sed in Table 2, and variants thereof having one, two, three or four substitutions ve to the CDRs shown in Table 2. Further de— scribed are TCR beta chains comprising at least one CDR ed from a beta chain CDR1, CDR2 and CDR3 shown in Table 2. Further described are TCR beta chains comprising a beta chain CDR3 shown in Table 2.
The description further relates to an ed or recombinant nucleic acid comprising a nu- cleotide ce encoding a TCR of the present description. In an embodiment, nucleic acids of the description encode a TCR alpha chain and/or a TCR beta chain as shown in Table The description further relates to a inant expression vector comprising a nucleic acid encoding a TCR alpha chain, beta chain, or both, as described herein.
The description further relates to an ed host cell comprising a recombinant expression vector expressing a c acid encoding the TCR alpha chain, beta chain, or both, as de- scribed herein.
The description further relates to an isolated host cell comprising a recombinant expression vector according to the present description, preferably wherein the cell is a human cell, pref- erably a peripheral blood lymphocyte (PBL), more preferably a CD4 or CD8 positive T lym- phocyte.
The description further relates to an isolated PBL comprising the recombinant expression vector of the description, wherein the PBL is a CD8+ T—cell or a CD4+ T—cell.
The description further relates to a population of cells comprising at least one host cell de- scribed herein.
The description r relates to TCRs and host cells of the present description for use in the treatment of proliferative diseases, such as, non—small cell lung cancer, small cell lung cancer, renal cell cancer, brain cancer, gastric cancer, colorectal cancer, cellular cancer, pan- creatic cancer, prostate cancer, leukemia, breast cancer, Merkel cell carcinoma, melanoma, ovarian , urinary bladder cancer, uterine cancer, gallbladder and bile duct cancer and esophageal cancer.
In an aspect, the host cell is a CD8+ T-cell or a CD4+ T-cell transfected with a nucleic acid encoding at least one TCR according to the description, n the TCR comprises at least one amino acid sequence disclosed in Table 2. In another aspect such host cells are used in the immunotherapy of small cell lung cancer, non-small cell lung cancer, small cell lung can- cer, renal cell cancer, brain cancer, gastric , colorectal cancer, cellular cancer, atic cancer, prostate cancer, leukemia, breast cancer, Merkel cell carcinoma, melano- ma, ovarian cancer, urinary bladder , e cancer, adder and bile duct cancer and esophageal cancer, and preferably non-small cell lung cancer.
The description further relates to methods of killing or reducing the number of cancer cells comprising contacting the cancer cells with a TCR, c acid, vector or host cell as de- scribed herein. Also provided are methods of ng cancer comprising administering to a subject in need thereof a TCR, nucleic acid, vector or host cell as described herein.
In r aspect, the present description relates to a MAG-003 peptide, for example an iso- lated peptide, comprising an amino acid sequence ing to the following general formula X1X2LEHVVRX3 (SEQ ID NO:25) Formula I wherein X1 is selected from the amino acids K and Y, X2 is selected from the amino acids V, L and A, and X3 is selected from V, L, A, and I, wherein said e binds to an HLA class I or class II molecule and/or induces T-cells cross—reacting with said e, or a pharmaceuti- cally able salt thereof. In an aspect, said peptide is not the underlying full-length poly- peptide.
Preferred is a sequence selected from the group consisting of SEQ ID NO:1 or a variant se- quence thereof which is at least 66%, preferably at least 77%, and more preferably at least 88% homologous (preferably at least 77% or at least 88% identical) to SEQ ID NO:1, wherein said variant binds to an HLA class I or class II molecule and/or induces T-cells cross-reacting with said peptide, or a pharmaceutically acceptable salt thereof, wherein said peptide is not the underlying full-length polypeptide.
The t description further relates to a peptide of the present description comprising a sequence that is selected from the group consisting of SEQ ID NO:1 or a variant thereof, which is at least 66%, preferably at least 77%, and more preferably at least 88% homologous (preferably at least 77% or at least 88% identical) to SEQ ID NO:1, n said peptide or variant thereof has an overall length of between 8 and 100, preferably between 8 and 30, and most preferably of n 8 and 14 amino acids.
The following tables show example peptides according to the present description, and their respective SEQ ID NOs. In an aspect, the peptides in Table 1 may bind to HLA—A*o2. In an- other aspect, TCRs described herein are capable of g or specifically binding to one or more peptides in Table 1.
Table 1: Peptides according to the present description SEQ ID NO: Sequence 1 KVLEHVVRV SEQ ID NO: Sequence 2 KVLEHVVRL 3 KVLEHVVRA 4 KVLEHVVRI KLLEHVVRV 6 KLLEHVVRL 7 KLLEHVVRA 8 VRI 9 KALEHVVRV KALEHVVRL 11 KALEHVVRA 12 KALEHVVRI 13 YLLEHVVRV 14 YLLEHVVRL YLLEHVVRA 16 YLLEHVVRI 17 YALEHVVRV 18 YALEHVVRL 19 YALEHVVRA YALEHVVRI 21 YVLEHVVRV 22 YVLEHVVRL 23 YVLEHVVRA 24 YVLEHVVRI In an aspect, the present description relates to the treatment of proliferative es, such as non-small cell lung cancer, small cell lung cancer, renal cell cancer, brain cancer, gastric can- cer, colorectal cancer, hepatocellular cancer, pancreatic cancer, prostate cancer, ia, breast cancer, Merkel cell carcinoma, melanoma, ovarian cancer, urinary bladder , uterine cancer, gallbladder and bile duct cancer and esophageal cancer by utilizing one or more peptides bed herein. ularly red are the peptides — alone or in combination — according to the present description selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:24. More pre- ferred are the peptides — alone or in ation — selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:24 (see Table 1), and their uses in the immunotherapy of non- small cell lung cancer, small cell lung cancer, renal cell cancer, brain cancer, gastric cancer, colorectal cancer, hepatocellular cancer, head and neck cancer, pancreatic cancer, prostate cancer, leukemia, breast cancer, Merkel cell carcinoma, melanoma, ovarian cancer, urinary bladder cancer, uterine , gallbladder and bile duct cancer and esophageal , and preferably non-small cell lung cancer.
In an aspect, the t description relates to peptides according to the present description that have the ability to bind to a molecule of HLA class-I or — in a longer form, such as a length—variant —HLA class-II.
In an aspect, the present description relates to the peptides according to the present descrip- tion wherein said peptides (each) comprise, consist of, or consist essentially of an amino acid sequence according to SEQ ID NO:1 to SEQ ID NO:24.
The present description further relates to the peptides according to the present description, wherein said peptide is modified and/or includes non-peptide bonds.
The present ption further relates to the peptides according to the present ption, wherein said e is part of a fusion protein, in particular fused to the N—terminal amino acids of the HLA—DR antigen—associated invariant chain (Ii), preferably the 80 N—terminal amino acids thereof, or fused to (or into the sequence of) an dy, such as, for example, an antibody that is specific for dendritic cells.
The description further relates to a nucleic acid encoding the peptides according to the de- scription. The description r s to the nucleic acid according to the description that is DNA, cDNA, PNA, RNA or combinations thereof.
The description further relates to an expression vector capable of expressing and/or express- ing a nucleic acid according to the ption.
The description further relates to a peptide according to the description, a nucleic acid ac- cording to the description or an expression vector according to the description for use in the ent of es and in medicine, in particular in the treatment of cancer.
The description further s to antibodies that specifically bind the peptides according to the present description or complexes of said peptides according to the description with MHC, and methods of making such antibodies.
The description further relates to a host cell comprising a nucleic acid ing to the de- scription or an expression vector as described before.
The description further s to the host cell according to the description that is an antigen presenting cell, and preferably is a dendritic cell.
The description further relates to a method for producing a peptide according to the p- tion, the method comprising culturing the host cell ing to the description, and isolating the peptide from said host cell or its culture medium.
The description further relates to methods according to the ption, wherein the antigen is loaded onto class I or II MHC molecules expressed on the surface of a suitable antigen- presenting cell or artificial antigen-presenting cell by contacting a sufficient amount of the antigen with an antigen—presenting cell or the antigen is loaded onto class I or II MHC te- tramers by tetramerizing the antigen/class I or II MHC x monomers.
The description r relates to the method according to the description, wherein the anti- gen-presenting cell comprises an expression vector capable of expressing or sing said peptide containing SEQ ID NO:1 to SEQ ID NO:24, preferably containing SEQ ID NO:1 to SEQ ID NO:24, or a variant amino acid sequence thereof.
The description further relates to activated T-lymphocytes, produced by the method accord- ing to the ption, wherein a T-cell ively recognizes a cell which expresses a poly- peptide sing an amino acid sequence according to the description.
The description r s to s of killing cancer and/or suppressing cells in a pa— tient which cancer cells aberrantly s a polypeptide comprising any amino acid se- quence according to the description, the methods comprising administering to the patient an effective number of T-cells as produced according to the description.
The description further relates to the use of any peptide described herein, nucleic acids ac- cording bed herein, expression vectors described herein, cells described herein, activat- ed T lymphocyte bed herein, T-cell ors, antibodies, or other peptide— and/or pep- HC-binding molecules according to the present description as a medicament or in the manufacture of a medicament. In an , the medicament is active against cancer.
Preferably, said medicament is a cellular therapy, a vaccine or a protein based on a TCR, a soluble TCR or antibody.
The present description further relates to a use according to the present description, wherein the cancer cells are non-small cell lung cancer, small cell lung cancer, renal cell cancer, brain cancer, gastric cancer, colorectal cancer, hepatocellular cancer, pancreatic cancer, prostate , leukemia, breast cancer, Merkel cell oma, melanoma, ovarian cancer, urinary bladder cancer, uterine cancer, gallbladder and bile duct cancer and esophageal cancer, and preferably all cell lung .
The t description further relates to biomarkers based on the peptides according to the present description, herein called "targets," that can be used in the diagnosis of cancer, pref- erably non-small cell lung cancer. The marker can be the over—presentation of the peptide(s) themselves, or over-expression of the corresponding gene(s). The markers may also be used to predict the probability of success of a treatment, preferably an immunotherapy, and most preferred an immunotherapy targeting the same target that is identified by the biomarker.
For example, an antibody or soluble TCR can be used to stain sections of the tumor to detect the presence of a peptide of interest in complex with MHC. Optionally the antibody or e TCR carries a further effector function such as an immune stimulating domain or toxin.
The present description further relates to the use of these novel targets for the fication of TCRs that recognize at least one of said targets, and preferably the identification of said TCRs that activate T-cells.
The present description also relates to the use of these novel targets in the context of cancer treatment.
BRIEF DESCRIPTION OF DRAWINGS shows 3 peptide presentation in healthy tissues and cancers.
FIGs. 2-4 show MAG-003 expression in cancer and healthy tissues.
FIGs. 5-7 show IFNy release from CD8+ T-cells electroporated with alpha and beta chain RNA of TCRs R7P1D5, R2oP1H7 and R1oP2G12 (Table 2), respectively, after co-incubation WO 58103 with target cells loaded with MAG-003 peptide (SEQ ID NO:1) or homologous but unrelated peptide RABGAP1L-001 (SEQ ID NO:91), AXIN1-001 (SEQ ID NO:92), o1 (SEQ ID NO:93), TPX2-001 (SEQ ID NO:94), SYNE3-001 (SEQ ID NO:95), MIA3-001 (SEQ ID NO:96), HERC4-001 (SEQ ID NO:97), PSME2-001 (SEQ ID NO:98), HEATR5A—001 (SEQ ID NO:99) or CNOT1-003 (SEQ ID NO:1oo) or control peptide NYESO1—001 (SEQ ID NO:101). IFNy release data were obtained with CD8+ T-cells derived from two different do- nors (donor 1 on right X-axis, donor 2 on left X—axis). RNA electroporated CD8+ T-cells alone or in co-incubation with unloaded target cells served as ls. show MHC/MAG-003 tetramer or MHC/NYESOl—001 tetramer staining of CD8+ T- cells electroporated with alpha and beta chain RNA of TCRs R7P1D5, R20P1H7 and R10P2G12 (Table 2), respectively. CD8+ s electroporated with RNA of 1G4 TCR that specifically binds to MHC/NYES01-001 complex and mock electroporated CD8+ T-cells served as controls.
FIGs. 9-11 show IFNy release from CD8+ T—cells electroporated with alpha and beta chain RNA of TCRs R7P1D5, R20P1H7 and R10P2G12 (Table 2), respectively, after co-incubation with target cells loaded with MAG-003 peptide (SEQ ID NO:1) or various MAG—003 alanine- substitution variants at positions 1-9 of SEQ ID N021. RNA-electroporated CD8+ T—cells alone or in co—incubation with target cells loaded with control peptide NYESOl—001 or un- loaded target cells served as controls. IFNy release data were obtained with CD8+ T-cells derived from two different donors (donor 1 on right X-axis, donor 2 on left X-axis).
IFNy release from CD8+ T-cells oporated with alpha and beta chain RNA of TCRs (A) R7P1D5, (B) R20P1H7, and (C) R10P2G12 after co-incubation with A—375 melano- ma cell line, T98G glioblastoma cell line and SK-BR-3 breast cancer cell line, respectively.
RNA-electroporated CD8+ T-cells alone served as a control.
T cells transfected with RNA coding for TCR , R10P2G12, R20P1H7, mock or the control TCR 1G4 (SEQ ID NO:X) were co-cultured with different primary human y tissue cells (see table 13 for abbreviations), the target negative tumor cell line MCF-7 and the MAGEA4 - and NY-ESOl—positive cell lines A—375 and NCI-H1755. TCRs R7P1D5, R10P2G12, R20P1H7 and 1G4 sion in T cells was achieved by electroporation using an RNA vector.
Human y tissue cell cultures did not lead to significant TCR-mediated recognition and T-cell activation for TCR R7P1D5, R10P2G12 or R20P1H7. E:T ratio 1:1, 20,000 cells each, mean of IFN-y e after 20 h from replicates is shown as measured by ELISA. Error bars indicate rd deviations. Results were normalized by subtraction of IFN-y release from TCR-transfected T cells only and IFN—y release due to co-culture of Target cells and T cells not expressing TCR of interest.
Fig. 14 Fig. 14 tive data from 4 donors screened for R7P1D5 TCR transgene expres- sion after transduction with 6 different lentiviral constructs (R71—R78). CD3+/CD8+ T—cells were ed by flow cytometry for tion of MHC/MAG—003 tetramer binding cells at 96 hours post transduction. Non-transduced T-cells (NT) d MHC/MAG—003 tetramer and 1G4 (NY-ESOl) TCR transduced T-cells stained with MHC/NYESOl—001 tetramer were used as negative and positive control, respectively. Cells were gated on Live CD3+CD8+ pop- ulation.
Fig. 15 A. Effector response of R7P1D5 TCR transduced T-cells measured by means of IFNy production upon co-culture MAGEA4 expressing tumor cell line A375 and MAGEA4 negative tumor cell line MCF—7. T-cells transduced with concentrated supernatant of R73 lentivirus encoding R7P1D5 TCR were compared with non-transduced cells (NT) both derived from PBMCs of 4 healthy donors. s are presented as meaniSEM of triplicates. B. IFNy re- sponse of R7P1D5 TCR transduced (R73 lentivirus) T-cells from PBMC of 2 healthy donors (Donor 6 and 7) upon co-incubation with T2 target cells pulsed with decreasing tra- tions of MAG—003 peptide. Results are presented as meaniSEM of triplicates measured 96 hours after transduction.
Fig. 16 (A, B) Cytotoxic response of R7P1D5 TCR (R73 lentivirus) transduced and non- transduced T-cells (NT) measured against MAGEA4 expressing tumor cell line A375 at dif- ferent E:T ratios in a 4h Cr51 release assay. Results are presented as meaniSEM of 3-4 repli— cates. (C) Combined data from 7 R7P1D5 TCR (R73 lentivirus) transduced T—cell products generated from 5 donors showing antigen specific killing of MAGEA4 expressing (A375) and MAGEA4-negative (MCF-7) tumor targets at E:T ration of 40:1.
ED DESCRIPTION The present ption relates to T-cell receptors (TCRs) comprising an alpha chain and/or a beta chain a/beta TCRs"). Also provided are MAG—003 peptides capable of g to TCRs and antibodies when presented by an MHC le. The present ption also relates to nucleic acids, vectors and host cells for expressing TCRs and peptides of the present description; and methods of using the same.
The object of the invention is therefore solved in a first aspect by an antigen recognizing con- struct sing at least one complementary determining region (CDR) 3 having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or preferably 100% sequence identity to an ami- no acid ce selected from SEQ ID NOS. 44, 52, 60, 68, 76, and 84.
The antigen recognizing construct according to the invention is preferably selected from an antibody, or derivative or fragment thereof, or a T cell receptor (TCR), or tive or frag- ment thereof. A derivative or fragment of an antibody or TCR of the invention shall prefera- bly retain the antigen binding/recognizing ability of the parent molecule, in particular its specificity and/or selectivity as explained above. Such binding functionality may be retained by the presence of a CDR3 region as d herein.
In an embodiment of the invention, the inventive TCRs are able to recognize TAA antigens in a major ompatibility complex (MHC) class ndent manner. "MHC class 1- dependent manner," as used herein, means that the TCR elicits an immune response upon binding to TAA antigens within the t of an MHC class I molecule. The MHC class I molecule can be any MHC class I molecule known in the art, e.g., HLA-A molecules. In a pre- ferred embodiment of the invention, the MHC class I molecule is an HLA—A*02 molecule.
The invention provides both single chain antigen recognizing construct and double chain izing constructs.
In an embodiment, the TCR alpha le domain has at least one mutation relative to a TCR alpha domain shown in Table 2; and/or the TCR beta variable domain has at least one mutation relative to a TCR alpha domain shown in Table 2. In an embodiment, a TCR comprising at least one mutation in the TCR alpha variable domain and/or TCR beta variable domain has a g affinity for, and/or a g half-life for, an TAA peptide- HLA molecule complex, which is at least double that of a TCR comprising the unmutated TCR alpha domain and/or unmutated TCR beta variable domain.
The TCR alpha chains of the present description may further comprise a TCR alpha transmembrane domain and/or a TCR alpha intracellular . The TCR beta chains of the pre-sent description may further comprise a TCR beta transmembrane domain and/or a TCR beta intracellular domain.
The invention in particular provides a TCR as antigen recognizing construct, or fragment or tive thereof. The TCR ably is of human, which is understood as being ted from a human TCR locus and therefore comprising human TCR sequences. Furthermore, the TCR of the invention may be characterized in that it is of human origin and specifically recognizes a TAA antigen of the invention as mentioned in table 1. r embodiment of the invention additionally or alternatively provides the antigen izing construct described above, which induces an immune response, preferably wherein the immune response is characterized by an increase in interferon (IFN) γ levels.
TCRs of the ion may be provided as single chain α or β, or γ and δ, molecules, or alter- natively as double chain constructs composed of both the α and β chain, or γ and δ chain.
Most preferably, in some additional embodiments, wherein the disclosure refers to antigen recognizing constructs comprising any one, two or all of the CDR1 to CDR3 regions of the herein disclosed TCR chains (see Table 2), such antigen recognizing ucts may be preferred, which comprise the respective CDR ce of the invention with not more than three, two, and preferably only one, modified amino acid residues. A modified amino acid residue may be selected from an amino acid insertion, deletion or substitution. Most preferred is that the three, two, preferably only one ed amino acid residue is the first or last amino acid residue of the respective CDR sequence. If the modification is a substitution then it is preferable in some embodiments that the substitution is a conservative amino acid substitution.
The inventive TCRs may further comprise a constant region derived from any suitable species, such as any mammal, e.g., human, rat, monkey, rabbit, donkey, or mouse. In an embodiment of the invention, the ive TCRs further comprise a human nt region.
In some preferred embodiments, the constant region of the TCR of the invention may be slightly modified, for example, by the introduction of heterologous sequences, preferably mouse sequences, which may increase TCR sion and stability.
In an embodiment of the invention, chimeric TCR are provided, wherein the TCR chains comprise sequences from multiple species. Preferably, a TCR of the invention may comprise an α chain comprising a human variable region of an α chain and, for example, a murine nt region of a murine TCR α chain.
In one embodiment, the TCR of the invention is a human TCR comprising human variable regions according to the above embodiments and human constant regions.
In some embodiments the antigen recognizing construct is murinized or humanized. These terms are used when amino acid sequences from a foreign s are introduced into a con- struct of the invention.
The TCR of the invention may be provided as a single chain TCR (scTCR). A scTCR according to the invention shall comprise in one polypeptide chain a full or partial alpha chain sequence and a full or partial beta chain sequence, preferably connected via a peptide linker. A scTCR can comprise a polypeptide of a variable region of a first TCR chain (e.g., an alpha chain) and a polypeptide of an entire (full—length) second TCR chain (e.g., a beta chain), or vice versa.
Furthermore, the scTCR can optionally comprise one or more s which join the two or more polypeptides together. The linker can be, for instance, a peptide, which joins together two single chains, as described herein. Also provided is such a scTCR of the invention, which is fused to a human cytokine, such as IL-2, IL—7 or IL—15.
The antigen recognizing construct according to the invention can also be provided in the form of a multimeric x, sing at least two scTCR molecules, wherein said scTCR molecules are each fused to at least one biotin moiety, or other interconnecting mole- cule/linker, and wherein said scTCRs are interconnected by -streptavidin interaction to allow the formation of said multimeric complex. Similar approaches known in the art for the generation of multimeric TCR are also possible and included in this disclosure. Also provided are multimeric complexes of a higher order, comprising more than two scTCR of the inven- tion.
For the purposes of the present invention, a TCR is a moiety having at least one TCR alpha or gamma and/or TCR beta or delta variable domain. Generally, they comprise both a TCR al- pha variable domain and a TCR beta variable domain, alternatively both a TCR gamma varia- ble domain and a TCR delta variable domain. They may be aB/VS heterodimers or may be in single chain format. For use in adoptive therapy, an (16 or v6 heterodimeric TCR may, for e, be transfected as full length chains having both cytoplasmic and transmembrane domains. If desired, an introduced disulfide bond n residues of the tive constant domains may be present.
In a preferred embodiment, the n recognizing construct is a human TCR, or nt or derivative thereof. A human TCR or fragment or derivative thereof is a TCR, which com- prises over 50% of the ponding human TCR sequence. Preferably, only a small part of the TCR sequence is of artificial origin or derived from other species. It is known, however, that chimeric TCRs, e.g. derived from human origin with murine sequences in the nt ns, are advantageous. Particularly preferred are, therefore, TCRs in accordance with the present invention, which contains murine sequences in the extracellular part of their con- stant domains.
Thus, it is also preferred that the ive n recognizing uct is able to recognize its antigen in a human leucocyte antigen (HLA) dependent manner, preferably in a HLA—A02 dependent . The term "HLA dependent manner" in the context of the present inven— tion means that the antigen recognizing construct binds to the antigen only in the event that the antigenic peptide is presented by said HLA.
The antigen recognizing construct in accordance with the invention in one embodiment pref- erably induces an immune response, preferably wherein the immune response is ter- ized by the increase in interferon (IFN) y levels.
Also provided by the invention is a polypeptide comprising a functional portion of any of the TCRs (or functional variants thereof) described herein, for es, of any one of the TCRs as provided in the example section and table 2. The term "poly-peptide" as used herein in- cludes oligopeptides and refers to a single chain of amino acids ted by one or more peptide bonds. With respect to the inventive polypeptides, the functional portion can be any portion comprising contiguous amino acids of the TCR (or functional variant thereof), of which it is a part, provided that the functional portion specifically binds to the TAA antigen, preferably as disclosed herein in Table 1. The term ional portion" when used in refer- ence to a TCR (or functional variant thereof) refers to any part or fragment of the TCR (or functional variant thereof) of the invention, which part or nt retains the biological activity of the TCR (or functional variant thereof), of which it is a part (the parent TCR or parent functional variant thereof). Functional portions ass, for example, those parts of a TCR (or functional variant thereof) that retain the ability to specifically bind to the TAA antigen (in an HLA dependent manner), or detect, treat, or prevent cancer, to a similar ex- tent, the same extent, or to a higher extent, as the parent TCR (or functional t thereof).
In reference to the parent TCR (or functional variant f), the functional portion can comprise, for instance, about 10%, 25%, 30%, 50%, 68%, 80%, 90%, 95%, or more, of the parent TCR variable sequences (or functional variant thereof).
The functional portion can comprise additional amino acids at the amino or carboxy termi- nus of the portion, or at both termini, in which additional amino acids are not found in the amino acid sequence of the parent TCR or functional variant thereof. Desirably, the addition- al amino acids do not interfere with the biological function of the functional portion, e.g., ically binding to the TAA antigens; and/or having the ability to detect cancer, treat or prevent cancer, etc. More desirably, the additional amino acids enhance the biological activi— ty, as com-pared to the ical activity of the parent TCR or functional variant thereof.
In some instances, the construct of the invention may comprise one or two polypeptide chains sing a ces according to any of the SEQ ID NO: 39 to 86 (CDR sequences, constant and variable s and full length sequences), or functional fragments thereof, and further comprise(s) other amino acid sequences, e.g., an amino acid sequence encoding an immunoglobulin or a portion f, then the inventive n can be a fusion protein.
In this regard, the invention also provides a fusion protein comprising at least one of the in- ventive polypeptides bed herein along with at least one other polypeptide. The other polypeptide can exist as a separate polypeptide of the fusion protein, or can exist as a poly- peptide, which is expressed in frame (in tandem) with one of the inventive polypeptides de- scribed . The other ptide may include any peptidic or proteinaceous molecule, or a portion f, including, but not limited to an immunoglobulin, CD3, CD4, CD8, an MHC molecule, a CD1 molecule, e.g., CD1a, CD1b, CD1c, CD1d, etc.
The fusion protein can se one or more copies of the inventive polypeptide and/or one or more copies of the other polypeptide. For instance, the fusion protein can comprise 1, 2, 3, 4, 5, or more, copies of the inventive ptide and/or of the other polypeptide. Suitable methods of making fusion proteins are known in the art, and include, for example, i- nant methods. In some embodiments of the invention, the TCRs (and functional portions and WO 58103 functional variants thereof), polypeptides, and proteins of the invention may be expressed as a single protein comprising a linker peptide g the or chain and the [3 chain, and linking the v chain and the 8 chain. In this regard, the TCRs (and functional variants and functional ns thereof), polypeptides, and proteins of the invention comprising the amino acid se- quences of the variable regions of the TCR of the invention and may further comprise a linker pep-tide. The linker e may advantageously tate the expression of a recombinant TCR (including functional portions and functional variants thereof), polypeptide, and/or pro- tein in a host cell. The linker e may comprise any suitable amino acid sequence. Linker sequences for single chain TCR constructs are well known in the art. Such a single chain con- struct may further comprise one, or two, constant domain ces. Upon expression of the construct including the linker peptide by a host cell, the linker peptide may also be cleaved, resulting in separated or and B chains, and separated y and 8 chain.
As already mentioned above, the binding functionality of the TCR of the invention may be ed in the framework of an antibody. For example, CDR sequences of the TCR of the invention, possibly including additional 3, 2 or 1 N and/or C terminal framework residues, may be directly grafted into an antibody variable heavy/light chain sequence. The term "anti- body" in its various grammatical forms is used herein to refer to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that con- tain an antigen-binding site or a paratope. Such les are also referred to as "antigen binding fragments" of immunoglobulin molecules. The invention further provides an anti— body, or antigen binding portion thereof, which specifically binds to the antigens described herein. The antibody can be any type of immunoglobulin that is known in the art. For in- stance, the antibody can be of any isotype, e.g., IgA, IgD, IgE, IgG, IgM, etc. The antibody can be monoclonal or polyclonal. The antibody can be a naturally-occurring antibody, e.g., an antibody isolated and/or purified from a mammal, e.g., mouse, rabbit, goat, horse, chicken, hamster, human, etc. atively, the antibody can be a genetically-engineered antibody, e. g., a humanized antibody or a chimeric dy. The antibody can be in monomeric 0r pol- ymeric form.
The term "antibody" includes, but is not limited to, cally engineered or otherwise modified forms of immunoglobulins, such as intrabodies, chimeric antibodies, fully human anti- bodies, zed antibodies (e.g. ted by rafting"), antibody fragments, and heteroconjugate antibodies (e.g., bispecific antibodies, diabodies, triabodies, tetra-bodies, etc.). The term "antibody" includes cys-diabodies and minibodies. Thus, each and every em- bodiment provided herein in regard to "antibodies", or "antibody like constructs" is also envi- sioned as, bi—specific antibodies, diabodies, scFv fragments, ic antibody receptor (CAR) constructs, diabody and/or minibody embodiments, unless itly d other- wise. The term "antibody" es a polypeptide of the immunoglobulin family or a p- tide comprising fragments of an immunoglobulin that is e of non-covalently, reversi- bly, and in a specific manner binding a corresponding antigen, preferably the TAA of the in- ven-tion, as disclosed herein. An exemplary dy structural unit comprises a tetramer. In some embodiments, a full length antibody can be composed of two identical pairs of polypep- tide chains, each pair having one "light" and one "heavy" chain (connected through a disul- fide bond). Antibody ure and es are well known to the skilled artisan (for example from Janeway's Immunobiology, 9th edition, 2016).
The recognized immunoglobulin genes of mammals include the kappa, lambda, alpha, gam- ma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin var- iable region genes (for more information on immunoglobulin genes see the international Im- MunoGeneTics information system®, Lefranc M-P et al, Nucleic Acids Res. 2015 Jan;43(Database issue):D413-22; and http://www.imgt.org/). For full-length chains, the light chains are classified as either kappa or . For full-length chains, the heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobu- lin classes, IgG, IgM, IgA, IgD, and IgE, respectively. The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these regions of light and heavy chains respectively. As used in this invention, an ody" en- compasses all variations of dy and fragments thereof. Thus, within the scope of this concept are full length antibodies, chimeric antibodies, humanized antibodies, single chain dies (scFv), Fab, Fab', and multimeric versions of these fragments (e.g., F(ab')2) with the same, ially the same or similar binding specificity. In some embodiments, the anti— body binds specifically to a peptide TAA of the invention. Preferred antigen recognizing con- structs according to the invention include an antibody heavy chain, preferably the variable domain thereof, or an antigen binding fragment thereof, and/or an antibody light chain, preferably the variable domain thereof, or an antigen binding fragment thereof. Similarly, disulfide-stabilized variable region fragments (dst) can be prepared by recombinant DNA logy, antibody fragments of the invention, however, are not limited to these exemplary types of antibody fragments. Also, the antibody, or antigen binding portion thereof, can be modified to comprise a detectable label, such as, for instance, a radioisotope, a fluorophore (e.g., fluorescein isothiocyanate (FITC), phycoerythrin (PE)), an enzyme (e.g., alkaline phos- phatase, horseradish peroxidase), and element particles (e.g., gold particles). In some in- s, the TCR CDR3 sequence may be slightly modified, but ably by not more than 3 amino acid residues, preferably only two and most preferably only one amino acid position, as compared to the CDR3 sequences provided in SEQ ID Nos 44, 52, 60, 68, 76 and 84. Pref- , the dies comprise the CDR3, preferably all of CDR1 to CDR3 regions in the combination, as indicated for the TCR of the invention in table 2, in each case independently, optionally with not more than three or two, ably one, amino acid substitution(s), inser- tion(s) and/or deletion(s) compared to these sequences.
Suitable methods of making antibodies are known in the art. For instance, standard hybrid- oma methods are described in, e.g., Kohler and Milstein, Eur. J. l, 5, 51 1-519 (1976), Harlow and Lane (eds.), Antibodies: A Laboratory Manual, CSH Press , and CA. y et al. (eds.), biology, 8 Ed., Garland Publishing, New York, NY (201 1)).
Alternatively, other methods, such as EBV—hybridoma methods (Haskard and Archer, J. Im- munol. Methods, 74(2), 361—67 (1984), and Roder et al, Methods Enzymol, 121, 140-67 (1986)), and bacteriophage vector expression s (see, e.g., Huse et al., Science, 246, 1 (1989)) are known in the art. Further, methods of producing dies in non- human animals are described in, e.g., US. Patents 5,545,806, 5,569,825, and 5,714,352, and US. Patent ation Publication No. 2002/0197266.
Some embodiments of the ion also pertain to TCRs, or functional fragments and poly- peptides thereof, which are soluble TCRs. As used herein, the term "soluble T—cell receptor" refers to heterodimeric truncated variants of native TCRs, which comprise extracellular por— tions of the TCR a-chain and B-chain, for example linked by a disulfide bond, but which lack the transmembrane and cytosolic domains of the native protein. The terms "soluble T-cell receptor a-chain ce and soluble T-cell receptor B-chain sequence" refer to TCR a- chain and n sequences that lack the transmembrane and cytosolic domains. The se- quence (amino acid or nucleic acid) of the e TCR or -chain and B-chains may be identi- cal to the corresponding ces in a native TCR or may comprise t soluble TCR achain and B-chain sequences, as compared to the corresponding native TCR sequences. The term "soluble T-cell receptor" as used herein asses soluble TCRs with variant or non- variant soluble TCR n and n sequences. The variations may be in the variable or constant regions of the soluble TCR (x-chain and B-chain sequences and can include, but are not limited to, amino acid deletion, insertion, substitution mutations as well as changes to the nucleic acid sequence, which do not alter the amino acid sequence. Soluble TCR of the invention in any case retain the binding onality of their parent les.
DEFINITIONS As used herein and except as noted otherwise all terms are defined as given below.
The term "T-cell or" (abbreviated TCR) refers to a heterodimeric molecule comprising an alpha polypeptide chain (alpha chain) and a beta polypeptide chain (beta chain), wherein the heterodimeric receptor is e of binding to a peptide antigen presented by an HLA molecule.
The term "T-cell response" means the specific proliferation and activation of effector func- tions induced by a peptide in vitro or in vivo. For MHC class I restricted cytotoxic T—cells, effector functions may be lysis of peptide-pulsed, peptide-precursor pulsed or naturally pep— tide-presenting target-cells, secretion of nes, preferably Interferon-gamma, TNF-alpha, or IL-2 induced by peptide, secretion of effector molecules, preferably granzymes or perforins induced by peptide, or ulation.
The term "peptide" is used herein to designate a series of amino acid residues, connected one to the other typically by peptide bonds between the alpha-amino and carbonyl groups of the adj acent amino acids. The peptides are preferably 9 amino acids in length, but can be as short as 8 amino acids in length, and as long as 10, 11, or 12 or longer, and in case of MHC class II peptides (longer variants of the peptides of the description) they can be as long as 13, 14, 15, 16, 17, 18, 19 or 20 or more amino acids in length. rmore, the term "peptide" shall e salts of a series of amino acid residues, con- nected one to the other typically by peptide bonds between the amino and carbonyl groups of the adjacent amino acids. Preferably, the salts are pharmaceutical able salts of the peptides, such as, for example, the chloride or acetate (trifluoroacetate) salts. It has to be noted that the salts of the peptides according to the present description differ substantially from the peptides in their state(s) in vivo, as the es are not salts in vivo.
The term "peptide" shall also include "oligopeptide". The term "oligopeptide" is used herein to designate a series of amino acid residues, connected one to the other typically by peptide bonds between the alpha—amino and carbonyl groups of the adjacent amino acids. The length of the oligopeptide is not critical to the description, as long as the correct epitope or epitopes are maintained therein. The oligopeptides are typically less than about 30 amino acid resi- dues in length, and greater than about 15 amino acids in length.
The term "polypeptide" designates a series of amino acid residues, connected one to the other typically by peptide bonds between the alpha-amino and carbonyl groups of the adjacent amino acids. The length of the polypeptide is not critical to the description as long as the cor- 2017/056260 rect epitopes are maintained. In contrast to the terms peptide or oligopeptide, the term poly- peptide is meant to refer to molecules containing more than about 30 amino acid residues.
A peptide, oligopeptide, protein or cleotide coding for such a molecule is "immuno- genic" (and thus is an "immunogen" within the present description), if it is capable of induc- ing an immune response. In the case of the present description, immunogenicity is more spe- cifically defined as the ability to induce a T-cell response. Thus, an "immunogen" would be a molecule that is capable of inducing an immune response, and in the case of the present de- scription, a molecule capable of inducing a T-cell response. In another aspect, the immuno- gen can be the peptide, the complex of the peptide with MHC, oligopeptide, and/or protein that is used to raise specific antibodies or TCRs against it.
A class I T-cell "epitope" requires a short peptide that is bound to a class I MHC receptor, forming a ternary complex (MHC class I alpha chain, beta-2—microglobulin, and peptide) that can be recognized by a T-cell bearing a matching T-cell receptor binding to the MHC/peptide complex with appropriate affinity. Peptides g to MHC class I molecules are lly 8- 14 amino acids in , and most typically 9 amino acids in length.
The nucleotide sequence coding for a particular peptide, oligopeptide, or polypeptide may be naturally occurring or they may be synthetically constructed. Generally, DNA segments en- coding the peptides, ptides, and proteins of this description are assembled from cDNA fragments and short oligonucleotide linkers, or from a series of oligonucleotides, to provide a synthetic gene that is capable of being sed in a inant riptional unit com- prising regulatory elements derived from a microbial or viral operon.
As used herein the term "a nucleotide coding for (or encoding) a peptide" refers to a nucleo- tide sequence coding for the peptide including artificial ade) start and stop codons ible for the biological system the sequence is to be expressed by, for example, a den- dritic cell or another cell system useful for the production of TCRs.
As used herein the term "a nucleotide coding for (or encoding) a TCR" refers to one or more nucleotide sequences coding for the TCR including artificial (man-made) start and stop codons compatible for the biological system the sequence is to be expressed by, for example, T- cell or another cell system useful for the production of TCRs.
As used herein, reference to a nucleic acid sequence includes both single stranded and double stranded nucleic acid. Thus, for example for DNA, the specific sequence, unless the context indicates otherwise, refers to the single strand DNA of such sequence, the duplex of such se- quence with its complement (double stranded DNA) and the complement of such sequence.
The term "coding region" refers to that portion of a gene which either naturally or ly codes for the expression product of that gene in its natural genomic environment, i.e., the region coding in vivo for the native sion product of the gene.
The coding region can be derived from a non-mutated ("normal"), d or altered gene, or can even be derived from a DNA sequence, or gene, wholly synthesized in the tory using s well known to those of skill in the art of DNA synthesis.
The term "expression product" means the polypeptide or protein that is the natural transla- tion product of the gene and any nucleic acid sequence coding equivalents resulting from genetic code degeneracy and thus coding for the same amino acid(s).
The term "fragment", when referring to a coding sequence, means a portion of DNA compris— ing less than the complete coding region, whose expression t retains essentially the same biological function or activity as the expression product of the complete coding region.
The term "DNA segment" refers to a DNA polymer, in the form of a te fragment or as a component of a larger DNA construct, which has been derived from DNA isolated at least once in ntially pure form, i.e., free of contaminating nous materials and in a quantity or tration enabling identification, manipulation, and recovery of the segment and its component tide sequences by standard biochemical methods, for e, by using a g vector. Such segments are provided in the form of an open reading frame un- upted by internal non-translated sequences, or introns, which are typically t in eukaryotic genes. Sequences of non-translated DNA may be present downstream from the open reading frame, where the same do not interfere with lation or expression of the coding regions.
The term "primer" means a short nucleic acid sequence that can be paired with one strand of DNA and provides a free 3'—OH end at which a DNA polymerase starts sis of a deoxyri- bonucleotide chain.
The term "promoter" means a region of DNA involved in binding of RNA polymerase to initi- ate transcription.
The term "isolated" means that the material is removed from its original environment (e.g., the natural environment, if it is naturally occurring). For example, a naturally-occurring pol- ynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleo- tide or polypeptide, separated from some or all of the coexisting als in the natural sys- tem, is isolated. In an aspect, such polynucleotides are part of a vector and/or such polynu- cleotides or polypeptides are part of a composition, and still are ed in that such vector or composition is not part of its natural environment.
The polynucleotides, and recombinant or immunogenic polypeptides, disclosed in accord- ance with the present description may also be in "purified" form. The term "purified" does not require absolute purity; rather, it is intended as a relative definition, and can include preparations that are highly purified or preparations that are only partially purified, as those terms are understood by those of skill in the relevant art. For example, individual clones iso- lated from a cDNA library have been tionally purified to electrophoretic homogeneity.
Purification of starting material or natural material to at least one order of ude, pref- erably two or three orders, and more preferably four or five orders of magnitude is expressly contemplated. Furthermore, a claimed polypeptide which has a purity of preferably 99.999%, or at least 99.99% or 99.9%; and even desirably 99% by weight or greater is expressly en- compassed.
The nucleic acids and polypeptide expression products disclosed ing to the present ption, as well as sion vectors containing such nucleic acids and/or such polypep- tides, may be in "enriched form". As used herein, the term "enriched" means that the concen- tration of the material is at least about 2, 5, 10, 100, or 1000 times its natural concentration (for example), advantageously 0.01%, by weight, preferably at least about 0.1% by weight.
Enriched preparations of about 0.5%, 1%, 5%, 10%, and 20% by weight are also contemplated.
The sequences, constructs, vectors, clones, and other materials comprising the present description can advantageously be in enriched or isolated form. The term "active fragment" means a fragment, usually of a peptide, polypeptide or nucleic acid sequence, that generates an immune response (i.e., has immunogenic activity) when stered, alone or optionally with a le adjuvant or in a vector, to an animal, such as a mammal, for example, a rabbit or a mouse, and also including a human, such immune se taking the form of stimulat- ing a T—cell response within the recipient , such as a human. Alternatively, the "active fragment" may also be used to induce a T-cell response in vitro.
As used herein, the terms on", "segment" and "fragment", when used in relation to pol— ypeptides, refer to a continuous sequence of residues, such as amino acid es, which sequence forms a subset of a larger sequence. For example, if a polypeptide were subjected to treatment with any of the common endopeptidases, such as trypsin or chymotrypsin, the oli- gopeptides ing from such treatment would represent ns, segments or fragments of the starting polypeptide. When used in relation to cleotides, these terms refer to the ts produced by treatment of said cleotides with any of the endonucleases.
In accordance with the present description, the term "percent identity" or "percent identica ", when referring to a sequence, means that a sequence is compared to a claimed or described sequence after alignment of the sequence to be compared (the "Compared Sequence") with the described or claimed sequence (the "Reference Sequence"). The percent identity is then determined according to the following formula: percent identity = 100 [1 -(C/R)] n C is the number of differences between the Reference Sequence and the Compared Sequence over the length of alignment between the Reference Sequence and the Compared Sequence, wherein (i) each base or amino acid in the Reference Sequence that does not have a ponding aligned base or amino acid in the Compared Sequence and (ii) each gap in the Reference Sequence and (iii) each aligned base or amino acid in the Reference Sequence that is different from an aligned base or amino acid in the Compared Sequence, constitutes a difference and (iv) the alignment has to start at position 1 of the d sequences; and R is the number of bases or amino acids in the Reference Sequence over the length of the alignment with the Compared Sequence with any gap created in the Reference ce also being counted as a base or amino acid.
If an ent exists between the Compared Sequence and the Reference ce for which the percent ty as calculated above is about equal to or greater than a specified minimum Percent ty then the Compared Sequence has the specified minimum percent identity to the Reference Sequence even though alignments may exist in which the herein above calculated percent identity is less than the specified percent identity.
In the description, the term "homologous" refers to the degree of identity (see percent identi- ty above) between sequences of two amino acid ces, i.e., peptide or polypeptide se- quences. The aforementioned "homology" is determined by comparing two sequences aligned under optimal conditions over the sequences to be compared. Such a sequence homology can WO 58103 be calculated by ng an ent using, for example, the ClustalW algorithm. Common- ly available sequence analysis software, more specifically, Vector NTI, GENETYX or other tools are provided by public databases.
A person skilled in the art will be able to assess, whether T-cells induced by a variant of a spe- cific peptide will be able to cross-react with the peptide itself (Appay et al., 2006; Colombetti et al., 2006; Fong et al., 2001; Zaremba et al., 1997).
By a "variant" of the given amino acid sequence the inventors mean that the side chains of, for example, one or two of the amino acid residues are d (for example by replacing them with the side chain of another naturally occurring amino acid residue or some other side chain) such that the peptide is still able to bind to an HLA molecule in substantially the same way as a peptide having the given amino acid sequence selected from the group consisting of SEQ ID NO:1 to SEQ ID NO:24. For example, a peptide may be modified so that it at least maintains, if not es, the ability to interact with and bind to the binding groove of a suitable MHC molecule, such as HLA-A*02 or -DR, and in that way it at least maintains, if not improves, the ability to bind to the TCR of activated T-lymphocytes. Similarly, a TCR may be modified so that it at least maintains, if not improves, the ability to interact with and bind to a suitable MHC molecule/KVLEHVVRV (SEQ ID NO:1) complex, such as HLA-A*02 or - DR, and in that way it at least maintains, if not improves, the ability to activate s.
These T-cells can subsequently cross-react with cells and kill cells that express a polypeptide that contains the natural amino acid sequence of the cognate peptide, such as KVLEHVVRV (SEQ ID NO:1), as defined in the aspects of the description. As can be d from the scien- tific literature and databases (Rammensee et al., 1999; Godkin et al., 1997), certain ons of HLA binding peptides are typically anchor residues forming a core sequence fitting to the binding motif of the HLA receptor, which is defined by polar, electrophysical, hydrophobic and l properties of the polypeptide chains constituting the binding groove. In an aspect, one skilled in the art would have the ability given the ngs of the description to modify the amino acid sequence of a TCR, by maintaining the known anchor es, and would be able to determine whether such TCR variants maintain the y to bind MHC class I or II molecules/KVLEHVVRV (SEQ ID NO:1) complexes. The TCR variants of the ption re- tain the y to bind MHC class I or II molecules/KVLEHVVRV (SEQ ID NO:1) complexes.
T-cells expressing the TCR variants of the description can subsequently kill cells that express a polypeptide ning the natural amino acid ce of the e peptide, such as VRV (SEQ ID NO:1).
In an aspect, the peptides or TCRs disclosed herein can be modified by the substitution of one or more es at different, possibly selective, sites within the peptide chain, if not oth- erwise stated. Preferably those substitutions are located at the end of the amino acid chain of said peptide. For TCRs, preferably those substitutions are located at variable domains of TCR alpha chain and TCR beta chain. Such substitutions may be of a conservative nature, for ex- ample, where one amino acid is replaced by an amino acid of similar structure and character- istics, such as where a hydrophobic amino acid is replaced by another hydrophobic amino acid. Even more conservative would be replacement of amino acids of the same or similar size and chemical nature, such as where leucine is replaced by isoleucine. In studies of se- quence ions in families of naturally occurring homologous proteins, certain amino acid substitutions are more often tolerated than others, and these are often show correlation with similarities in size, charge, polarity, and hydrophobicity between the original amino acid and its replacement, and such is the basis for defining "conservative substitutions." Conservative substitutions are herein defined as exchanges within one of the following five groups: Group 1-small aliphatic, nonpolar or slightly polar residues (Ala, Ser, Thr, Pro, Gly); Group 2—polar, negatively charged residues and their amides (Asp, Asn, Glu, Gln); Group 3- polar, positively charged residues (His, Arg, Lys); Group 4-large, aliphatic, nonpolar residues (Met, Leu, Ile, Val, Cys); and Group 5—large, aromatic residues (Phe, Tyr, Trp).
Less conservative substitutions might involve the replacement of one amino acid by another that has similar characteristics but is at different in size, such as replacement of an alanine by an isoleucine residue. Highly non-conservative replacements might involve substi- tuting an acidic amino acid for one that is polar, or even for one that is basic in ter.
Such "radica " substitutions , however, be dismissed as potentially ctive since chemical s are not totally predictable and radical substitutions might well give rise to serendipitous effects not otherwise predictable from simple chemical principles.
In an aspect, such substitutions may involve structures other than the common L-amino ac- ids. Thus, o acids might be substituted for the L-amino acids commonly found in the antigenic peptides of the description and yet still be encompassed by the disclosure herein. In addition, non-standard amino acids (i.e., other than the common lly occurring pro— teinogenic amino acids) may also be used for substitution purposes to produce immunogens and immunogenic polypeptides according to the present description.
If substitutions at more than one position are found to result in a peptide with substantially equivalent or greater antigenic ty as defined below, then ations of those substi- tutions will be tested to determine if the combined substitutions result in additive or syner- gistic s on the antigenicity of the e. At most, no more than 4 positions within the peptide would be simultaneously substituted.
As used herein, the term e" or "human," when ing to an antigen recognizing con- struct, or a TCR, or any component of a TCR described herein (e.g., complementarity deter- mining region (CDR), variable region, constant region, or chain, and/or [3 chain), means a TCR (or component thereof), which is derived from a mouse or a human unrearranged TCR locus, respectively.
T-CELL RECEPTORS (TCRS) In a preferred embodiment, the description relates a TCR comprising a TCR alpha chain shown in Table 2, and variants thereof; and a TCR beta chain shown in Table 2, and ts thereof. In an aspect, a TCR bed herein has the ability to bind or specifically bind to a molecule of the human major histocompatibility complex (MHC) I/ KVLEHVVRV (SEQ ID NO:1)/complex or to class II/KVLEHVVRV (SEQ ID NO:1)/complex.
Table 2: Representative TCRs according to present description TCR ID Description Sequence alpha chain MEKMLECAFIVLWLQLGWLSGEDQVTQSPEALRLQEGESSS LNCSYTVSGLRGLFWYRQDPGKGPEFLFTLYSAGEEKEKERL KATLTKKESFLHITAPKPEDSATYLCAVQGENSGYSTLTFGKG TMLLVSPDIQNPDPAVYQLRDSKSSDKSVCLFI‘DFDSQTNVS QSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANA FNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGF VAGFNLLMTLRLWSS (SEQ ID NO:39) L segment CAFIVLWLQLGWLSG (SEQ ID NO:40) (TRAV20) V chain MEKMLECAFIVLWLQLGWLSGEDQVTQSPEALRLQEGESSS R20P1H7_ (TRAV20) LNCSYTVSGLRGLFWYRQDPGKGPEFLPTLYSAGEEKEKERL alpha Cham KATLTKKESFLHITAPKPEDSATYLCAVQ (SEQ ID NO:41) CDR1 VSGLRG (SEQ ID NO:42) CDR2 LYS (SEQ ID NO:43) CDR3 CAVQGENSGYSTLTF (SEQ ID NO:44) J segment NSGYSTLTFGKGTMLLVSP (SEQ ID NO:45) (TRAJ11) Constant re- DIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDV gion (TRAC) YITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPE DTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVA GFNLLMTLRLWSS (SEQ ID NO:46) beta chain GYVVLCLLGAGPLEAQVTQNPRYLITVTGKKLTVTC SQNMNHEYMSWYRQDPGLGLRQIYYSMNVEVTDKGDVPEG YKVSRKEKRNFPLILESPSPNQTSLYFCASSLGPGLAAYNEQF FGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLA TGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRY CLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRA KPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKAT LYAVLVSALVLMAMVKRKDSRG (SEQ ID NO:47) L segment MGPQLLGYVVLCLLGAGPL (SEQ ID NO:48) V chain MGPQLLGYVVLCLLGAGPLEAQVTQNPRYLITVTGKKLTVTC R20P1H7 _ (TRBV27) SQNMNHEYMSWYRQDPGLGLRQIYYSMNVEVTDKGDVPEG beta Chm YKVSRKEKRNFPLILESPSPNQTSLYFCASSL (SEQ ID NO:49) CDR1 MNHEY (SEQ ID NO:50) CDR2 SMNVEV (SEQ ID NO:51) CDR3 CASSLGPGLAAYNEQF (SEQ ID NO:52) J chain YNEQFFGPGTRLTVL (SEQ ID NO:53) (TRBJ2-1) constant re- EDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVEL gion (TRBC2) SWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSA TFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA WGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVL MAMVKRKDSRG (SEQ ID NO:54) alpha chain MKTFAGFSFLFLWLQLDCMSRGEDVEQSLFLSVREGDSSVIN CTYTDSSSTYLYWYKQEPGAGLQLLTYIFSNMDMKQDQRLTV KHLSLRIADTQTGDSAIYFCAEYSSASKIIFGSGTRLS IRPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDS DVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSII PEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLK VAGFNLLMTLRLWSS (SEQ ID NO:55) L segment MKTFAGFSFLFLWLQLDCMSR (SEQ ID NO:56) (TRAV5) V chain MKTFAGFSFLFLWLQLDCMSRGEDVEQSLFLSVREGDSSVIN R P11)7 5, a1_ (TRAV5) CTYTDSSSTYLYWYKQEPGAGLQLLTYIFSNMDMKQDQRLTV pha Cham LLNKKDKHLSLRIADTQTGDSAIYFCAE (SEQ ID NO:57) CDR1 Y (SEQ ID NO:58) CDR2 IFS (SEQ ID NO:59) CDR3 CAEYSSASKIIF ((SEQ ID NO:60) J segment YSSASKIIFGSGTRLSIRP (SEQ ID NO:61) (TRAJ3) Constant re- NIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDV gion (TRAC) YITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPE DTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVA GFNLLMTLRLWSS (SEQ ID NO:62) beta chain MGSWTLCCVSLCILVAKHTDAGVIQSPRHEVTEMGQEVTLR CKPISGHDYLFWYRQTMMRGLELLIYFNNNVPIDDSGMPED PNASFSTLKIQPSEPRDSAVYFCASRANTGELFFGEG SRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFY PDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSS RLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVT QIVSAEAWGRADCGFI‘SESYQQGVLSATILYEILLGKATLYAV LVSALVLMAMVKRKDSRG (SEQ ID NO:63) L t MGSWTLCCVSLCILVAKHT (SEQ ID N0:64) (TRBV12—4) V chain MGSWTLCCVSLCILVAKHTDAGVIQSPRHEVTEMGQEVTLR R7P1D5 beta (TRBV12—4) CKPISGHDYLFWYRQTMMRGLELLIYFNNNVPIDDSGMPED chain RFSAKMPNASFSTLKIQPSEPRDSAVYFCAS (SEQ ID NO:65) CDR1 SGHDY (SEQ ID NO:66) CDR2 FNNNVP (SEQ ID NO:67) CDR3 CASRANTGELFF (SEQ ID NO:68) J chain NTGELFFGEGSRLTVL (SEQ ID NO:69) constant re- EDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVEL gion (TRBC2) SWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSA TFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA WGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVL MAMVKRKDSRG (SEQ ID NO:70) alpha chain MLTASLLRAVIASICVVSSMAQKVTQAQTEISVVEKEDVTLDC VYETRDTTYYLFWYKQPPSGELVFLIRRNSFDEQNEISGRYS WNFQKSTSSFNFI‘ITASQVVDSAVYFCALSEGNSGNTPLVFGK GTRLSVIANIQNPDPAVYQLRDSKSSDKSVCLFI‘DFDSQTNVS QSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANA FNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGF RILLLKVAGFNLLMTLRLWSS (SEQ ID NO:71) L segment MLTASLLRAVIASICVVSSM (SEQ ID NO:72) (TRAV19) V chain MLTASLLRAVIASICVVSSMAQKVTQAQTEISVVEKEDVTLDC R10P2G12 _ (TRAV19) TI‘YYLFWYKQPPSGELVFLIRRNSFDEQNEISGRYS alpha Cham WNFQKSTSSFNFTITASQVVDSAVYFCALSE (SEQ ID NO:73) CDR1 TRDTIYY (SEQ ID NO:74) CDR2 RNSF (SEQ ID NO:75) CDR3 CALSEGNSGNTPLVF (SEQ ID NO:76) J segment LVFGKGTRLSVIA (SEQ ID NO:77) (TRAJ29) Constant re- NIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDV gion (TRAC) YITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPE DTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVA GFNLLMTLRLWSS (SEQ ID NO:78) beta chain MGIRLLCRVAFCFLAVGLVDVKVTQSSRYLVKRTGEKVFLEC VQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDIPEG YSVSREKKERFSLILESASTNQTSMYLCASSLSSGSHQETQYF GPGTRLLVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLAT GFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYC LSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKP VTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLY AVLVSALVLMAMVKRKDSRG (SEQ ID NO:79) L segment MGIRLLCRVAFCFLAVGLV (SEQ ID NO:80) V chain MGIRLLCRVAFCFLAVGLVDVKVTQSSRYLVKRTGEKVFLEC :ffigube (TRBV28) VQDMDHENMFWYRQDPGLGLRLIYFSYDVKMKEKGDIPEG YSVSREKKERFSLILESASTNQTSMYLCASSL (SEQ ID NO:81) CDR1 MDHEN (SEQ ID NO:82) CDR2 SYDVKM (SEQ ID NO:83) CDR3 CASSLSSGSHQETQYF (SEQ ID NO:84) J chain QETQYFGPGTRLLVL (SEQ ID NO:85) (TRBJ2-5) constant re- EDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVEL gion (TRBC2) SWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSA RNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA WGRADCGFI‘SESYQQGVLSATILYEILLGKATLYAVLVSALVL MAMVKRKDSRG (SEQ ID NO:86) The alpha and beta chains of alpha/beta TCR's, and the gamma and delta chains of gam- ma/delta TCRS, are lly regarded as each having two "domains", namely variable and constant domains. The variable domain consists of a concatenation of variable region (V), and joining region (J). The le domain may also include a leader region (L). Beta and delta chains may also include a diversity region (D). The alpha and beta constant domains may also include C-terminal transmembrane (TM) domains that anchors the alpha and beta chains to the cell membrane.
In the t description, the term "TCR alpha variable domain" ore refers to the con— catenation of the TCR alpha V (TRAV) region without leader region (L), and the TCR alpha J (TRAJ) region; and the term "TCR alpha constant domain" refers to the extracellular TRAC , or to a C-terminal truncated TRAC sequence, and optionally an alpha transmembrane domain (VIGFRILLLKVAGFNLLMTL (SEQ ID NO: 87)).
Likewise the term "TCR beta variable " refers to the concatenation of the TCR beta V (TRBV) region without leader region (L), and the TCR beta D/J (TRBD/TRBJ) region; and the term TCR beta constant domain refers to the ellular TRBC region, or to a C— terminal truncated TRBC sequence, and optionally a beta transmembrane domain (TILYEILLGKATLYAVLVSALVL (SEQ ID NO:88)).
With t to gamma/delta TCRs, the term "TCR gamma variable domain" as used herein refers to the concatenation of the TCR gamma V (TRGV) without leader region (L), and TCR gamma J (TRGJ) regions; and the term TCR gamma nt domain refers to the extracellu- lar TRGC region, or to a C-terminal truncated TRGC sequence. Likewise the term "TCR delta variable domain" refers to the concatenation of the TCR delta V (TRDV) without leader re- gion (L), and TCR delta D/J (TRDD/TRDJ) s; and the term TCR delta constant domain refers to the extracellular TRDC region, or to a C-terminal truncated TRDC sequence.
In an embodiment, a TCR of the present description comprises or consists of a TCR alpha chain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 90%, 95%, 96%, 97%, 98%, or 99% identical, to a TCR alpha chain shown in Table 2. The TCR alpha chains shown in Table 2 contain a leader (L) segment; a V chain; three complimentary determining s (CDR1, CDR2 and CDR3); a joining region (J) and a constant region, as defined in Table 2.
In an embodiment, a TCR of the present description comprises or consists of a TCR alpha variable domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 90%, 95%, 96%, 97%, 98%, or 99% identical, to a TCR alpha variable domain shown in Table 2.
In an embodiment, a TCR of the present description comprises or ts of, a TCR alpha constant domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 75% identical, to a TCR alpha constant domain shown in Table 2.
In an embodiment, a TCR of the present description comprises, or consists of, a TCR alpha variable domain comprising at least one alpha chain complementarity determining region (CDR) ed from the group consisting of an alpha chain CDR1, CDR2 and CDR3 shown in Table 2. In a preferred embodiment, the TCR alpha variable domain comprises an alpha chain CDR3 shown in Table 2. In another preferred embodiment, the TCR alpha variable domain comprises an alpha chain CDR1, CDR2 and CDR3 shown in Table 2.
In a ularly preferred embodiment, a TCR of the present description ses, or con- sists of, a TCR alpha variable domain having at least 90% sequence identity to a TCR alpha variable domain of Table 2, and comprises CDR1, CDR2 and CDR3 of the same alpha variable domain of Table 2.
In an embodiment, a TCR of the present description comprises, or consists of, a TCR beta chain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 90%, 95%, 96%, 97%, 98%, or 99% identical, to a TCR beta chain shown in Table 2. The TCR beta chains shown in Table 2 contain a leader (L) segment; a V chain; three com- plimentary determining regions (CDR1, CDR2 and CDR3); a joining region (J) and a constant region, as defined in Table 2.
In an embodiment, a TCR of the t description comprises, or consists of, a TCR beta variable domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 90%, 95%, 96%, 97%, 98%, or 99% cal, to a TCR beta variable do— main shown in Table 2.
In an embodiment, a TCR of the present description comprises, or consists of, a TCR beta constant domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 75% identical, to a TCR beta constant domain shown in Table 2.
In an embodiment, a TCR of the present description comprises, or consists of, a TCR beta variable domain comprising at least one beta chain complementarity determining region (CDR) selected from the group consisting of a beta chain CDR1, CDR2 and CDR3 shown in Table 2. In a preferred ment, the TCR beta variable domain comprises a beta chain CDR3 shown in Table 2. In another preferred embodiment, the TCR beta variable domain comprises a beta chain CDR1, CDR2 and CDR3 shown in Table 2.
In a particularly preferred embodiment, a TCR of the t description comprises, or con- sists of, a TCR beta variable domain having at least 90% or 95% sequence ty to a TCR beta variable domain of Table 2, and comprises CDR1, CDR2 and CDR3 of the same TCR beta variable domain of Table 2.
The alpha chain le domain may comprise one or more alpha CDR domains having one, two, three or four amino acid tutions relative to the corresponding CDR sequence shown in Table 2. Likewise, the beta chain variable domain may comprise one or more beta CDR s having one, two, three or four amino acid substitutions relative to the corre- sponding beta CDR ce shown in Table 2.
The TCR alpha chain and TCR beta chain may be fused to form a single chain TCR. Alterna- tively, the TCR alpha and beta chains may be expressed as separate proteins which can be assembled into a heterodimer.
In one embodiment, any TCR alpha chain of Table 2 is paired with any TCR beta chain of Table 2 to produce a TCR that specifically binds to a 3 e-HLA molecule com- pleX.
TCR R20P1Hz In one embodiment, a TCR of the present description comprises, or consists of, the alpha chain and/or beta chain of TCR R20P1H7, corresponding to SEQ ID NOs:39 and 47, respec- tively. 2017/056260 The TCR alpha variable domain of TCR R20P1H7 comprises, or alternatively consists of, amino acids 22 to 133 of SEQ ID NO:39; the TCR alpha constant domain of TCR R20P1H7 comprises, or alternatively consists of, amino acids 5 of SEQ ID NO:39; the TCR beta variable domain of TCR R20P1H7 comprises, or alternatively consists of, amino acids 20 to 135 of SEQ ID NO:47; and the TCR beta constant domain comprises, or alternatively consists of, amino acids 136 to 315 of SEQ ID NO:47.
In a particular embodiment, a TCR of the present ption comprises a TCR alpha chain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, a- bly 90%, 95%, 96%, 97%, 98%, or 99% identical, to the TCR alpha chain of SEQ ID NO:39.
In another embodiment, a TCR of the present description ses a TCR alpha le domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identi- cal, preferably 90%,95%, 96%, 97%, 98%, or 99% identical, to the TCR alpha variable domain of SEQ ID NO:39.
In an embodiment, a TCR of the present description comprises a TCR alpha constant domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% cal, prefer- ably 75% identical, to the TCR alpha constant domain of SEQ ID NO:39.
In an embodiment, a TCR of the present description comprises a TCR alpha variable domain comprising at least one alpha chain complementarity determining region (CDR) selected from the group ting of the alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:39. In a preferred embodiment, the TCR alpha variable domain comprises the alpha chain CDR3 of SEQ ID NO:39. In another preferred embodiment, the TCR alpha variable domain comprises the alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:39.
In a particularly red ment, a TCR of the present description ses a TCR alpha variable domain having at least 90% or 95% sequence identity to the TCR alpha varia- ble domain of SEQ ID NO:39, and comprises the CDR1, CDR2 and CDR3 of SEQ ID NO:39.
In another particular embodiment, a TCR of the present description comprises a TCR beta chain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 90%, 95%, 96%, 97%, 98%, or 99% identical, to the TCR beta chain of SEQ ID NO:47.
In an embodiment, a TCR of the present description comprises a TCR beta variable domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, prefer- ably 90%, 95%, 96%, 97%, 98%, or 99% identical, to the TCR beta variable domain of SEQ ID NO:47.
In an embodiment, a TCR of the present description comprises a TCR beta constant domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, prefer- ably 75% identical, to the TCR beta constant domain of SEQ ID NO:47.
In an embodiment, a TCR of the present description comprises a TCR beta variable domain comprising at least one beta chain complementarity determining region (CDR) selected from the group consisting of the beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:47. In a pre- ferred embodiment, the TCR beta variable domain comprises the beta chain CDR3 of SEQ ID NO:47. In another preferred embodiment, the TCR beta variable domain comprises the beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:47.
In a particularly preferred embodiment, a TCR of the present description comprises a TCR beta variable domain having at least 90% or 95% sequence identity to the TCR beta variable domain of SEQ ID NO:47, and comprises CDR1, CDR2 and CDR3 of SEQ ID NO:47.
The alpha chain variable domain may comprise one or more alpha CDR domains having one, two, three or four amino acid substitutions relative to the corresponding CDR sequence of SEQ ID NO:39. Likewise, the beta chain variable domain may comprise one or more beta CDR domains having one, two, three or four amino acid substitutions relative to the corre- sponding beta CDR sequence of SEQ ID NO:47.
TCR R2P1D5 In one embodiment, a TCR of the present description comprises, or consists of, the alpha chain and/or beta chain of TCR R7P1D5, corresponding to SEQ ID NOs:55 and 63, - tively.
The TCR alpha variable domain of TCR R7P1D5 comprises, or alternatively consists of, amino acids 22 to 131 of SEQ ID NO:55; the TCR alpha nt domain of TCR R7P1D5 comprises, or alternatively consists of, amino acids 132 to 272 of SEQ ID NO:55; the TCR beta variable domain of TCR R7P1D5 comprises, or alternatively consists of, amino acids 20 to 131 of SEQ ID NO:63; and the TCR beta constant domain comprises, or alternatively consists of, amino acids 132 to 310 of SEQ ID NO:63.
In a particular embodiment, a TCR of the present description comprises a TCR alpha chain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, prefera- bly 90%, 95%, 96%, 97%, 98%, or 99% identical, to the TCR alpha chain of SEQ ID NO:55.
In another embodiment, a TCR of the present description comprises a TCR alpha le domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identi- cal, preferably 90%, 95%, 96%, 97%, 98%, or 99% identical, to the TCR alpha variable do- main of SEQ ID NO:55.
In an embodiment, a TCR of the present description comprises a TCR alpha constant domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% cal, prefer— ably 75% identical, to the TCR alpha constant domain of SEQ ID NO:55.
In an ment, a TCR of the t ption comprises a TCR alpha le domain comprising at least one alpha chain complementarity determining region (CDR) selected from the group consisting of the alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:55. In a preferred embodiment, the TCR alpha variable domain comprises the alpha chain CDR3 of SEQ ID NO:55. In another preferred embodiment, the TCR alpha variable domain comprises the alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:55.
In a particularly preferred embodiment, a TCR of the present description ses a TCR alpha variable domain having at least 90% or 95% sequence identity to the TCR alpha varia- ble domain of SEQ ID NO:55, and comprises the CDR1, CDR2 and CDR3 of SEQ ID NO:55.
In another ular embodiment, a TCR of the present description comprises a TCR beta chain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 90% or 95% identical, to the TCR beta chain of SEQ ID NO:63.
In an embodiment, a TCR of the present description ses a TCR beta variable domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, prefer- ably 90%, 95%, 96%, 97%, 98%, or 99% cal, to the TCR beta variable domain of SEQ ID NO:63.
In an embodiment, a TCR of the present description comprises a TCR beta constant domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, prefer- ably 75% identical, to the TCR beta constant domain of SEQ ID NO:63.
In an embodiment, a TCR of the present ption comprises a TCR beta variable domain comprising at least one beta chain complementarity determining region (CDR) selected from the group consisting of the beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:63. In a pre- ferred embodiment, the TCR beta le domain comprises the beta chain CDR3 of SEQ ID NO:63. In another preferred embodiment, the TCR beta variable domain comprises the beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:63.
In a particularly preferred embodiment, a TCR of the t description comprises a TCR beta variable domain having at least 90% or 95% sequence identity to the TCR beta variable domain of SEQ ID NO:63, and comprises CDR1, CDR2 and CDR3 of SEQ ID NO:63.
The alpha chain variable domain may comprise one or more alpha CDR domains having one, two, three or four amino acid substitutions relative to the corresponding CDR sequence of SEQ ID NO:55. Likewise, the beta chain variable domain may comprise one or more beta CDR domains having one, two, three or four amino acid substitutions relative to the corre- sponding beta CDR sequence of SEQ ID NO:63.
TCR R10P2G12 In one embodiment, a TCR of the present description ses, or consists of, the alpha chain and/or beta chain of TCR R10P2G12, corresponding to SEQ ID NOs:71 and 79, respec- tively.
The TCR alpha le domain of TCR R10P2G12 comprises, or alternatively consists of, amino acids 21 to 136 of SEQ ID NO:71; the TCR alpha constant domain of TCR R10P2G12 comprises, or alternatively consists of, amino acids 137 to 277 of SEQ ID NO:71; the TCR beta variable domain of TCR 12 comprises, or alternatively consists of, amino acids 20 to 134 of SEQ ID NO:79; and the TCR beta constant domain comprises, or alternatively consists of, amino acids 135 to 313 of SEQ ID NO:79.
In a particular ment, a TCR of the present description comprises a TCR alpha chain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, prefera— bly 90%, 95%, 96%, 97%, 98%, or 99% identical, to the TCR alpha chain of SEQ ID NO:71.
In another embodiment, a TCR of the present ption comprises a TCR alpha variable domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identi- cal, preferably 90%, 95%, 96%, 97%, 98%, or 99% identical, to the TCR alpha variable do- main of SEQ ID NO:71.
In an embodiment, a TCR of the present description comprises a TCR alpha constant domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, — ably 75% identical, to the TCR alpha constant domain of SEQ ID NO:71.
In an ment, a TCR of the present description comprises a TCR alpha variable domain comprising at least one alpha chain complementarity determining region (CDR) selected from the group consisting of the alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:71. In a preferred embodiment, the TCR alpha variable domain comprises the alpha chain CDR3 of SEQ ID NO:71. In another preferred embodiment, the TCR alpha variable domain comprises the alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:71.
In a particularly preferred embodiment, a TCR of the present description comprises a TCR alpha variable domain having at least 90% or 95% sequence identity to the TCR alpha varia- ble domain of SEQ ID NO:71, and comprises the CDR1, CDR2 and CDR3 of SEQ ID NO:71.
In another particular embodiment, a TCR of the present description comprises a TCR beta chain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, preferably 90%, 95%, 96%, 97%, 98%, or 99% identical, to the TCR beta chain of SEQ ID NO:79.
In an embodiment, a TCR of the present description comprises a TCR beta variable domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, prefer- ably 90%, 95%, 96%, 97%, 98%, or 99% cal, to the TCR beta variable domain of SEQ ID NO:79.
In an embodiment, a TCR of the present ption comprises a TCR beta constant domain at least 75%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical, prefer- ably 75% identical, to the TCR beta constant domain of SEQ ID NO:79.
In an embodiment, a TCR of the present description comprises a TCR beta variable domain comprising at least one beta chain complementarity ining region (CDR) selected from the group consisting of the beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:79. In a pre- ferred embodiment, the TCR beta le domain comprises the beta chain CDR3 of SEQ ID NO:79. In another preferred embodiment, the TCR beta le domain comprises the beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:79.
In a particularly preferred embodiment, a TCR of the present description comprises a TCR beta variable domain having at least 90% or 95% sequence identity to the TCR beta variable domain of SEQ ID NO:79, and comprises CDR1, CDR2 and CDR3 of SEQ ID NO:79.
The alpha chain variable domain may se one or more alpha CDR domains having one, two, three or four amino acid substitutions relative to the corresponding CDR sequence of SEQ ID NO:71. Likewise, the beta chain variable domain may comprise one or more beta CDR domains having one, two, three or four amino acid substitutions ve to the corre- sponding beta CDR sequence of SEQ ID NO:79.
In a further red embodiment, a TCR of the present ption specifically binds to a MAG—003 peptide-HLA molecule complex, wherein the MAG—003 peptide is selected from KVLEHVVRV (SEQ ID NO:1) and ts thereof, such as those shown in SEQ ID N02 to SEQ ID NO:24. In an ment the HLA molecule is a class I MHC molecule selected from the group consisting of HLA-A, HLA-B, and HLA-C molecules. In one embodiment the HLA molecule is HLA-A*02. In another embodiment, the HLA molecule is a class II MHC molecule ed from the group consisting of HLA-DP, HLA-DQ, and HLA-DR.
TCRs of the present description ably bind to a MAG-003 peptide-HLA molecule com- plex with a binding affinity (KB) of about 100 uM or less, about 50 uM or less, about 25 uM or less, or about 10 uM or less. More preferred are high affinity TCRs having binding affinities of about 1 uM or less, about 100 nM or less, about 50 nM or less, about 25 nM or less. Non- limiting examples of preferred binding affinity ranges for TCRs of the present description include about 1 nM to about 10 nM; about 10 nM to about 20 nM; about 20 nM to about 30 nM; about 30 nM to about 40 nM; about 40 nM to about 50 nM; about 50 nM to about 60 nM; about 60 nM to about 70 nM; about 70 nM to about 80 nM; about 80 nM to about 90 nM; and about 90 nM to about 100 nM.
As used herein in connect with TCRs of the present description, "specific binding" and grammatical variants thereof are used to mean a TCR having a binding affinity (KD) for a MAG—003 peptide-HLA molecule complex of 100 uM or less.
Alpha/beta heterodimeric TCRs of the present description may have an introduced disulfide bond between their nt domains. Preferred TCRs of this type include those which have a TRAC constant domain sequence and a TRBC1 or TRBC2 nt domain sequence except that Thr 48 of TRAC and Ser 57 of TRBC1 or TRBC2 are replaced by cysteine residues, the said cysteines g a disulfide bond between the TRAC constant domain sequence and the TRBC1 or TRBC2 constant domain sequence of the TCR.
With or without the introduced inter-chain bond mentioned above, alpha/beta heterodimeric TCRs of the t ption may have a TRAC constant domain sequence and a TRBC1 or TRBC2 constant domain sequence, and the TRAC constant domain sequence and the TRBC1 or TRBC2 nt domain sequence of the TCR may be linked by the native disulfide bond between Cys4 of exon 2 of TRAC and Cys2 of exon 2 ofTRBC1 or TRBC2.
TCRs of the present description may comprise a detectable label selected from the group con- sisting of a radionuclide, a fluorophore and biotin. TCRs of the present description may be conjugated to a therapeutically active agent, such as a radionuclide, a herapeutic agent, or a toxin.
In an embodiment, a TCR of the present description having at least one mutation in the alpha chain and/or having at least one mutation in the beta chain has modified glycosylation com- pared to the ted TCR.
In an embodiment, a TCR comprising at least one mutation in the TCR alpha chain and/or TCR beta chain has a binding affinity for, and/or a binding half-life for, a MAG-003 peptide- HLA molecule complex, which is at least double that of a TCR sing the unmutated TCR alpha chain and/or unmutated TCR beta chain. Affinity—enhancement of tumor-specific TCRs, and its exploitation, relies on the existence of a window for optimal TCR affinities. The existence of such a window is based on observations that TCRs specific for HLA—A2-restricted pathogens have KD values that are generally about 10—fold lower when compared to TCRs specific for HLA—A2-restricted tumor—associated self-antigens (Aleksic et al. 2012; Kunert et al. 2013). It is now known, although tumor antigens have the potential to be immunogenic, because tumors arise from the dual’s own cells only mutated proteins or proteins with altered translational processing will be seen as foreign by the immune system. Antigens that are upregulated or overexpressed (so called self-antigens) will not necessarily induce a func- tional immune response against the tumor: T—cells expressing TCRs that are highly reactive to these antigens will have been negatively selected within the thymus in a process known as central tolerance (Xing et al. 2012; Ruella et al. 2014; Sharpe et al. 2015), meaning that only s with low-affinity TCRs for self-antigens remain. Therefore, affinity of TCRs or vari- ants of the present description to 3 have been enhanced by methods well known in the art as described below.
MAG—003 PEPTIDES The description provides a peptide comprising a sequence that is selected from the group of consisting of SEQ ID NO:1 to SEQ ID NO:24 or a variant thereof which is 88% homologous to SEQ ID NO:1 to SEQ ID NO:24, or a variant thereof that will induce T—cells cross-reacting with a peptide described herein. In an aspect, the peptides of the description have the ability to bind to a le of the human major histocompatibility complex (MHC) class-I or long- er ns of a peptide described herein to class II. In an , a TCR described herein is capable of binding to or specifically g to a peptide bed .
In humans there are three different genetic loci that encode MHC class I molecules (the MHC-molecules of the human are also designated human leukocyte ns (HLA)): HLA—A, HLA—B, and HLA—C. HLA—A*01, HLA—A*02, and HLA—B*07 are examples of different MHC class I alleles that can be expressed from these loci.
Table 3: sion ncies F of HLA—A*02 and HLA—A*24 and the most frequent HLA- DR serotypes. Frequencies are deduced from haplotype frequencies Gf within the American tion adapted from Mori et al. (Mori et al., 1997) employing the Hardy-Weinberg for- mula F = 1 — (1-Gf)2. Combinations of A*02 or A*24 with certain HLA—DR alleles might be enriched or less frequent than expected from their single frequencies due to linkage disequilibrium.
For details refer to Chanock et al. (Chanock et al., 2004).
Table 3 Allele tion Calculated phenotype from allele fre- quency A*02 Caucasian (North America) 49.1% A*02 African an (North America) 34.1% A*02 Asian American (North America) 43.2% A*02 Latin American (North American) 48.3% DR1 ian (North America) 19.4% DR2 Caucasian (North America) 28.2% DR3 Caucasian (North America) 20.6% DR4 Caucasian (North America) 30.7% DR5 Caucasian (North America) 23.3% DR6 Caucasian (North America) 26.7% Allele Population Calculated phenotype from allele fre- quency DR7 ian (North America) 24.8% DR8 Caucasian (North America) 5.7% DR9 Caucasian (North America) 2.1% DR1 African (North) American 13.20% DR2 African (North) American 29.80% DR3 African (North) American 24.80% DR4 n (North) American 11.10% DR5 African (North) American 31.10% DR6 African (North) American 33.70% DR7 African (North) American 19.20% DR8 African (North) American 12.10% DR9 African (North) American 5.80% DR1 Asian (North) American 6.80% DR2 Asian (North) American 33.80% DR3 Asian (North) American 9.20% DR4 Asian (North) American 28.60% DR5 Asian (North) American 30.00% DR6 Asian (North) American 25.10% DR7 Asian (North) American 13.40% DR8 Asian ) an 12.70% DR9 Asian (North) American 18.60% DR1 Latin (North) American 15.30% DR2 Latin ) American 21.20% DR3 Latin (North) American 15.20% DR4 Latin (North) an 36.80% DR5 Latin (North) American 20.00% DR6 Latin ) American 31.10% DR7 Latin (North) American 20.20% DR8 Latin (North) an 18.60% DR9 Latin (North) American 2.10% A*24 Philippines 65% A*24 Russia Nenets 61% A*24:o2 Japan 59% A*24 Malaysia 58% A*24:02 Philippines 54% A*24 India 47% A*24 South Korea 40% A*24 Sri Lanka 37% A*24 China 32% A*24:o2 India 29% A*24 Australia West 22% A*24 USA 22% Allele tion Calculated ype from allele fre- quency A*24 Russia Samara 20% A*24 South America 20% A*24 Europe 18% MAGM. Gene This gene is a member of the MAGEA gene family. The members of this family encode pro- teins with 50 to 80% sequence identity to each other. The promoters and first exons of the MAGEA genes show considerable variability, suggesting that the existence of this gene family enables the same function to be expressed under different transcriptional controls. The MAGEA genes are clustered at chromosomal location Xq28. They have been implicated in some hereditary disorders, such as dyskeratosis ita. At least four variants encoding the same protein have been found for this gene. (Provided by RefSeq, Jul 2008).
MAGEA4 localization has been described as cytoplasmic (Kim et al., 2015). However, MAGEA4 staining has also been detected in nuclei, with ential bution between nucleus and cytoplasm in ifferentiated versus less differentiated cancers (Sarcevic et al., 2003).
MAGEA4 is used as a male germ cell marker. It is not expressed in gonocytes, but expressed in pre-spermatogonia and mature germ cells (Mitchell et al., 2014).
Table 4: General cancer target Antigen properties Evaluation Over—expression in [cancer of interest] reported in literature Over-expression in other cancers reported in literature + T-cell ses against source protein-derived targets described Oncofetal expression pattern Expression by cancer stem cells Roles in cell cycle progression and tumor cell proliferation Involvement in tumor invasion, migration and metastasis Link to -associated signaling pathways1 poptotic effects Pro-angiogenic effects / Neovascularisation Over-expression linked to poor prognosis in cancer Over-expression associated with advanced cancer stages General cancer target Sub-cellular localization2 CY Characterization of source n in literature (-, +, ++, +++) + Cell type association3 TU 1 TGF = orming growth factor; P13K = Phosphatidylinositide 3-kinases; p53 = cellular tumor antigen p53; EGFR = epithelial growth factor receptor; FGF2 = fibroblast growth fac- tor 2; Wnt = Wnt / beta—catenin pathway (embryogenesis); Ras = Rat sarcoma proto— oncogene; NF-kB = Nuclear factor Kappa B yotic transcription factor) 2 CY = cyto- plasmic; 3 TU = tumor cells 2017/056260 pMHC as target A phase I clinical trial investigated adoptive er of TCR—engineered gous CTLs reactive towards MAGEA4(143-151) bound to HLA—A*24:02 in esophageal cancer patients.
Patients were given TCR—transduced lymphocytes once, without preconditioning ent, followed by subcutaneous immunizations with MAGEA4 peptide after 2 and 4 weeks. No ob- jective tumor regression was observed, possibly due to the lack of lymphodepleting regimen and administration of IL2 (Kageyama et al., 2015). Preclinical studies in mice had demonstrated that transferred T-cells ted growth of MAGEA4-expressing tumor cell lines in- ed in the mice, and that additional peptide vaccination ed this antitumor activi- ty (Shirakura et al., 2012).
Targeting MAGEA4 with adoptive CTL transfer is proposed as a ent option of EBV- negative Hodgkin and non-Hodgkin lymphoma. d CTLs targeting EBV—derived pep- tides have been described to induce complete ions in EBV(+) lymphoma patients.
Therefore, targeting other antigens expressed by lymphoma, including MAGEA4, is being explored as a possible treatment option (Cruz et al., 2011; Gerdemann et al., 2011).
Several studies have demonstrated the generation of MAGEA4 specific CD4(+) T-cells from healthy donors and cancer patients after incubation with autologous antigen-presenting cells pulsed with overlapping peptide pools (Cesson et al., 2011; Gerdemann et al., 2011; Ohkuri et al., 2009).
MAG-003 peptide, i.e., KVLEHVVRV (SEQ ID NO:1), is a HLA—A*0201-restricted cytotoxic T lymphocyte (CTL) epitope of MAGEA4 (amino acids 286-294). (Jia et al. 2010; Wu et al. 2011), the contents of which are hereby incorporated by nce in their entirety. In an aspect, MAG—003 elicits peptide-specific CTLs both in vitro from HLA—A*0201-positive PBMCs and in HLA—A*0201/Kb enic mice. In another aspect, the induced CTLs lyse target-cells in an HLA—A*0201-restricted fashion, demonstrating that MAG-003 is HLA— A*0201-restricted CTL epitope and serve as a target for therapeutic antitumoral vaccination (Jia et al. 2010), the content of which is hereby incorporated by reference in its entirety. shows MAG-003 peptide presentation in healthy tissues and cancers. The results are summarized in Table 5. Specifically, about 4,000 and 2,000 copies of MAG-003 per cell are estimated in tumor tissues from n cancer (0C) and non-small cell lung cancer (NSCLC), respectively.
Table 5: MAG-003 presentation in healthy tissues and s.
A*02 Samples Mean intensity chore Healthy 0 of 245 --— ——- Cancer 14 of 397 1.1e+07 0.000 H_CC 1 of 16 2.9e+06 0.000 m 0 of 3 0.0e+00 @ 2 of 20 7 0.000 pNSCLC 11 of 91 1.0e+07 0.000 Expression profiling of genes encoding the es of the description Over-presentation or specific tation of TAAs on tumor cells compared to healthy cells is sufficient for its usefulness in immunotherapy, and some peptides are tumor-specific de- spite their source n occurring also in healthy tissues. Still, mRNA expression profiling adds an additional level of safety in selection of peptide targets for immunotherapies. Espe- cially for therapeutic options with high safety risks, such as affinity-matured TCRs, the ideal target peptide will be derived from a protein that is unique to the tumor and not found on healthy tissues.
RNA sources and preparation Surgically removed tissue specimens were provided as indicated above after n informed consent had been obtained from each patient. Tumor tissue specimens were snap-frozen im- ely after surgery and later homogenized with mortar and pestle under liquid nitrogen.
Total RNA was prepared from these samples using TRI Reagent (Ambion, Darmstadt, Ger- many) followed by a cleanup with RNeasy (QIAGEN, Hilden, y); both s were performed according to the manufacturer's protocol.
RNAseq experiments Gene expression analysis of tumor and healthy tissue RNA samples was performed by next generation sequencing (RNAseq) by CeGaT (Tiibingen, y). Sequencing libraries are prepared using the Illumina HiSeq v4 reagent kit according to the provider’s ol (Illu- mina Inc, San Diego, CA, USA), which es RNA fragmentation, cDNA conversion and addition of sequencing adaptors. Libraries derived from multiple samples are mixed equimo- larly and sequenced on the Illumina HiSeq 2500 sequencer according to the manufacturer’s instructions, generating 50 bp single end reads. Processed reads are mapped to the human genome (GRCh38) using the STAR software. Expression data are provided on transcript level as RPKM (Reads Per Kilobase per Million mapped reads, generated by the software Cuf- flinks) and on exon level (total reads, generated by the software Bedtools), based on annota- tions of the ensembl sequence se (Ensembl77). Exon reads are normalized for exon length and alignment size to obtain RPKM values.
As shown in FIGs. 2-4, MAG-003 is highly expressed in cancer tissues and in low risk healthy tissues, such as testis, as compared with that is high risk and medium risk healthy tissues.
Tables 6-8 show RNASeq data (expression scores) of MAG-003 sion in various cancers Table 6: RNASeq Score 1 Tumor type thcore exonScore exonScore exonScore (27242) (317034) (593984) BRCA 1.57 1.23 1.23 1.51 CRC 1.65 1.00 1.00 1.76 HCC 12.10 11.98 11.97 6.15 0C 56.60 18.45 18.44 57.74 OSCAR 58.42 3.49 3.49 60.40 PC 12.10 10.78 10.77 4.74 pGB 0.88 0.95 0.95 0.74 pNSCLC 100.83 1.52 1.52 98.57 RCC 0.93 0.95 0.95 0.77 SCLC 56.41 28.32 28.30 152.27 Table 7: RNASeq Score 3 Tumor type thcore ore exonScore exonScore (27242) (317034) (593984) BRCA 7.48 5.11 5.11 6.01 CRC 8.35 1.05 1.05 7.90 HCC 123.03 210.33 210.30 42.22 0C 612-59 333-74 333-69 447-29 OSCAR 632.95 47.41 47.40 468.45 PC 122.95 187.07 187.05 31.15 pGB 0.31 0.18 0.18 0.25 pNSCLC 1100.05 10.26 10.25 768.23 RCC 0.78 0.18 0.18 0.43 SCLC 611.00 524.23 524.17 1190.36 Table 8: Tumor expression Tumor type tgtumor40 Exontumor40 Exontumor40 Exontumor40 ) (317034) (593984) BRCA 0.12 0.04 0.04 0.17 CRC 0.14 0.01 0.01 0.22 HCC 2.05 1.82 1.82 1.18 0C 11.19 3.16 3.16 13.72 OSCAR 10.89 0.42 0.42 13.11 PC 2.09 1.65 1.65 0.89 pGB 0.00 0.00 0.00 0.01 pNSCLC 19.25 0.09 0.09 22.58 RCC 0.01 0.00 0.00 0.01 SCLC 10.18 4.53 4.53 33.35 In an aspect, a peptide consisting essentially of the amino acid sequence as indicated herein can have one or two non-anchor amino acids (see below regarding the anchor motif) ex- changed without that the ability to bind to a molecule of the human major histocompatibility complex (MHC) class-I or —II is substantially changed or is negatively affected, when com- pared to the non-modified peptide. In another embodiment, in a peptide consisting essential- ly of the amino acid ce as indicated herein, one or two amino acids can be exchanged with their conservative exchange partners (see herein below) without that the ability to bind to a molecule of the human major histocompatibility x (MHC) I or —II is sub- stantially changed, or is negatively affected, when ed to the non-modified peptide.
The amino acid residues that do not substantially contribute to interactions with the TCR can be modified by replacement with other amino acids whose incorporation do not substantially affect T-cell reactivity and does not eliminate binding to the relevant MHC. Thus, apart from the proviso given, the peptide of the description may be any peptide (by which term the in- s include oligopeptide or polypeptide), which includes the amino acid ces or a portion or variant thereof as given.
Table 9: Variants and motif of the peptides Position 1 2 3 5 6 7 8 9 SEQ ID NOs:1-24 K V L H V V R V Variants l L >>>>FFFF>>>>FFFF H>r¢ H>r¢ *<1’- In an , peptides of the description can be elongated by up to 1, 2, 3, or 4 amino acids, that is 1, 2, 3 or 4 amino acids can be added to either end of the peptide in any combination between 8 and 11 amino acids long. It is preferred that the residues that flank between 4:0 and 0:4. Combinations of the elongations according to the description can be found in Table Table 10: Combinations of the elongations of peptides of the description C-terminus inus OHNW-h O OOI‘l 00r1or2 00r10r2or3 00r10r2or3or4 N-terminus C-terminus ounce-1:. O OOI‘l OOI‘101‘2 00r10r20r3 00r10r2or3or4 The amino acids for the elongation/extension can be the peptides of the original sequence of the protein or any other amino acid(s). The elongation can be used to enhance the stability or solubility of the peptides.
Thus, the epitopes of the present description may be identical to naturally occurring tumor- associated or specific epitopes or may include epitopes that differ by no more than four residues from the reference e, as long as they have substantially identical antigen- ic activity.
In an alternative embodiment, the peptide is elongated on either or both sides by more than 4 amino acids, preferably to a total length of up to 30 amino acids. In an aspect, this elongation leads to MHC class II binding peptides. Binding to MHC class II can be tested by methods known in the art.
Accordingly, the present description provides peptides and variants ofMHC class I epitopes, wherein the peptide or variant has an overall length of between 8 and 100, preferably be- tween 8 and 30, and most preferred between 8 and 14, namely 8, 9, 1o, 11, 12, 13, 14 amino acids, in case of the longer class II g peptides the length can also be 15, 16, 17, 18, 19, 2o, 21 or 22 amino acids.
In an aspect, the peptide or variant according to the present description will have the ability to bind to a molecule of the human major histocompatibility complex (MHC) class I or II.
Binding of a peptide or a variant to a MHC complex may be tested by methods known in the art.
Preferably, when the T—cells specific for a e according to the present description are tested against the substituted peptides, the peptide concentration at which the substituted peptides achieve half the maximal increase in lysis relative to background is no more than about 1 mM, ably no more than about 1 uM, more preferably no more than about 1 nM, and still more ably no more than about 100 pM, and most ably no more than about 10 pM. It is also preferred that the substituted peptide be recognized by T-cells from more than one individual, at least two, and more preferably three individuals.
As used herein, the term "complex" refers to a le that specifically binds to an (e.g., antigenic) determinant. In one ment, a complex is able to direct the entity to which it is attached (e.g., a (second) antigen binding moiety) to a target site, for example to a specific type of tumor cell or tumor stroma bearing the antigenic determinant (e.g., the complex of a peptide with MHC, according to the application at hand). In another embodiment a complex is able to activate signaling through its target antigen, for example a T—cell receptor complex antigen. Complexes include but are not limited to antibodies and fragments thereof, antigen binding domains of an antibody, comprising an antibody heavy chain variable region and an antibody light chain variable , binding ns comprising at least one ankyrin repeat motif and single domain antigen binding (SDAB) molecules, aptamers, (soluble) TCRs and (modified) cells such as allogenic or autologous T-cells. To assess whether a molecule is a complex binding to a target, binding assays can be performed. fic" g means that the complex (e.g. TCR) binds the peptide-MHC-complex of interest better than other naturally occurring peptide-MHC—complexes, to an extent that a complex armed with an active molecule that is able to kill a cell g the specific target is 2017/056260 not able to kill another cell without the specific target but presenting other peptide-MHC complex(es). Binding to other peptide—MHC complexes is irrelevant if the peptide of the cross-reactive peptide-MHC is not naturally occurring, i.e., not derived from the human HLA-peptidome. Tests to assess -cell killing are well known in the art. They should be performed using -cells (primary cells or cell lines) with unaltered peptide-MHC presen- tation, or cells loaded with peptides such that naturally occurring peptide-MHC levels are reached.
Each complex can comprise a labelling which provides that the bound complex can be detect- ed by determining the ce or absence of a signal ed by the label. For example, the complex can be labeled with a fluorescent dye or any other applicable cellular marker mole- cule. Such marker molecules are well known in the art. For e a fluorescence-labelling, for example provided by a fluorescence dye, can provide a visualization of the bound aptamer by cence or laser scanning microscopy or flow cytometry.
Each complex can be conjugated with a second active molecule such as for example IL-21, anti-CD3, and anti-CD28.
Further information on polypeptide complexes may be found, for example, in the background n ofWC 2014/071978A1, which is incorporated by reference in its entirety.
A aceutical composition" is a composition suitable for administration to a human be- ing in a medical setting. Preferably, a pharmaceutical composition is sterile and produced ing to GMP guidelines.
Pharmaceutical compositions of the present description also include at least one TCR, soluble TCR, nucleic acid, and/or host cell expressing a TCR of the present description, in a pharma- ceutically acceptable carrier.
Pharmaceutical compositions of the present description may also include pharmaceutically acceptable excipients and/or stabilizers.
This composition is used for parenteral administration, such as subcutaneous, intradermal, intramuscular or oral administration. For this, the es and optionally other molecules are dissolved or suspended in a pharmaceutically acceptable, preferably aqueous carrier. In addition, the composition can contain excipients, such as buffers, g agents, blasting agents, diluents, flavors, lubricants, etc. An extensive listing of excipients that can be used in such a composition, can be, for example, taken from A. Kibbe, ok of ceutical Excipients (Kibbe, 2000). The composition can be used for a tion, prophylaxis and/or therapy of adenomateous or cancerous diseases. Exemplary formulations can be found in, for example, EP2112253, which is herein incorporated by reference in its entirety.
A further aspect of the description provides nucleic acids (for example polynucleotides) en- coding a e, peptide variants, TCRs and TCR variants of the description. The polynucle- otide may be, for example, DNA, cDNA, PNA, RNA or ations thereof, either single— and/or double-stranded, or native or stabilized forms of polynucleotides, such as, for example , polynucleotides with a orothioate backbone and it may or may not contain in- trons so long as it codes for the peptide. Of course, only es that contain naturally oc- g amino acid residues joined by naturally occurring peptide bonds are encodable by a polynucleotide. A still further aspect of the description provides an expression vector capable of expressing a polypeptide according to the description.
A variety of methods have been developed to link polynucleotides, especially DNA, to vectors for example via complementary cohesive termini. For instance, complementary homopoly- mer tracts can be added to the DNA segment to be inserted to the vector DNA. The vector and DNA segment are then joined by hydrogen bonding between the complementary homopoly- meric tails to form recombinant DNA molecules.
Synthetic linkers containing one or more restriction sites e an alternative method of joining the DNA segment to vectors. Synthetic linkers containing a variety of ction en- donuclease sites are commercially available from a number of sources including International Biotechnologies Inc. New Haven, CN, USA.
A desirable method of ing the DNA encoding the polypeptide of the description em- ploys the rase chain reaction as disclosed by Saiki RK, et al. (Saiki et al., 1988). This method may be used for introducing the DNA into a suitable vector, for example by engineer- ing in suitable restriction sites, or it may be used to modify the DNA in other useful ways as is known in the art. If viral vectors are used, pox— or adenovirus vectors are preferred.
In one aspect, to obtain T-cells expressing TCRs of the t description, nucleic acids en- coding TCR—alpha and/or ta chains of the present description are cloned into expres- sion vectors, such as gamma retrovirus or lentivirus. The inant viruses are generated and then tested for functionality, such as antigen specificity and functional avidity. An aliquot of the final product is then used to transduce the target T-cell population (generally purified from patient PBMCs), which is expanded before infusion into the patient.
In another aspect, to obtain T—cells sing TCRs of the present description, TCR RNAs are synthesized by techniques known in the art, e.g., in vitro transcription systems. The in synthesized TCR RNAs are then introduced into primary CD8+ T-cells obtained from healthy donors by electroporation to re-express tumor specific TCR-alpha and/or TCR—beta chains.
TCR chains introduced into a peripheral T-cell may e with endogenous TCR chains for association with the CD3 complex, which is necessary for TCR e expression. Because a high level of TCR surface expression is essential to confer appropriate sensitivity for trigger- ing by cells expressing the target tumor antigen r et al., 2000; Labrecque et al., 2001), gies that enhance TCR-alpha and TCR-beta gene expression levels are an important consideration in TCR gene therapy.
To increase the expression, nucleic acids encoding TCRs of the present description may be operably linked to strong promoters, such as retroviral long al repeats (LTRs), cyto- megalovirus (CMV), murine stem cell virus (MSCV) U3, oglycerate kinase (PGK), B- actin, ubiquitin, and a simian virus 40 /CD43 composite promoter (Cooper et al., 2004; Jones et al., 2009), elongation factor (EF)-1a (Tsuji et at, 2005) and the spleen focus- forming virus (SFFV) promoter (Joseph et al., 2008). In a preferred embodiment, the pro- moter is heterologous to the nucleic acid being expressed.
In addition to strong promoters, TCR expression cassettes of the present description may contain additional elements that can enhance transgene expression, including a central poly- purine tract (cPPT), which promotes the r translocation of lentiViral ucts (Fol- lenzi et al., 2000), and the woodchuck tis Virus posttranscriptional regulatory element (WPRE), which increases the level of ene expression by increasing RNA stability rey et al., 1999).
The alpha and beta chains of a TCR of the present invention may be encoded by nucleic acids located in separate vectors, or may be encoded by polynucleotides located in the same vector. ing high-level TCR surface expression requires that both the TCR-alpha and ta chains of the introduced TCR be transcribed at high levels. To do so, the TCR-alpha and TCR- beta chains of the present description may be cloned into bicistronic constructs in a single vector, which has been shown to be capable of overcoming this obstacle. The use of a Viral intraribosomal entry site (IRES) between the TCR-alpha and TCR-beta chains results in the coordinated expression of both chains, because the TCR-alpha and TCR-beta chains are gen- erated from a single transcript that is broken into two proteins during translation, ensuring that an equal molar ratio of TCR-alpha and TCR-beta chains are produced. (Schmitt et al. 2009) Nucleic acids encoding TCRs of the present description may be codon optimized to increase expression from a host cell. Redundancy in the genetic code allows some amino acids to be encoded by more than one codon, but certain codons are less "optimal" than others because of the relative availability of matching tRNAs as well as other factors (Gustafsson et al., 2004). Modifying the TCR-alpha and TCR-beta gene sequences such that each amino acid is encoded by the optimal codon for mammalian gene expression, as well as eliminating mRNA instability motifs or cryptic splice sites, has been shown to significantly enhance TCR-alpha and TCR-beta gene sion (Scholten et al., 2006).
Furthermore, mispairing between the introduced and nous TCR chains may result in the ition of specificities that pose a icant risk for autoimmunity. For example, the formation of mixed TCR dimers may reduce the number of CD3 molecules ble to form properly paired TCR complexes, and therefore can icantly decrease the functional avidi- ty of the cells expressing the introduced TCR (Kuball et al., 2007).
To reduce mispairing, the C-terminus domain of the introduced TCR chains of the present description may be ed in order to e interchain affinity, while decreasing the ability of the introduced chains to pair with the endogenous TCR. These strategies may in- clude replacing the human TCR-alpha and TCR-beta C—terminus domains with their murine counterparts (murinized C-terminus domain); generating a second interchain disulfide bond in the C-terminus domain by introducing a second ne e into both the TCR-alpha and TCR-beta chains of the uced TCR (cysteine modification); swapping interacting residues in the TCR-alpha and TCR-beta chain C-terminus domains ("knob-in-hole"); and fusing the variable domains of the TCR-alpha and ta chains directly to CD3§ (CD3C fusion). (Schmitt et al. 2009).
The DNA (or in the case of retroviral vectors, RNA) may then be expressed in a suitable host to produce a polypeptide comprising the peptide or variant of the description. Thus, the DNA encoding the peptide or variant of the description may be used in accordance with known techniques, appropriately modified in view of the teachings contained herein, to construct an expression vector, which is then used to transform an appropriate host cell for the expression and production of the polypeptide of the description. Such techniques include those dis- closed, for example, in US 4,440,859, 4,530,901, 4,582,800, 4,677,063, 4,678,751, 4,704,362, 4,710,463, 4,757,006, 4,766,075, and 4,810,648, which are herein incorporated by reference in their entirety.
The DNA (or in the case of retroviral vectors, RNA) encoding the polypeptide constituting the compound of the description may be joined to a wide variety of other DNA sequences for in- troduction into an appropriate host. The companion DNA will depend upon the nature of the host, the manner of the introduction of the DNA into the host, and r al maintenance or integration is desired.
Generally, the DNA is inserted into an expression vector, such as a plasmid, in proper orien- tation and correct reading frame for sion. If ary, the DNA may be linked to the appropriate transcriptional and translational regulatory l tide sequences recog- nized by the d host, although such controls are generally available in the sion vector. The vector is then introduced into the host through standard techniques. Generally, not all of the hosts will be transformed by the vector. Therefore, it will be necessary to select for ormed host cells. One selection technique involves incorporating into the expression vector a DNA sequence, with any necessary control elements, that codes for a selectable trait in the transformed cell, such as antibiotic resistance. atively, the gene for such selectable trait can be on r vector, which is used to co- transform the desired host cell.
Host cells that have been transformed by the recombinant DNA of the description are then ed for a ient time and under appropriate conditions known to those skilled in the art in view of the ngs disclosed herein to permit the expression of the polypeptide, which can then be recovered.
Many expression systems are known, including bacteria (for example E. coli and Bacillus subtilis), yeasts (for example Saccharomyces cerevisiae), ntous fungi (for example Aspergillus spec), plant—cells, animal cells and insect—cells. Preferably, the system can be ian cells such as CHO cells available from the ATCC Cell Biology Collection.
In an embodiment, a host cell is engineered to express a TCR of the present description. In preferred embodiments, the host cell is a human T-cell or T-cell progenitor. In some embod- iments the T-cell or T—cell progenitor is obtained from a cancer patient. In other embodi- ments the T—cell or T—cell progenitor is obtained from a healthy donor. Host cells of the pre- sent description can be allogeneic or autologous with respect to a patient to be treated. In one embodiment, the host is a gamma/delta T—cell transformed to express an alpha/beta TCR.
A typical mammalian cell vector plasmid for constitutive sion comprises the CMV or SV40 promoter with a suitable poly A tail and a resistance marker, such as neomycin. One example is pSVL ble from Pharmacia, Piscataway, NJ, USA. An example of an inducible mammalian expression vector is pMSG, also available from Pharmacia. Useful yeast plasmid vectors are pRS403-406 and pRS413-416 and are generally available from Stratagene Clon- ing s, La Jolla, CA 92037, USA. ds pRS403, pRS404, pRS405 and pRS406 are Yeast Integrating plasmids (YIps) and incorporate the yeast selectable markers HIS3, TRP1, LEU2 and URA3. Plasmids pRS413-416 are Yeast Centromere plasmids (chs). CMV pro- moter—based vectors (for example from Sigma-Aldrich) e transient or stable - sion, cytoplasmic expression or secretion, and N-terminal or C-terminal tagging in various combinations of FLAG, 3xFLAG, c-myc or MAT. These fusion proteins allow for detection, purification and analysis of recombinant protein. Dual-tagged fusions provide flexibility in detection.
The strong human galovirus (CMV) promoter regulatory region drives tutive protein expression levels as high as 1 mg/L in COS cells. For less potent-cell lines, protein levels are typically ~0.1 mg/L. The presence of the SV40 replication origin will result in high levels of DNA replication in SV40 replication permissive COS cells. CMV vectors, for exam- ple, can contain the pMB1 (derivative of pBR322) origin for replication in ial cells, the b-lactamase gene for ampicillin resistance selection in bacteria, hGH polyA, and the f1 origin.
Vectors containing the pre-pro-trypsin leader (PPT) sequence can direct the secretion of FLAG fusion proteins into the culture medium for purification using ANTI-FLAG antibodies, resins, and plates. Other vectors and expression systems are well known in the art for use with a variety of host cells.
In another embodiment two or more peptides or peptide variants of the description are en- coded and thus expressed in a successive order (similar to "beads on a string" constructs). In doing so, the es or peptide variants may be linked or fused together by stretches of linker amino acids, such as for example LLLLLL, or may be linked without any onal e(s) between them. These constructs can also be used for cancer therapy, and may in- duce immune responses both involving MHC I and MHC II.
The present description also relates to a host cell ormed with a polynucleotide vector construct of the t description. The host cell can be either prokaryotic or eukaryotic.
Bacterial cells may be preferred prokaryotic host cells in some circumstances and typically are a strain of E. coli such as, for example, the E. coli s DH5 available from Bethesda Research Laboratories Inc., Bethesda, MD, USA, and RR1 available from the American Type Culture Collection (ATCC) of Rockville, MD, USA (No ATCC 31343). Preferred eukaryotic host cells include yeast, insect and mammalian cells, preferably vertebrate cells such as those from a mouse, rat, monkey or human fibroblastic and colon cell lines. Yeast host cells include , YPH500 and YPH501, which are generally available from Stratagene Cloning Sys- tems, La Jolla, CA 92037, USA. Preferred mammalian host cells e Chinese hamster ovary (CHO) cells available from the ATCC as CCL61, NIH Swiss mouse embryo cells NIH/3T3 available from the ATCC as CRL 1658, monkey —derived COS-1 cells available from the ATCC as CRL 1650 and 293 cells which are human embryonic kidney cells. Pre- ferred insect-cells are Sf9 cells which can be transfected with baculovirus expression vectors.
An ew regarding the choice of suitable host cells for expression can be found in, for example, the textbook of Paulina Balbas and Argelia Lorence "Methods in Molecular Biology Recombinant Gene Expression, Reviews and Protocols," Part One, Second Edition, ISBN 978-1—58829—262-9, and other literature known to the person of skill. ormation of appropriate cell hosts with a DNA construct of the present description is accomplished by well-known methods that typically depend on the type of vector used. With regard to transformation of prokaryotic host cells, see, for example, Cohen et al. (Cohen et al., 1972) and (Green and ok, 2012) . Transformation of yeast-cells is described in n et al. (Sherman et al., 1986) . The method of Beggs (Beggs, 1978) is also useful.
With regard to vertebrate cells, reagents useful in transfecting such cells, for example calcium phosphate and DEAE—dextran or liposome ations, are available from Stratagene Clon- ing Systems, or Life logies Inc., Gaithersburg, MD 20877, USA. Electroporation is also useful for transforming and/or transfecting cells and is well known in the art for transform- ing yeast-cell, bacterial cells, insect-cells and vertebrate cells.
Successfully transformed cells, i.e., cells that contain a DNA construct of the present descrip- tion, can be identified by well—known techniques such as PCR. Alternatively, the presence of the protein in the supernatant can be detected using antibodies.
It will be appreciated that certain host cells of the description are useful in the preparation of the peptides of the description, for example bacterial, yeast and insect-cells. However, other host cells may be useful in certain therapeutic methods. For example, antigen-presenting cells, such as dendritic cells, may usefully be used to express the peptides of the ption such that they may be loaded into appropriate MHC molecules. Thus, the current description es a host cell comprising a c acid or an expression vector according to the de- scription.
In a preferred embodiment the host cell is an antigen presenting cell, in particular a dendritic cell or antigen presenting cell. APCs loaded with a recombinant fusion protein containing prostatic acid phosphatase (PAP) were approved by the US. Food and Drug Administration (FDA) on April 29, 2010, to treat asymptomatic or minimally symptomatic metastatic HRPC (Sipuleucel-T) (Rini et al., 2006; Small et al., 2006).
A r aspect of the description provides a method of producing a peptide or its variant, the method comprising culturing a host cell and isolating the peptide from the host cell or its culture medium.
In another ment the TCRs, the nucleic acid or the expression vector of the description are used in medicine. For example, the peptide or its variant may be prepared for intravenous (iv) injection, sub-cutaneous (s.c.) injection, intradermal (i.d.) injection, intraperitoneal (i.p.) injection, intramuscular (i.m.) injection. Preferred methods of peptide injection e s.c., i.d., i.p., i.m., and iv. Preferred methods of DNA injection include i.d., i.m., s.c., i.p. and iv. Doses of e.g., between 50 pg and 1.5 mg, preferably 125 pg to 500 pg, of peptide or DNA may be given and will depend on the tive peptide or DNA. Dosages of this range were successfully used in previous trials (Walter et al., 2012).
The polynucleotide used for active vaccination may be substantially pure, or contained in a suitable vector or delivery system. The nucleic acid may be DNA, cDNA, PNA, RNA or a com- bination thereof. Methods for designing and introducing such a c acid are well known in the art. An overview is provided by e.g., Teufel et al. (Teufel et al., 2005). cleotide vaccines are easy to prepare, but the mode of action of these vectors in inducing an immune response is not fully understood. Suitable vectors and delivery s e viral DNA and/or RNA, such as systems based on adenovirus, ia virus, retroviruses, herpes virus, associated virus or hybrids containing elements of more than one virus. Non-viral de- livery systems include cationic lipids and cationic rs and are well known in the art of DNA delivery. Physical delivery, such as via a "gene-gun" may also be used. The peptide or peptides encoded by the nucleic acid may be a fusion protein, for example with an epitope that stimulates T-cells for the respective opposite CDR as noted above.
The present description further relates to aptamers. Aptamers (see for example WC 2014/191359 and the literature as cited therein which are herein incorporated by nce in their entirety) are short single-stranded nucleic acid les, which can fold into defined three—dimensional structures and ize specific target structures. They have appeared to be suitable alternatives for ping targeted therapies. Aptamers have been shown to se- lectively bind to a variety of complex targets with high affinity and specificity.
Aptamers recognizing cell surface located les have been identified within the past dec- ade and e means for developing diagnostic and therapeutic approaches. Since ap- tamers have been shown to possess almost no toxicity and immunogenicity they are promis- ing candidates for biomedical applications. Indeed rs, for example prostate-specific membrane-antigen izing aptamers, have been sfully employed for targeted ther- apies and shown to be functional in xenograft in vivo models. Furthermore, aptamers recog- nizing specific tumor cell lines have been identified.
DNA aptamers can be selected to reveal broad-spectrum recognition properties for s cancer cells, and particularly those derived from solid tumors, while non-tumorigenic and primary healthy cells are not recognized. If the identified aptamers recognize not only a spe— cific tumor sub-type but rather ct with a series of tumors, this renders the aptamers applicable as so-called broad-spectrum diagnostics and therapeutics.
Further, igation of cell-binding behavior with flow cytometry showed that the aptamers revealed very good nt affinities that are within the nanomolar range. rs are useful for diagnostic and therapeutic purposes. In an aspect, at least one or more aptamers are taken up by tumor cells and thus can function as molecular vehicles for the targeted delivery of anti-cancer agents such as siRNA into tumor cells.
Aptamers can be selected against complex targets such as cells and tissues and complexes of the peptides or the TCRs comprising, ably consisting of, a sequence according to any of SEQ ID NO 25 to SEQ ID NO 26, according to the description at hand with the MHC mole- cule, using the cell-SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique.
In one embodiment the description es a method of ing a TCR as described here- in, the method sing culturing a host cell capable of expressing the TCR under condi- tions suitable to promote expression of the TCR.
The present description r relates to a method of identifying and isolating a TCR accord- ing to the present description, said method comprising incubating PBMCs from HLA—A*02— negative healthy donors with A2/MAG—003 monomers, incubating the PBMCs with tetramer- phycoerythrin (PE) and isolating the high avidity T-cells by fluorescence activated cell sorting (FACS)—Calibur analysis.
The present description further relates to a method of identifying and isolating a TCR accord- ing to the present description, said method comprising incubating PBMCs from HLA—A*02— WO 58103 negative healthy donors with A2/p286-1Y2L monomers, ting the PBMCs with tetram- coerythrin (PE) and isolating the high avidity s by fluorescence ted cell sorting —Calibur analysis.
The t description further relates to a method of identifying and ing a TCR accord- ing to the present description, said method comprising incubating PBMCs from HLA—A*o2— negative healthy donors with A2/p286-1Y2L9L monomers, incubating the PBMCs with te- tramer-phycoerythrin (PE) and isolating the high avidity T-cells by fluorescence activated cell sorting —Calibur analysis.
The present description further relates to a method of identifying and isolating a TCR - ing to the present description, said method comprising obtaining a transgenic mouse with the entire human TCRaB gene loci (1.1 and 0.7 Mb), whose T-cells express a diverse human TCR repertoire that compensates for mouse TCR deficiency, immunizing the mouse with MAG- 003, incubating PBMCs obtained from the transgenic mice with tetramer-phycoerythrin (PE), and isolating the high avidity T—cells by fluorescence activated cell sorting (FACS)— Calibur analysis.
The present description further relates to a method of identifying and isolating a TCR accord- ing to the present description, said method comprising obtaining a transgenic mouse with the entire human TCRaB gene loci (1.1 and 0.7 Mb), whose T-cells express a diverse human TCR repertoire that compensates for mouse TCR deficiency, immunizing the mouse with p286- 1Y2L, incubating PBMCs obtained from the transgenic mice with tetramer-phycoerythrin (PE), and isolating the high avidity T—cells by fluorescence activated cell g (FACS)— Calibur analysis.
The present description further relates to a method of identifying and isolating a TCR accord- ing to the present description, said method comprising obtaining a transgenic mouse with the entire human TCRaB gene loci (1.1 and 0.7 Mb), whose T-cells express a diverse human TCR repertoire that compensates for mouse TCR deficiency, immunizing the mouse with p286- 1Y2L9L, incubating PBMCs obtained from the transgenic mice with tetramer-phycoerythrin (PE), and isolating the high avidity T—cells by fluorescence activated cell sorting (FACS)— Calibur analysis.
The present description r relates to the method according to the description, wherein the T—cell comprises an expression vector capable of expressing A TCR according to the pre- sent description.
The present description further relates to a method of killing target-cells in a patient which -cells aberrantly express MAG—003, the method comprising administering to the pa- tient an effective number of TCRs, soluble TCRs and/or s as according to the present description.
The present description further relates to the use of any TCR described, a nucleic acid accord- ing to the present description, an expression vector ing to the present description, a cell ing to the present description, or an activated cytotoxic T lymphocyte ing to the present description as a medicament or in the manufacture of a medicament. The present description r relates to a use ing to the present ption, wherein the medic- ament is active against cancer.
The present description further relates to a use according to the description, wherein said cancer cells are non-small cell lung cancer cells or other solid or haematological tumor cells such as all cell lung cancer, small cell lung cancer, renal cell cancer, brain cancer, gas- tric cancer, ctal cancer, hepatocellular cancer, pancreatic cancer, prostate cancer, leu— kemia, breast cancer, Merkel cell carcinoma, melanoma, ovarian cancer, urinary bladder can- cer, e cancer, gallbladder and bile duct cancer and esophageal cancer.
The present description further relates to a method of killing cancer cells comprising contact the cancer cells with a host cell of the t description. In one embodiment, the host cell expresses a TCR of the present description. In one embodiment the host cell is a T-cell or T- cell progenitor. In one embodiment, In a preferred embodiment the cancer cells are selected from non-small cell lung cancer cells or other solid or haematological tumor cells such as non-small cell lung cancer, small cell lung , renal cell cancer, brain , c can- cer, colorectal cancer, hepatocellular cancer, pancreatic cancer, prostate , leukemia, breast cancer, Merkel cell carcinoma, melanoma, ovarian cancer, urinary bladder cancer, uterine cancer, gallbladder and bile duct cancer and esophageal . In some embodi- ments, the TCR is conjugated to a therapeutically active agent. In certain ments the therapeutically active agent is selected from the group consisting of a radionuclide, a chemo- therapeutic agent, and a toxin.
The present invention further relates to a method of treating cancer comprising administer- ing to a subject in need f a host cell of the present invention. In one embodiment, the host cell ses a TCR of the t description. In one embodiment the host cell is a T- cell or T-cell progenitor. In one ment the host cell is autologous to the subject to be treated. In another embodiment the host cell is neic to the subject to be treated. In a preferred embodiment the cancer cells are selected from non-small cell lung cancer cells or other solid or haematological tumor cells such as non—small cell lung cancer, small cell lung cancer, renal cell cancer, brain cancer, gastric cancer, colorectal cancer, hepatocellular can- cer, pancreatic cancer, prostate cancer, leukemia, breast cancer, Merkel cell carcinoma, mel- anoma, n cancer, urinary bladder cancer, uterine cancer, gallbladder and bile duct can- cer and geal cancer.
In some embodiments, the TCR is conjugated to a therapeutically active agent. As used here- in, the term "therapeutically active agent" means a compound used to treat or prevent a dis- ease or undesirable medical condition. In one embodiment, the therapeutically active agent is used to treat or prevent cancer. In certain embodiments the therapeutically active agent is selected from the group consisting of a radionuclide, a chemotherapeutic agent, and a toxin.
TCRs, nucleic acids and host cells of the present description, and pharmaceutical composi- tions thereof, may be administered to a subject in need thereof by routes known in the art, and may vary depending on the type of cancer to be treated. Routes of stration in- clude, for e, local administration (such as intratumoral) and parenteral administra- tion such as subcutaneous, intraperitoneal, intramuscular, intravenous, intraportal and in- trahepatic. In a red embodiment, TCRs, nucleic acids or host cells of the present de- ion, or pharmaceutical compositions thereof, are administered to a subject by local in- fusion, for example using an infusion pump and/or catheter system, to a site to be treated, such as a solid tumor. In one embodiment, a composition of the present description is in- fused into a solid tumor, a blood vessel that feeds a solid tumor, and/or the area nding a solid tumor.
In preferred embodiments, itions of the present description are administered to a subject using a dosing regimen of at least two administrations separated by at least 24 hours.
Dosing regimens suitable for administering compositions of the present description include, for example, once a day, once every two days, and once every three days. More preferred dos- ing ns include once a week, twice a week, once every other week, once a month, and twice a month. In particular embodiments, a dose escalation regimen is used, wherein a se- ries of increasing doses is stered to a subject over a period of days, weeks or months.
Effective doses of host cells sing TCRs of the t invention include, for example at least about 104, at least about 105, at least about 106, at least about 107, at least about 108, at least about 109, and at least 1010 host cells per dose. In one embodiment, host cells of the present description are administered in a dose of between about 104 to about 1010 cells per dose, preferably in a dose of between about 105 to about 109 cells per dose. In preferred em- bodiments, doses are administered in a dosing regimen over the course of at least two or more dosing cycles.
The present invention also relates to a method of treating cancer comprising administering a TCR, a nucleic acid, or a host cell of the present description in combination with at least one chemotherapeutic agent and/or radiation therapy.
Also provided is a method of treating cancer in a subject in need thereof, comprising: a) isolating a cell from said t; b) transforming the cell with at least one vector encoding a TCR of the present descrip- tion to produce a transformed cell; c) expanding the transformed cell to produce a plurality of transformed cells; and d) administering the plurality of transformed cells to said subject.
Also provided is a method of ng cancer in a subject in need thereof, comprising: a) isolating a cell from a healthy donor; b) transforming the cell with a vector encoding a TCR of the present description to pro- duce a transformed cell; c) expanding the transformed cell to produce a plurality of transformed cells; and d) stering the plurality of transformed cells to said subject.
Also provided is a method of detecting cancer in a biological sample comprising: a) contacting the biological sample with a TCR of the present description; b) detecting binding of the TCR to the biological sample.
In some embodiments the method of detecting cancer is carried out in vitro, in vivo or in situ.
The present description r relates to particular marker ns and biomarkers based on the es according to the present description, herein called ts" that can be used in the diagnosis and/or prognosis of non-small cell lung cancer. The present description also relates to the use of these novel targets for cancer treatment.
WO 58103 It is a further aspect of the ption to provide a method for producing a soluble T-cell receptor (sTCR) recognizing a specific peptide—MHC complex. Such soluble T—cell receptors can be ted from specific T-cell clones, and their affinity can be increased by mutagene- sis targeting the complementarity-determining regions. For the purpose of T—cell receptor selection, phage display can be used (US 2010/0113300, (Liddy et al., 2012)). For the pur- pose of stabilization of T-cell receptors during phage display and in case of practical use as drug, alpha and beta chain can be linked e.g., by non—native de bonds, other covalent bonds (single—chain T-cell receptor), or by dimerization domains (Boulter et aL, 2003; Card et al., 2004; Willcox et al., 1999). The T-cell receptor can be linked to toxins, drugs, cytokines (see, for example, US 2013/0115191), domains recruiting effector cells such as an anti—CD3 domain, etc., in order to e ular functions on -cells. In another aspect, it is expressed in T-cells used for adoptive transfer. See, for example, A1, WO 2004/074322A1, and A1, the contents of which are incorporated by refer— ence in their entirety.
In on, the peptides and/or the TCRs or antibodies or other binding molecules of the present description can be used to verify a pathologist’s diagnosis of a cancer based on a bi- opsied sample.
The antibodies or TCRs may also be used for in vivo diagnostic assays. Generally, the anti- body or TCR is labeled with a radionucleotide (such as 111In, 99Tc, 14C, 1311, 3H, 32F or 358) so that the tumor can be localized using scintiography. In one embodiment, antibodies or fragments thereof bind to the extracellular domains of two or more s of a protein selected from the group consisting of the above-mentioned proteins, and the affinity value (Kd) is less than 1 x 10uM.
Antibodies or TCRs for diagnostic use may be labeled with probes suitable for detection by s imaging methods. Methods for detection of probes include, but are not limited to, fluorescence, light, confocal and electron microscopy; magnetic resonance imaging and spec- troscopy; fluoroscopy, computed aphy and positron emission aphy. Suitable probes e, but are not limited to, fluorescein, rhodamine, eosin and other fluorophores, radioisotopes, gold, gadolinium and other lanthanides, paramagnetic iron, fluorine-18 and other positron-emitting radionuclides. Additionally, probes may be bi- or multi-functional and be detectable by more than one of the methods listed. These antibodies and/or TCRs may be directly or indirectly d with said probes. ment of probes to the antibodies and/or TCRs includes covalent attachment of the probe, incorporation of the probe into the antibody or TCR, and the covalent attachment of a chelating compound for binding of probe, amongst others well recognized in the art. For immunohistochemistry, the disease tissue sample may be fresh or frozen or may be embedded in paraffin and fixed with a preservative such as formalin. The fixed or embedded section contains the sample are contacted with a d primary antibody and secondary antibody, wherein the antibody is used to detect the expression of the proteins in situ.
The invention further pertains to the ing items: Item 1. A TCR comprising an alpha chain and a beta chain, n the alpha chain comprises a TCR alpha variable domain at least 90% identical to the amino acid sequence of any of SEQ ID NO:39, SEQ ID NO:55 and SEQ ID NO:71; and the beta chain comprises a TCR beta variable domain at least 90% identical to any of SEQ ID NO:47, SEQ ID NO:63 and SEQ ID NO:79, and wherein the TCR specifically binds to a MAG-003 peptide-MHC mole- cule complex.
Item 2. The TCR of item 1, further sing a TCR alpha constant domain and a TCR beta constant domain, wherein the TCR alpha constant domain is at least 70% identical to a TCR alpha constant domain of any of SEQ ID NO:39, SEQ ID NO:55 and SEQ ID NO:71, and the beta constant domain is at least 70% identical to a TCR beta constant domain of any of SEQ ID NO:47, SEQ ID NO:63 and SEQ ID NO:79.
Item 3. The TCR of any of items 1 or 2, wherein the alpha constant domain comprises the alpha transmembrane domain VIGFRILLLKVAGFNLLMTL (SEQ ID NO:97) and the beta constant domain comprises the beta transmembrane domain TILYEILLGKATLYAVLVSALVL (SEQ ID NO:88).
Item 4. The TCR of any of items 1 to 3, wherein the TCR alpha variable domain con- sists of the amino acid sequence of SEQ ID NO:39; and the TCR beta variable domain consists of the amino acid sequence of SEQ ID NO:47.
Item 5. The TCR of any of items 1 to 3, wherein the TCR alpha variable domain con- sists of the amino acid sequence of SEQ ID NO:55; and the TCR beta le domain con- sists of the amino acid sequence of SEQ ID NO:63.
Item 6.The TCR of any of items 1 to 3, wherein the TCR alpha variable domain consists of the amino acid sequence of SEQ ID NO:71; and the TCR beta variable domain consists of the amino acid ce of SEQ ID NO:79.
Item 7. The TCR of any of items 1 to 6, wherein the TCR alpha constant domain con- sists of the TCR alpha constant domain of SEQ ID NO:39, and the TCR beta constant domain consists of the TCR beta constant domain of SEQ ID NO:47.
Item 8. The TCR of any of items 1 to 6, wherein the TCR alpha constant domain con- sists of the TCR alpha constant domain of SEQ ID NO:55, and the TCR beta constant domain consists of the TCR beta constant domain of SEQ ID NO:63.
Item 9. The TCR of any of items 1 to 6, wherein the TCR alpha constant domain con- sists of the TCR alpha constant domain of SEQ ID NO:71, and the TCR beta nt domain consists of the TCR beta constant domain of SEQ ID NO:79.
Item 10. The TCR of any of items 1 to 9, comprising an alpha chain consisting of SEQ ID NO:39 and a beta chain consisting of SEQ ID NO:47.
Item 11. The TCR of any of items 1 to 9, comprising an alpha chain ting of SEQ ID NO:55 and a beta chain consisting of SEQ ID NO:63.
Item 12. The TCR of any of items 1 to 9, comprising an alpha chain ting of SEQ ID NO:71 and a beta chain consisting of SEQ ID NO:79.
Item 13. The TCR of any of items 1 to 12, wherein the TCR alpha chain comprises at least one alpha chain complementarity determining region (CDR) selected from the group consisting of an alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:39, SEQ ID NO:55 and SEQ ID NO:71; and/or the TCR beta chain comprises at least one beta chain complementarity determining region (CDR) selected from the group consisting of a beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:47, SEQ ID NO:63 and SEQ ID NO:79.
Item 14. The TCR of any of items 1 to 13, wherein the TCR alpha chain comprises all three CDRs of SEQ ID NO:39, SEQ ID NO:55 or SEQ ID NO:71.
Item 15. The TCR of any of items 1 to 13, n the TCR beta chain comprises all three CDRs of SEQ ID NO:47, SEQ ID NO:63 or SEQ ID NO:79.
Item 16. The TCR of any of items 1 to 15, wherein the alpha chain and beta chain are fused to form a single chain TCR.
Item 17. The TCR of any of items 1 to 16, wherein the alpha and/or beta chain compris- es a detectable label.
Item 18. The TCR of item 17, wherein the detectable label is selected from the group consisting of a uclide, a fluorophore and biotin.
Item 19. The TCR of any of items 1 to 18, wherein the alpha and/or beta chain is conju- gated to a therapeutically active agent.
Item 20. The TCR of item 19, wherein the therapeutically active agent is selected from the group ting of a radionuclide, a chemotherapeutic agent and a toxin.
Item 21. A TCR comprising a gamma chain and a delta chain, wherein the gamma chain comprises at least one complementarity determining region (CDR) ed from the group consisting of an alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:39, SEQ ID NO:55 and SEQ ID NO:71; and/or the TCR delta chain comprises at least one complementarity deter- mining region (CDR) selected from the group consisting of a beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:47, SEQ ID NO:63 and SEQ ID NO:79, and wherein the TCR specifically binds to a MAG-003 peptide-MHC molecule complex.
Item 22. The TCR of any of items 1 to 21, wherein the TCR specifically binds to a MAG- 003 peptide-MHC molecule complex, wherein the MAG-003 peptide is selected from the group ting of SEQ ID NOs:1-24, and the MHC molecule is an HLA class I or HLA class II molecule.
Item 23. A nucleic acid encoding the alpha chain and/or beta chain of the TCR of any of items 1 to 20, or the gamma chain and/or delta chain of the TCR of item 21.
Item 24. An sion vector comprising the c acid of item 23 operably linked to at least one promoter sequence.
Item 25. A host cell transformed with the expression vector of item 24.
Item 26. The host cell of item 25 which is a T cell or T cell progenitor.
Item 27. The host cell of item 26 wherein the T cell or T cell progenitor is obtained from a cancer patient.
Item 28. The host cell of item 26 wherein the T cell or T cell progenitor is obtained from a healthy donor.
Item 29. A pharmaceutical composition comprising the TCR of any of items 1 to 22, a nucleic acid of item 23, an expression vector of item 24, and/or a host cell of any one of items to 28; and a pharmaceutically acceptable r, and optionally, pharmaceutically ac- ceptable excipients and/or stabilizers.
Item 30. A method for producing a TCR that specifically binds to the peptide of SEQ ID NO:1 when presented by an MHC molecule, said method comprising culturing the host cell of any one of items 25 to 28 under conditions suitable to promote expression of the TCR.
Item 31. A method of treating cancer comprising administering to a t in need thereof the TCR of any of items 1 to 22, the nucleic acid of item 23, the expression vector of item 24, the host cell of any one of items 25 to 28, and/or the pharmaceutical composition of item 29.
Item 32. The method of item 31, wherein the TCR is expressed on the surface of a host cell.
Item 33. The method of item 31, wherein the host cell is selected from the group con- sisting of a T cell or T cell progenitor.
Item 34. The method of item 33, wherein the T cell or T cell progenitor is autologous.
Item 35. The method of item 33, wherein the T cell or T cell progenitor is allogeneic.
Item 36. The method of item 31, wherein the TCR is conjugated to a eutically active agent.
Item 37. The method of item 36, wherein the therapeutically active agent is selected from the group consisting of a radionuclide, a chemotherapeutic agent and a toxin.
Item 38. The method of any of items 31 to 37, wherein the cancer is non-small cell lung cancer, small cell lung , renal cell cancer, brain cancer, gastric cancer, colorectal can- cer, hepatocellular , pancreatic cancer, prostate cancer, leukemia, breast , Mer- kel cell carcinoma, melanoma, ovarian cancer, urinary bladder cancer, uterine cancer, gallbladder and bile duct , esophageal , or a combination f.
Item 39. The method of any of items 31 to 38, further comprising administering to the subject at least one chemotherapeutic agent.
Item 40. The method of any of items 31 to 39, further comprising administering radia- tion therapy to the subject.
Item 41. A method of treating cancer in a subject in need f, comprising: a) isolating a cell from said subject; b) transforming the cell with a vector encoding the TCR of any of items 1 to 22 to pro- duce a ormed cell; c) expanding the transformed cell to produce a plurality of ormed cells; and d) administering the plurality of transformed cells to said subject.
Item 42. The method of item 41, wherein the cell is ed from a T cell or a T cell pro- genitor.
Item 43. A method of treating cancer in a subject in need thereof, comprising: a) isolating a cell from a healthy donor; b) transforming the cell with a vector encoding the TCR of any of items 1 to 22 to pro- duce a transformed cell; c) expanding the transformed cell to produce a plurality of ormed cells; and d) administering the plurality of transformed cells to said t.
Item 44. The method of item 43, wherein the cell is ed from a T cell or a T cell progenitor.
Item 45. A method of detecting cancer in a biological sample comprising: a) contacting the biological sample with the TCR of any of items 1 to 22, and b) ing binding of the TCR to the biological sample.
Item 46. The method of item 45, wherein the TCR comprises a detectable label.
Item 47. The method of item 46, wherein the detectable label is selected from the group consisting of a radionuclide, a fluorophore and .
Item 48. The method of any of items 45 to 47, wherein said detecting is carried out in vitro, in vivo or in situ.
Item 49. The method of any of items 45 to 48, wherein said cancer is non-small cell lung cancer, small cell lung cancer, renal cell , brain cancer, gastric cancer, colorectal cancer, hepatocellular cancer, pancreatic cancer, prostate cancer, leukemia, breast cancer, Merkel cell carcinoma, melanoma, ovarian cancer, urinary bladder cancer, uterine cancer, gallbladder and bile duct cancer, esophageal cancer, or a combination thereof.
Item 50. The host cell of any of items 25 to 28 wherein the T cell is a gamma/delta T cell.
Item 51. A method of killing target-cells in a patient which target-cells aberrantly ex- press MAG-003, the method comprising administering to the patient an effective number of T-cells expressing a TCR of any of items 1 to 22, the nucleic acid of item 23, the expression vector of item 24, the host cell of any one of items 25 to 28, and/or the pharmaceutical com- position of item 29.
Item 52. The TCR of any of items 1 to 22 which is a soluble TCR. 2017/056260 Item 53. The TCR of any of items 1 to 22, wherein the alpha chain comprises a TCR al- pha variable domain at least 95% identical to the amino acid sequence of any of SEQ ID NO:39, SEQ ID NO:55 and SEQ ID NO:71; and the beta chain comprises a TCR beta variable domain at least 95% identical to any of SEQ ID NO:47, SEQ ID NO:63 and SEQ ID NO:79, and wherein the TCR specifically binds to a MAG-003 e-MHC molecule complex.
Item 54. The TCR of any of items 1 to 22 having at least one mutation in the alpha chain relative to SEQ ID NO:39, SEQ ID NO:55 or SEQ ID NO:71 and/or having at least one muta- tion in the beta chain relative to SEQ ID NO:47, SEQ ID NO:63 and SEQ ID NO:79, and wherein the TCR has a binding affinity for, and/or a binding half-life for, a MAG-003 pep- tide-HLA molecule complex, which is at least double that of the unmutated TCR for the same peptide.
Item 55. The TCR of any of items 1 to 22 having at least one mutation in the alpha chain relative to SEQ ID NO:39, SEQ ID NO:55 or SEQ ID NO:71 and/or having at least one muta- tion in the beta chain relative to SEQ ID NO:47, SEQ ID NO:63 and SEQ ID NO:79, and wherein the TCR has modified glycosylation compared to the unmutated TCR.
Item 56. The method of any of items 31 to 44 or 51, wherein the TCR of any of items 1 to 22, the nucleic acid of item 23, the expression vector of item 24, the host cell of any of items to 28 or the pharmaceutical composition of item 29 is administered in at least two admin- istrations separated by at least 24 hours.
Item 57. The method of item 56, wherein the TCR of any of items 1 to 22, the nucleic acid of item 23, the expression vector of item 24, the host cell of any of items 25 to 28 or the phar- maceutical composition of item 29 is administered to the subject over a period of days, weeks or .
Item 58. The method of items 56 or 57, n the TCR of any of items 1 to 22, the nucleic acid of item 23, the expression vector of item 24, the host cell of any of items 25 to 28 or the pharmaceutical composition of item 29 is stered by local infusion.
Item 59. The method of any of item 58, wherein the local infusion is administered by an on pump and/or a catheter system.
Item 60. The method of items 58 or 59, wherein said local infusion is into a solid tumor, a blood vessel that feeds a solid tumor, and/or the area surrounding a solid tumor.
Item 61. The method of any of items 31 to 44, 51 or 56 to 60, wherein the TCR of any of items 1 to 22, the nucleic acid of item 23, the expression vector of item 24, the host cell of any of items 25 to 28 or the pharmaceutical composition of item 29 is administered in a dose of about 104 to about 1010 cells per dose.
Item 62. A TCR comprising at least one alpha chain complementarity determining re- gion (CDR) selected from the group ting of an alpha chain CDR1, CDR2 and CDR3 of SEQ ID NO:39, SEQ ID NO:55 and SEQ ID NO:71; and/or at least one beta chain - mentarity determining region (CDR) selected from the group consisting of a beta chain CDR1, CDR2 and CDR3 of SEQ ID NO:47, SEQ ID NO:63 and SEQ ID NO:79, and n the TCR specifically binds to a MAG-003 peptide-MHC molecule complex.
Allo—reactive settings can be used to circumvent self-tolerance and yield T-cells with a higher avidity when compared to s derived from autologous settings, i.e., patients. Examples of such settings include in vitro generation of allo-HLA reactive, peptide—specific T-cells (Sa- dovnikova et al. 1998; Savage et al. 2004; Wilde et al. 2012), and immunization of mice transgenic for MHC or human TCR (Stanislawski et al. 2001; Li et al. 2010).
Example 1: In vitro generation of allo-HLA reactive, peptide-specific T—cells (Savage et al. 2004) PBMCs from HLA—A*o2-positive and HLA—A*02-negative healthy donors were used after obtaining informed consent. Recombinant biotinylated HLA-A2 class I monomers and A2 fluorescent tetramers containing 3 were obtained from MBLI (Woburn, MA).
PBMCs were ted with anti-CD2OSA diluted in ate buffered saline (PBS) for 1 hour at room ature, washed, and ted with the biotinylated A2/MAG-003 mon- omers for 30 minutes at room temperature, washed, and plated at 3x106 cells/well in 24-well plates in RPMI with 10% human AB serum. Interleukin 7 (IL-7; R&D Systems, polis, MN) was added on day 1 at 10 ng/mL and IL-2 (Chiron, Harefield, United Kingdom) was added at 10 U/mL on day 4. Over a 5-week period cells were restimulated weekly with fresh PBMCs, mixed with responder cells at a 1:1 ratio, and plated at 3x106/well in 24—well plates.
To obtain high avidity T-cells, approximately 106 PBMCs with HLA—A2/MAG—003 tetramer- phycoerythrin (PE) (obtained from MBLI) were incubated for 30 minutes at 37°C, followed by anti—CD8—fluorescein isothiocyanate (FITC)/allophycocyanin (APC) for 20 minutes at 4°C, followed by fluorescence activated cell sorting (FACS)—Calibur analysis. Sorting was done with a FACS-Vantage (Becton Dickinson, Cowley, Oxford, United Kingdom). Sorted tetramer-positive cells were ed in 24-well plates using, per well, 2x105 sorted cells, 2x106 irradiated A2-negative PBMCs as s, 2x104 CD3/CD28 beads/mL (Dynal, Oslo ), and IL-2 (1000 U/mL). The high avidity T-cells, thus obtained, were then used to identify and isolate TCRs using techniques known in the art, such as single cell 5’ RACE (Rapid Amplification of cDNA Ends). Non-redundant TCR DNAs were then analyzed for amino acid/DNA sequences determination and g into expression vectors using meth- ods well known in the art.
Example 2: Immunization of mice transgenic for human-MHC or human TCR 3 are used to immunize transgenic mice with the entire human TCROLB gene loci (1.1 and 0.7 Mb), whose T-cells express a diverse human TCR repertoire that compensates for mouse TCR deficiency. (Li et al. 2010). To obtain high avidity s, PBMCs obtained from the transgenic mice are incubated with tetramer-phycoerythrin (PE) followed by cell sorting as described above. The high avidity s, thus obtained, are then used to identify and iso- late TCRs for amino acid/DNA sequences determination and cloning into expression vectors using methods described in the art.
In an aspect, MAG-003 and its variants, i.e., p286-1Y2L (having 2 amino acid substitutions, SEQ ID NO:13) and p286-1Y2L9L (having 3 amino acid substitutions, SEQ ID NO:14) exhibit potent binding affinity and stability towards HLA—A*0201 molecule. In particular, p286- 1Y2L9L showed the capability to induce specific CTLs which, in an aspect, lyse the target can- cer cells from both PBMCs of healthy donors and HLA-A2.1/Kb transgenic mice. See, for ex- ample, (Wu et al. 2011), the content of which is hereby incorporated by reference in its en- tirety.
To obtain high avidity TCRs for MHC I or II/p286-1Y2L or p286-1Y2L9L complexes, these peptides can be used in methods described in Examples 1 and 2. The high avidity T-cells, thus obtained, are then used to identify and isolate TCRs for amino acid/DNA ces determi- nation and cloning into expression vectors using methods described are in the art.
Example 3: Cloning ofTCRs Methods of cloning TCRs are known in the art, for example, as described in US. 8,519,100, which is hereby incorporated by reference in its entirety for said methods. The alpha chain variable region sequence specific ucleotide A1 (ggaattccatatgagtcaacaaggagaagaagatcc SEQ ID NO:26) which encodes the restriction site NdeI, an introduced methionine for effi- cient initiation of expression in bacteria, and an alpha chain constant region sequence specific oligonucleotide A2 (ttgtcagtcgacttagagtctctcagctggtacacg SEQ ID NO:27) which encodes the restriction site SalI are used to y the alpha chain variable region. In the case of the beta chain, a beta chain variable region sequence specific ucleotide B1 (tctctcat— atggatggtggaattactcaatccccaa SEQ ID NO:28) which s the restriction site NdeI, an in- ed methionine for efficient tion of expression in bacteria, and a beta chain con- stant region sequence specific oligonucleotide B2 (tagaaaccggtggccaggcacaccagtgtggc SEQ ID NO:29) which encodes the restriction site AgeI are used to y the beta chain variable region.
The DNA sequences encoding the TCR alpha chain cut with NdeI and SalI are ligated into pGMT7+Ca vector, which was cut with NdeI and XhoI. The DNA sequences encoding the TCR beta chain cut with NdeI and AgeI was ligated into separate pGMT7+CB vector, which was also cut with NdeI and AgeI. Ligated plasmids are transformed into competent Esche— richia coli strain XL1-blue cells and plated out on r plates containing 100 ug/ml ampicillin.
Following incubation overnight at 37° C., single colonies are picked and grown in 10 ml LB containing 100 ug/ml ampicillin ght at 37° C. with shaking. Cloned plasmids are purified using a Miniprep kit (Qiagen) and the insert is ced using an ted DNA sequencer (Lark Technologies).
Three TCRs (R20P1H7, R7P1D5 and R10P2G12, see table 2), each encoding tumor ic pha and ta chains, were isolated and ied from T-cells of healthy donors.
Cells from healthy donors were in vitro stimulated according to the method described in Wal- ter et. al. 2003. Target-specific cells were single-cell sorted using target-specific multimers for subsequent TCR isolation. TCR sequences were isolated via 5’ RACE by standard methods as described by e.g. Molecular Cloning a laboratory manual fourth edition by Green and Sambrook. All three TCRs were derived from HLA—A2 positive donors. The alpha and beta variable s of TCRs R20P1H7, R7P1D5 and R10P2G12 were sequenced.
The R20P1H7 TCR alpha variable domain was found to have an amino acid ce corre- sponding to residues 22-133 of SEQ ID NO:39. The R20P1H7 TCR beta variable domain was found to have an amino acid sequence corresponding to residues 20-135 of SEQ ID NO:47.
WO 58103 The R7P1D5 TCR alpha variable domain has an amino acid sequence corresponding to residues 22-131 of SEQ ID NO:55. The R7P1D5 TCR beta le domain has an amino acid sequence corresponding to residues 20—131 of SEQ ID N0:63.
The R10P2G12 TCR alpha variable domain has an amino acid sequence corresponding to residues 21-136 of SEQ ID NO:71. The R10P2G12 TCR beta variable domain has an amino acid sequence corresponding to residues 20-134 of SEQ ID NO:79.
Phage display can be used to generate libraries of TCR variants to identify high affinity mu- tants. The TCR phage display and screening methods described in (Li et al, (2005) Nature h 23 (3): 349-354) can be applied to a reference TCR ed from the TCRs described in Table 2.
For example, all three CDR regions of the alpha chain sequence of SEQ ID NOs: 39, 55 and 71; and all three CDR regions of the beta chain sequence of SEQ ID NOs: 47, 55 and 79 can be targeted by mutagenesis, and each CDR library panned and screened separately.
Accordingly, TCRs with affinities and/or binding half—lives at least twice that of a reference TCR (and therefore impliedly at least twice that of the native TCR) are identified.
TCR heterodimers are refolded using the method including the introduced cysteines in the constant regions to provide the artificial inter—chain disulphide bond. In that way TCRs are prepared, ting of (a) the reference TCR beta chain, together with mutated alpha ; (b) the reference TCR alpha chain together with mutated beta chains; and (c) various combi- nations of beta and alpha chains including the mutant variable domains.
The interaction between high affinity soluble disulfide—linked TCRs, and TCR variants, and the native peptide KVLEHVVRV (SEQ ID NO:1) HLA-A*02 x can be analysed using the BIAcore .
High avidity TCR variants can also be selected from a library of CDR mutants by yeast, or T- cell display (Holler et al. 2003; Chervin et al. 2008). Candidate TCR variants, thus, provide guidance to design mutations of the TCR’s CDRs to obtain high avidity TCR variants (Rob- bins et al. 2008; Zoete et al. 2007).
Example 4: Autologous T-cell engineering T-cells can be engineered to express high avidity TCRs (so-called TCR therapies) or protein- fusion derived chimeric antigen receptors (CARs) that have ed antigen specificity to MHC I/MAG—003 complex or MHC II/MAG—003 complex. In an aspect, this ch over- comes some of the tions associated with central and peripheral tolerance, and generate T-cells that will be more efficient at targeting tumors without the requirement for de novo T- cell activation in the patient.
In one aspect, to obtain s expressing TCRs of the present description, nucleic acids en- coding the tumor specific TCR—alpha and/or TCR-beta chains identified and isolated, as de- scribed in es 1-3, are cloned into expression s, such as gamma retrovirus or len- tivirus. The recombinant viruses are generated and then tested for functionality, such as an- tigen specificity and onal avidity. An aliquot of the final t is then used to trans- duce the target T-cell population (generally purified from patient PBMCs), which is expanded before infusion into the patient.
In another aspect, to obtain T-cells expressing TCRs of the present description, TCR RNAs were sized by techniques described in the art, e.g., in vitro transcription systems. The in vitro-synthesized TCR RNAs were then introduced into primary CD8+ T-cells obtained from y donors by oporation to re—express tumor ic TCR-alpha and/or TCR- beta chains.
To determine specificity and affinity of TCRs, the transformed CD8+ T-cells were co- incubated with MAGloaded target cells or with target cells loaded with homologous but unrelated peptide RABGAP1L—001 (SEQ ID NO:91), AXIN1-001 (SEQ ID NO:92), ANO5-001 (SEQ ID NO:93), TPX2-001 (SEQ ID NO:94), SYNE3-001 (SEQ ID NO:95), 01 (SEQ ID NO:96), HERC4-001 (SEQ ID NO:97), 001 (SEQ ID NO:98), HEATR5A—001 (SEQ ID NO:99) or CNOT1-003 (SEQ ID NO:100) or control peptide NYES01-001 (SEQ ID NO:101), followed by IFN—y release assay. Unloaded target cells and CD8+ T-cells alone served as controls. IFN—v secretion from CD8+ T-cells is indicative of T—cell activation with cytotoxic activity.
Table 11 TCR TCR Code Donor/HLA— IFNy EC50 % MAG-003 % NYESOl— No. A2 (pg/ml) sitive 001 TET- (+ or -) primary positive pri- CD8+ T—cells mary CD8+ T—cells 1 R7P1D5 HBC-583/(+) 400- ~3 nM 7.99 0.87 1050 2 R20P1H7 HBC- 200-900 ~10 nM 5.73 0.87 689/(+) 3 R10P2G12 HBC-673/(+) 200- ~10 nM 5.38 0.87 1500 As shown in FIGS. 5-7 all primary CD8+ T-cells transformed with TCRs of the present disclo- sure, after co-incubation with MAGloaded target cells, released much higher levels of IFN—y than that stimulated by unrelated peptide-loaded target cells, and the controls. Target peptide titration analysis showed EC50 ranges from about 3 nM to about 10 nM (Table 11).
These results suggest that TCRs of the present invention can activate cytotoxic T-cell activity, e. g., IFN—y release, through specific interaction with the MHC/MAG-003 complex.
T-cell activation was r med using a tetramer staining technique to detect Gbinding ted cytotoxic T-cells. As shown in and Table 11, a higher percentage of TCR-expressing CD8+ T-cells were stained positive cent—labeled MHC/MAG-003 tetramer than that with MHC/NYES01-001 control tetramer or mock con- trol. As a control, primary CD8+ T-cells ormed with TCRs, such as 1G4 TCR, which is known to bind specifically to MHC/NYES01-001 complex, was readily activated by NYESOl— 001-loaded target cells. The alpha and beta chains of TCR 1G4 are shown in SEQ ID NO:89 and 90, respectively: 2017/056260 1G4 alpha chain (SEQ ID N089): METLLGLLILWLQLQWVSSKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKG LTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVRPTSGGSYIPTFGRGT SLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMD FKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIG FRILLLKVAGFNLLMTLRLWSS 1G4 beta chain (SEQ ID NO:90): MSIGLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPG MGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYVGNTGELF LTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEV HSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQD RAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVLMAMVKR KDSRG To determine the binding motif of the TCRs for the MAG-003/MHC complex, positional ala- nine scanning analysis was performed at each of the 9 amino acids of the MAG-003 peptide.
Alanine—substituted MAG-003 peptides are shown in Table 12.
Table 12 Position: MAG-003 (SEQ ID NO:1) MAG—003 A1 (SEQ ID NO:3o) 3 A2 (SEQ ID NO:31) MAG-003 A3 (SEQ ID NO:32) MAG-003 A4 (SEQ ID NO:33) MAG-003 A5 (SEQ ID NO:34) MAG—003 A6 (SEQ ID NO:35) MAG-003 A7 (SEQ ID NO:36) MAG-003 A8 (SEQ ID NO:37) 3 A9 (SEQ ID NO:38) ww>wH <<<<<<<>mmmm4> mumm>mmmmmm <<<><<<<<<<<<<<<< Results of positional alanine scanning analysis are shown in FIGs. 9—11 and summarized in Table 13.
Table 13 TCR MAG-003 positions enable TCR binding R7P1D5 1, 3, 5, 7, 8 R2oP1H7 1, 3, 4, 5, 7, 8 R10P2G12 1, 2, 3, 4, 5, 8 A genome-wide screen for inding peptides with an identical motif revealed no poten- tially cross—reactive peptides for the TCRs R20P1H7, R7P1D5 and 12, respectively.
These results suggest that the TCRs described herein exhibit a very specific recognition pat- tern with a reduced risk of off-target effects.
To determine efficacy of s expressing TCRs described herein, primary CD8+ T—cells electroporated with RNA of the TCRs R7P1D5, R20P1H7 and R10P2G12 were co-incubated with different human cancer cell lines, e.g., A-375 (human melanoma cell line, which is posi- tive for HLA-A2 and MAG—003 expression), T98G (human glioblastoma cell line, which is HLA—A2-positive and MAGnegative), and SK-BR—3 (human breast cancer cell line, which is HLA—A2-negative and MAGnegative), followed by IFNy release assay.
As shown in A-C, IFNy e was observed in A—375 cells, which are HLA—A2- positive and MAG-003—positive, but not in T98G and 3 cells, which have basal levels of IFNy release that is comparable to that of effector cell only control. In addition, CD8+ T- cells transformed with TCR R7P1D5, but not controls, also ted increased IFNy release when co-incubated with the human non-small cell cancer cell line, H1755 (data not shown).
These results indicate that T—cells expressing TCRs R7P1D5, R20P1H7 and R10P2G12 can specifically induce cytotoxic activity targeting cancer cells in a HLA-A2/MAG—003 specific manner.
The present description provides TCRs that are useful in treating s/tumors, preferably melanoma and non-small cell lung cancer that over- or exclusively present MAG-003.
Example 5: Allogeneic T-cell engineering Gamma delta (y8) T cells, which are non-conventional T lymphocyte effectors implicated in the first line of defense against pathogens, can interact with and eradicate tumor cells in a MHC-independent manner through activating receptors, among others, TCR-gamma and TCR-delta chains. These y6 T cells display a preactivated phenotype that allows rapid cyto- kine tion , TNF—a) and strong cytotoxic se upon activation. These T—cells have anti-tumor activity against many cancers and suggest that y8 T cell-mediated - y is feasible and can induce objective tumor responses. (Braza et al. 2013).
Recent advances using immobilized antigens, agonistic monoclonal antibodies (mAbs), tu- mor—derived artificial antigen presenting cells (aAPC), or combinations of activating mAbs and aAPC have been successful in expanding gamma delta T-cells with lonal or polyclonal TCR repertoires. For example, lized major histocompatibility complex Class-I chain-related A was a stimulus for y8 s expressing TCR61 isotypes, and plate-bound activating dies have expanded V61 and V82 cells ex vivo. Clinically sufficient quantities of TCR61, TCR62, and TCR61negTCR62neg have been ed following co-culture on aAPC, and these subsets displayed differences in memory phenotype and reactivity to tumors in vitro and in vivo. (Deniger et al. 2014).
In on, y6 T-cells are amenable to genetic modification as evidenced by introduction of TCR-alpha and ta . (Hiasa et al. 2009). Another aspect of the present descrip- tion s to production of y6 T-cells expressing TCR-alpha and TCR-beta that bind to MAG—003. To do so, y6 T-cells are expanded by methods described by Deniger et al. 2014, followed by transducing the recombinant viruses expressing the TCRs that bind to 3 (as described in Example 3) into the expanded y8 T-cells. The virus-transduced y8 T-cells are then infused into the patient.
Example 6: Safety ofMAG—003-specific TCRs Three MAGspecific TCRs (R7P1D5, R10P2G12, R20P1H7, see Table 2), each encoding tumor specific TCR-alpha and TCR-beta chains, were isolated and amplified from s of healthy donors. Cells from healthy donors were in vitro stimulated according to a method previously described (Walter et al., 2003 J Immunol, Nov 15;171(10):4974—8) and target- specific cells were -cell sorted using HLA—A*02 multimers and then used for subse- quent TCR isolation. TCR sequences were isolated via 5’ RACE by standard methods as de- scribed by e.g. Molecular Cloning a laboratory manual fourth edition by Green and Sambrook.
The alpha and beta variable regions of TCRs R7P1D5, R10P2G12 and R20P1H7 were sequenced and cloned for further functional characterization. TCRs R7P1D5, R10P2G12 and R20P1H7 are derived from a HLA—A*02 positive donor.
Table 13: Target Cell Types eered Human Neurons HN cells TCRs of interest were sed in human T cells via RNA electroporation and the T cells were assessed for IFN—y release after co-culture with different target cells, such as T2 cells loaded with different peptides as well as tumor cell lines and primary cells from healthy tis- sues. T—cell activation data are shown in absolute IFN—y levels or a normalized way as t- ed below.
Efficacy of CD8+ T cells expressing TCRs R7P1D5, R10P2G12 and R20P1H7 was determined by T cell tion studies (IFN—y release) using different tumor cell lines as target cells. The characterization of the safety profile of TCRs of interest was approached by testing the poten- tial activation of TCR—expressing T cells upon co-culture with isolated primary cell types from healthy s and d otent stem cell (iPSC)-derived cell types from HLA—A*o2- positive donors (Fehler! Verweisquelle konnte nicht gefunden werden.). Cell types were selected in a manner to cover most of the critical organs like e.g. brain, heart and liver and different cell types as epithelium, elium or smooth muscle. Tumor cell lines were analyzed side—by-side as positive and negative controls.
Normalization method for IFNy release: Meannorm (TCRoi; co) = [mean(TCRoi; co)'mean(TCRoi; effector only)]‘[mean(mock; co)'mean(mock; effector only)] The respective CVnorm was calculated: CVnorm (TCRoi; co) = [CV(TCRoi; co)2 + CV(TCRoi; effector only)2 + ("/(moclqco)2 + CV(mock; effector only)2] A [1/2] TCRoi = effector cells expressing TCR of interest Mock = effector cells without exogenous TCR expression Co = effector cells co-cultured with target cells Effector only = effector cells not co—cultured Meammrm) = mean IFNy e (normalized) CV(norm) = coefficient of variation (normalized) Results: For CD8+ T cells expressing TCR R7P1D5, R10P2G12 or 7, no activation was ob- served upon co-culture with HLA-A*02 positive cell types from healthy tissues (see Figure 13), while there was a ty towards the tumor cell lines A—375 and NCI-H1755 expressing HLA-A*o2 and MAGEA4 as source gene for MAG-003 peptide. A similar pattern of vity was observed with CD8+ T cells expressing the NYESOl-specific TCR 1G4, which were found to be reactive towards NYESOl sing HLA-A*02 positive tumor cell lines but not to- wards the indicated panel of healthy tissue cells.
T-cell activation upon co-culture with cell lines expressing HLA—A*o2 and MAGEA4 reflects the recognition of endogenously expressed and processed target pHLA by TCRs R7P1D5, R10P2G12 and R20P1H7.
The safety analysis indicates the absence of un-expected cross-reactivity or potential alloreac- tivity of TCR R7P1D5, R10P2G12 and R20P1H7 towards healthy tissue primary cells. This is noteworthy as the tested primary cell types represent thousands of normal HLA ligands in the context of HLA-A*o2 and likely also ent additional allogeneic HLA alleles that vary from normal cell type to normal cell type.
Example 7: Lentiviral Expression ofTCR ofthe Invention T cell products were generated starting from bulk total Peripheral Blood Mononuclear Cells (PBMCs) isolated from healthy donors ing a small scale ACTengine cturing pro- cess. The lentiviral vector backbone expressing R7P1D5 TCR of the invention for manufactur- ing ine T cells was designed based on previous studies and multiple clinical trials (Porter et al., 2011; Kalos et al., 2011; and others) Briefly, thawed and rested PBMCs were activated with CD3/CD28 dies and uced with concentrated viral supernatants ctured using various lentiviral vectors carrying R7P1D5 TCR transgene with different orientations of a and B chains and various combinations of promotors and enhancer se- s (constructs were denoted as R71-R78). Two of the 8 constructs (R74, R75) were eliminated due to low titers and/or poor productivity. Cells transduced with the remaining 6 viral supernatants were expanded and evaluated for ene expression by flow cytometry.
Orientations were as s: Alpha-beta: R71, R72, 75, 76; beta-alpha: R73, R74, R77, 78, IG4.
All T cell products showed able viability, percentage of lymphocytes as well as CD3+ T-cells. Percentage of CD4+ and CD8+ T-cells varied among the donors. No differences were observed in terms of toxicity among all 6 viral supernatants. R7P1D5 TCR lentiviral construct R73 consistently induced higher TCR expression as detected on the surface by tetramer bind- ing. Based on transgene expression lentiviral constructs follow the order: R73>R78>R77>R71>R76>R72 (Fig 14).
Additional experiments with 2 new donors were done to m the transducibility of the R7P1D5 TCR R73 virus. Transduced cell from all experiments were tested for functional eval- uation in cytokine release and killing assays. In all donors tested, R73 transduced T cells de— rived from whole PBMCs of four donors exhibited significantly higher IFNv production upon co-culturing with A375 cells sing MAGE—A4 antigen as compared to non—transduced T cells (Fig.15A). IFNy response was strictly antigen specific as induction in presence of MCF-7 cells lacking MAGE-A4 expression was below background levels. In addition, EC50 value de- rived from T2 titration curves representing IFNy quantities detected in response to decreas- ing concentration of MAG-003 peptide was 10.0 nM in both donors (Fig 15B).
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Claims (44)

1. An antigen recognizing construct ically binding to the amino acid sequence of SEQ ID NO: 1 comprised in a peptide of 9 to 14 amino acids length and in complex with a human leucocyte antigen (HLA) class I molecule, wherein said antigen recognizing 5 construct comprises a g n of a T cell receptor (TCR) comprising (i) the complementary determining regions (CDRs) according to amino acid ce of SEQ ID NO: 58, SEQ ID NO: 59 and SEQ ID NO: 60 and the CDRs according to amino acid sequence of SEQ ID NO: 66, SEQ ID NO: 67 and SEQ ID NO: 68; 10 (ii) the complementarity determining regions (CDRs) according to amino acid sequence of SEQ ID NO: 42, SEQ ID NO: 43 and SEQ ID NO: 44 and the CDRs according to amino acid sequence of SEQ ID NO: 50, SEQ ID NO: 51 and SEQ ID NO: 52; or (iii) the complementary determining s (CDRs) according to amino acid sequence 15 of SEQ ID NO: 74, SEQ ID NO: 75 and SEQ ID NO: 76 and the CDRs according to amino acid sequence of SEQ ID NO: 82, SEQ ID NO: 83 and SEQ ID NO: 84; and wherein said antigen recognizing construct comprises the respective CDR amino acid sequences with not more than one amino acid substitution, wherein the substitution is with a conservative amino acid.
2. The antigen izing construct according to claim 1, wherein the antigen recognizing construct is an α/β-TCR, or fragment or derivative thereof; or the antigen recognizing uct is a γ/δ-TCR, or a fragment or derivative thereof. 25
3. The antigen recognizing construct ing to any one of claims 1 to 2, wherein said antigen recognizing construct is capable of ng an immune response in a subject.
4. The antigen recognizing construct according to claim 3, wherein the immune response is characterized by an increase in interferon (IFN) γ levels.
5. The antigen recognizing construct according to any one of claims 1 to 4, wherein the construct is humanized, chimerized and/or murinized.
6. The antigen recognizing construct according to any one of claims 1 to 5, comprising a TCR α or γ chain; and a TCR β or δ chain, wherein (i) said TCR α or γ chain ce comprises the CDR1 to CDR3 sequences according to SEQ ID NO: 58 to 60, and said TCR β or δ chain sequence comprises the CDR1 5 to CDR3 sequences according to SEQ ID NO: 66 to 68; or (ii) wherein said TCR α or γ chain comprises the CDR1 to CDR3 sequences according to SEQ ID NO: 42 to 44, and said TCR β or δ chain sequence comprises the CDR1 to CDR3 sequences according to SEQ ID NO: 50 to 52; or (iii) wherein said TCR α or γ chain sequence ses the CDR1 to CDR3 sequences 10 according to SEQ ID NO: 74 to 76, and said TCR β or δ chain sequence comprises the CDR1 to CDR3 sequences according to SEQ ID NO: 82 to 84.
7. The antigen recognizing construct according to any one of claims 1 to 6, wherein the construct is a TCR, or a nt f, comprising at least one TCR α and one TCR β 15 chain sequence,wherein (i) said TCR α chain sequence comprises a variable region sequence having the amino acid sequence of SEQ ID NO: 57 or a variable region at least 90% identical to the amino acid sequence of SEQ ID NO: 57, wherein said le region ce at least 90% identical to the amino acid sequence of SEQ ID NO: 57 comprises the 20 CDRs having the amino acid sequence of SEQ ID NO: 58, SEQ ID NO: 59 and SEQ ID NO: 60, and wherein said TCR β chain sequence comprises a variable region sequence having the amino acid sequence of SEQ ID NO: 65 or a variable region at least 90% identical to the amino acid sequence of SEQ ID NO: 65, wherein said le region sequence at least 90% identical to the amino acid sequence of 25 SEQ ID NO: 65 comprises the CDRs having the amino acid sequence of SEQ ID NO: 66, SEQ ID NO: 67 and SEQ ID NO: 68; or (ii) said TCR α chain sequence comprises a variable region sequence having the amino acid sequence of SEQ ID NO: 41 or a variable region at least 90% identical to the amino acid sequence of SEQ ID NO: 41, wherein said variable region sequence at 30 least 90% identical to the amino acid sequence of SEQ ID NO: 41 comprises the CDR1 to CDR3 sequences of SEQ ID NO: 42, SEQ ID NO: 43 and SEQ ID NO: 44, and n said TCR β chain sequence comprises a variable region sequence having the amino acid ce of SEQ NO: 49 or a variable region at least 90% identical to the amino acid sequence of SEQ ID NO: 49, wherein said variable region sequence at least 90% cal to the amino acid sequence of SEQ ID NO: 49 comprises the CDRs having the amino acid sequence of SEQ ID NO: 50, SEQ ID NO: 51 and SEQ ID NO: 52; or (iii) wherein said TCR α chain sequence comprises a variable region sequence having 5 the amino acid sequence of SEQ ID NO: 73 or a variable region at least 90% identical to the amino acid ce of SEQ ID NO: 73, wherein said variable region sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 73 comprises the CDRs having the amino acid sequence of SEQ ID NO: 74, SEQ ID NO: 75 and SEQ ID NO: 76, and wherein said TCR β chain sequence comprises 10 a variable region sequence having the amino acid sequence of SEQ ID NO: 81, or a variable region at least 90% identical to the amino acid ce of SEQ ID NO: 81, n said variable region sequence at least 90% identical to the amino acid ce of SEQ ID NO: 81 ses the CDRs having the amino acid sequence of SEQ ID NO: 82, SEQ ID NO: 83 and SEQ ID NO: 84.
8. The antigen recognizing construct according to any one of claims 1 to 7, wherein the construct is a TCR, or a fragment thereof, further comprising a TCR constant region having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 62, 70, 46, 54, 78 and 86; 20 preferably wherein the TCR is composed of at least one TCR α and one TCR β chain sequence, wherein the TCR α chain sequence comprises a constant region having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 62, 46 and 78; and wherein the TCR β chain sequence comprises a constant region having at least 50%, 60%, 70%, 80%, 90%, 95%, 25 98%, 99% or 100% ce identity to an amino acid sequence ed from SEQ ID NOs: 70, 54 and 86.
9. The TCR according to claim 8 comprising or consisting of a TCR α chain according to SEQ ID NO: 55 and a TCR β chain according to SEQ ID NO: 63.
10. The TCR according to claim 8 comprising or consisting of a TCR α chain according to SEQ ID NO: 39 and a TCR β chain according to SEQ ID NO: 47.
11. The TCR according to claim 8 comprising or ting of a TCR α chain according to SEQ ID NO: 71 and a TCR β chain ing to SEQ ID NO: 79.
12. A nucleic acid encoding the antigen recognizing construct according to any one of claims 5 1 to 8.
13. A nucleic acid or two separate nucleic acids encoding the TCR according to claim 9.
14. A nucleic acid or two separate nucleic acids encoding the TCR according to claim 10.
15. A nucleic acid or two separate nucleic acids ng the TCR according to claim 11.
16. A vector comprising the nucleic acid ing to claim 12. 15
17. A vector comprising the nucleic acid or the nucleic acids according to claim 13.
18. A vector comprising the c acid or the nucleic acids according to claim 14.
19. A vector comprising the nucleic acid or the nucleic acids according to claim 15.
20. A host cell comprising the antigen recognizing construct according to any one of claims 1 to 8, or the nucleic acid according to claim 12, or the vector according to claim 16, wherein the host cell is not a cell in a human body. 25
21. A host cell comprising the TCR according to claim 9 or the nucleic acid or nucleic acids according to claim 13 or the vector according to claim 17, wherein the host cell is not a cell in a human body.
22. A host cell comprising the TCR according to claim 10 or a nucleic acid or nucleic acids 30 according to claim 14 or the vector ing to claim 18, wherein the host cell is not a cell in a human body.
23. A host cell comprising the TCR according to claim 11 or a nucleic acid or nucleic acids according to claim 15 or the vector according to claim 19, wherein the host cell is not a cell in a human body. 5
24. The host cell according to any one of claims 20 to 23, wherein the host cell is a lymphocyte.
25. The host cell according to claim 24, wherein the lymphocyte is a T lymphocyte or T lymphocyte progenitor.
26. The host cell ing to claim 25, wherein the T lymphocyte is a CD4 positive, or CD8 positive T cell.
27. A pharmaceutical ition comprising the antigen recognizing construct according to 15 any one of claims 1-8, or the TCR according to any one of claims 9-11 or the nucleic acid or nucleic acids according to any one of claims 12-15, or the vector according to any one of claims 16-19, or the host cell according to any one of claims 20-26, and a pharmaceutical acceptable carrier, stabilizer and/or excipient. 20
28. Use of the antigen recognizing construct according to any one of claims 1-8, or the TCR according to any one of claims 9-11 or the c acid or nucleic acids according to any one of claims 12-15, or the vector according to any one of claims 16-19, or the host cell according to any one of claims 20-26, or the pharmaceutical composition ing to claim 27, in the manufacture of a medicament.
29. Use of the antigen recognizing uct according to any one of claims 1-8, or the TCR according to any one of claims 9-11 or the nucleic acid or nucleic acids ing to any one of claims 12-15, or the vector ing to any one of claims 16-19, or the host cell according to any one of claims 20-26, or the pharmaceutical composition according to 30 claim 27, in the manufacture of a medicament, wherein the medicament is for diagnosing, preventing, and/or treating a proliferative disease, wherein the disease comprises a malignant or benign tumor disease.
30. A use according to claim 29, wherein the tumor disease is characterized by the expression of a tumor associated antigen (TAA) in a tumor cell of the tumor disease.
31. A use according to any one of claims 28 to 30, wherein the medicament is for immune 5 therapy.
32. A use according to claim 31, wherein the immune therapy comprises an adoptive cell transfer. 10
33. A use according to claim 31, wherein the immune therapy comprises adoptive autologous or heterologous T-cell therapy.
34. A method of manufacturing a tumor associated antigen (TAA) specific n recognizing construct expressing cell line, comprising 15 a. providing a le host cell, wherein the host cell is not a cell in a human body, b. ing a genetic construct comprising a coding sequence encoding the n recognizing construct according to any one of claims 1 to 8 or the TCR according to any one of claims 9-11, c. introducing into said suitable host cell said genetic construct, 20 d. expressing said genetic uct by said suitable host cell.
35. The method according to claim 34, further comprising cell surface presentation of said antigen recognizing construct. 25
36. The method according to claim 34 or 35, wherein the genetic construct is an expression construct comprising a promoter sequence ly linked to said coding sequence.
37. The method ing to any one of claims 34-36, wherein said antigen recognizing uct is of mammalian origin, preferably of human origin.
38. The method according to any one of claims 34-37, wherein said suitable host cell is a mammalian cell.
39. The method according to claim 38, wherein said mammalian cell is selected from a human cell or a human T lymphocyte.
40. The method according to any one of claims to 34-39, n said antigen recognizing 5 construct is a modified TCR, wherein said modification comprises the addition of a functional domain comprising a label, or an ative domain comprising a membrane anchor domain.
41. The method according to claim 40, wherein said modified TCR is an alpha/beta TCR, 10 gamma/delta TCR, or a single chain TCR (scTCR).
42. The method ing to any one of claims 34-41, wherein said genetic construct is introduced into said suitable host cell by iral transfection. 15
43. The method according to any one of claims 34-42, further comprising the isolation and purification of the n recognizing construct from the suitable host cell.
44. The method according to claim 43, wherein the method further comprises the reconstitution of the antigen recognizing construct in a T-cell.
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Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201662308975P 2016-03-16 2016-03-16
GB1604492.7 2016-03-16
GBGB1604492.7A GB201604492D0 (en) 2016-03-16 2016-03-16 Transfected t-cells and t-cell receptors for use in immunotherapy against cancers
US62/308,975 2016-03-16
PCT/EP2017/056260 WO2017158103A1 (en) 2016-03-16 2017-03-16 Transfected t-cells and t-cell receptors for use in immunotherapy against cancers

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